The older MAPS forecast issued on July 21, 2026 continues to track well with the observations. The days after the preliminary estimate start will continue to fill in, so do not be deceived by the dip. Here is the model forecast for matching dates. Expands the observations to indicate 600,000 NDIs when the new updates arrive tonight.

And here is the entire forecast.

It appears that PJ.2.1 has arrived in the US. Expect that to start dominating in another month or so. It is a saltation, with numerous changes to the S protein. This is shown clearly in the image below.

I will have a new forecast ready by Sunday and will post it then. The new version of MAPS continues to go through a learning cycle, and the forecasts will become more accurate with time.

Executive Summary

● DR Congo’s Ebola outbreak (Bundibugyo strain, Ituri province) is now the country’s fastest-growing epidemic on record: 5,514 cases and 2,642 deaths as of ~Aug 24, with a case-fatality rate of 40–60% by health zone and officials describing transmission as outpacing the response. This is the top story this cycle.

● Measles: Pennsylvania’s Lancaster County outbreak produced the first two US measles deaths this year (both unvaccinated, one a newborn); a recent national tally added 211 cases (89 in PA, 73 in OH), and rising kindergarten vaccine-exemption rates raise back-to-school transmission risk.

● Avian flu is expanding on two fronts: continued H5N1 spillover into US dairy cattle and poultry (72 dairy-cow detections year-to-date; new detections in TX, UT, ID) plus Australia’s first-ever wild-bird H5N1 detections (ending its H5N1-free status); China continues reporting human H9N2 cases, including in young children.

● Mpox (clade I) deaths in DR Congo have passed 600, with the Republic of Congo reporting its first cases — a regional expansion — and research suggesting true infections may outnumber diagnosed cases by roughly 33 to 1.

Pathogen-by-Pathogen Briefing

1. SARS-CoV-2 / COVID-19

Status:

● No acute outbreak or surge signal was identified this cycle; coverage skewed toward long COVID research.

● UK data: roughly 1 in 4 infected healthcare workers developed long COVID, with support described as “inconsistent and insufficient.”

● Long COVID symptoms persist into a second year for most affected; exercise intolerance affects about 36% of that group.

● Night-shift workers show an 88% higher long COVID risk, suggesting circadian disruption compounds recovery risk.

● Severe acute COVID has been linked to arterial plaque growth, raising heart attack/stroke risk for up to a year afterward.

● Data gap this cycle: current variant mix (e.g., any successor to recent dominant lineages) and wastewater/test-positivity trends could not be confirmed from accessible sources.

Severity: Low–Moderate

Trend: Stable acute activity; substantial ongoing long COVID burden

Why it matters now: The acute picture looks quiet, but the long COVID data reinforce that prevention — masking in high-risk settings, staying current on boosters, cleaner indoor air — still pays off well after the infection itself resolves.

2. Measles

Status:

● Lancaster County, PA outbreak produced the first two US measles deaths of the year, both unvaccinated; one was a newborn whose death may trace to maternal measles infection.

● A recent CDC tally added 211 new cases nationally (Pennsylvania 89, Ohio 73), and officials suspect the Pennsylvania outbreak may be undercounted.

● US kindergarten vaccine-exemption rates rose again in the last school year, a trend public-health officials link to elevated outbreak risk.

● A cost study estimated ~$60,000 per case for the 2025 outbreak wave, roughly $134 million in total.

● Pediatricians are actively preparing for further measles activity as the new school year begins.

Severity: High

Trend: Rising

Why it matters now: Falling vaccination coverage plus school-year mixing is a well-understood recipe for measles resurgence — the first US deaths this year are a signal this isn’t a hypothetical risk anymore.

3. Diphtheria

Status:

● Data gap this cycle: CDC’s diphtheria outbreak page and CIDRAP’s diphtheria topic page were both unreachable (404) from available sources, so no current case data could be confirmed.

Severity: Unknown — monitor

Trend: Unknown this cycle

Why it matters now: Diphtheria stays on this briefing’s core list because global vaccine-coverage gaps and conflict-zone disruptions keep it a recurring risk; we’ll attempt a fresh check next cycle.

4. Avian Flu (H5N1 / H9N2)

Status:

● US: H5N1 continues in dairy cattle (new detections in Texas, Utah, Idaho; 72 dairy-cow detections nationally year-to-date) and in poultry, including Utah egg-laying operations.

● Australia recorded its first-ever wild-bird H5N1 detections, ending the continent’s H5N1-free status.

● Cambodia confirmed a human H5N1 case in an infant.

● China continues reporting human H9N2 infections — roughly 16–20 cases in the past six months, including young children (one case in a 1-year-old girl).

Severity: Moderate

Trend: Expanding — geographically and across species

Why it matters now: No sustained human-to-human transmission has been documented, but continued mammalian adaptation (dairy cattle) and spread into previously unaffected regions (Australia) both push the long-run pandemic-risk picture in the wrong direction.

5. Pertussis (Whooping Cough)

Status:

● Data gap this cycle: the CIDRAP pertussis topic page returned no accessible results, so no current case counts or locations could be confirmed.

Severity: Unknown — monitor

Trend: Unknown this cycle

Why it matters now: Pertussis resurgence tied to waning vaccine coverage has been a multi-year trend in several countries; it stays on the watchlist pending a confirmed update.

6. Ebola

Status:

● DR Congo’s Ituri-province outbreak (Bundibugyo strain) is now the country’s fastest-growing Ebola epidemic on record: 5,514 cases and 2,642 deaths as of ~Aug 24, more than 100 days since declaration.

● Case fatality rate is running 40–60% depending on health zone.

● WHO’s IHR Emergency Committee has held its second meeting on the outbreak; officials describe transmission as currently outpacing the response.

● A “Congo River Without Ebola” initiative is underway to protect the Kisangani–Kinshasa river corridor from further spread.

● An experimental monoclonal antibody (MBP134) has shown promising early results in the response effort.

● Separately, Uganda’s own Ebola outbreak has officially ended, at 20 cases and 2 deaths.

Severity: High/Severe

Trend: Rising sharply — described as tracking toward one of the largest Ebola epidemics ever recorded

Why it matters now: This is the most urgent item in today’s briefing: a case-fatality rate above 40% combined with transmission reportedly outrunning containment is a genuine international health emergency, not a routine watch item.

7. RSV

Status:

● No acute seasonal-surge signal this cycle; the Northern Hemisphere is currently between RSV seasons.

● Maternal RSV vaccination during pregnancy is linked to about a 70% reduction in infant RSV hospitalizations.

● Newborn RSV immunization was also linked to a 36% lower risk of invasive pneumococcal disease, a possible dual-protection benefit.

● Mayo Clinic data show asthma, chronic kidney disease, and similar conditions nearly double severe RSV risk in adults under 50 — a group not broadly targeted for vaccination today.

Severity: Low

Trend: Stable / pre-season

Why it matters now: The under-50, high-risk-condition finding is worth watching as a possible future vaccine-policy gap, even though current activity is quiet.

8. Influenza A

Status:

● Data gap this cycle: accessible CIDRAP flu coverage did not include Southern Hemisphere season severity or current strain-predominance data.

● Coverage did note flu vaccine availability messaging for the coming Northern Hemisphere season.

Severity: Unknown this cycle — monitor

Trend: Unknown this cycle

Why it matters now: Strain composition data from the Southern Hemisphere season normally previews what the Northern Hemisphere should expect and how well this year’s vaccine is matched; that read isn’t available yet.

9. Influenza B

Status:

● Data gap this cycle: no current strain-specific or case-trend data on Influenza B could be confirmed from accessible sources.

Severity: Unknown this cycle — monitor

Trend: Unknown this cycle

Why it matters now: Influenza B’s co-circulation pattern with influenza A affects total respiratory disease burden each season; will revisit once season data becomes available.

Other Outbreaks of Interest

Mpox (Clade I, Central Africa and beyond)

Status:

● DR Congo’s clade I mpox outbreak has surpassed 600 deaths.

● The Republic of Congo has reported its first cases — a notable regional expansion.

● CDC’s clade I detection test was flagged as “most likely not reliable” for distinguishing substrains, complicating surveillance.

● Research suggests actual infections may outnumber diagnosed cases by roughly 33 to 1, driven partly by asymptomatic transmission.

● A CDC assessment suggests mpox is becoming endemic in affected regions; separate research found nonsexual-contact transmission is uncommon, and a dose-sparing Jynneos vaccination strategy is showing effectiveness.

● An older item (dated February 2025) describing a New Hampshire congregate-living cluster (clade Ib; one case exposing 17 contacts across two group homes) also appeared in source coverage — flagged here as historical context, not a new development.

Severity: Moderate–High (Central Africa) / Low (US)

Trend: Expanding regionally; likely becoming endemic

Why it matters now: Spread to a new country plus evidence of substantial underdiagnosis suggest the true regional burden and transmission risk are larger than confirmed case counts show.

Andes Hantavirus (flagged by ECDC as an emerging threat)

Status:

● ECDC’s newsroom listed an “Andes hantavirus outbreak” among current emerging/ongoing threats, but no case counts, fatality data, or specific location could be confirmed from the accessible page content.

● Data gap this cycle — flagged for direct verification next cycle rather than reporting unconfirmed figures.

Severity: Unknown — monitor

Trend: Unknown this cycle

Why it matters now: Andes virus is the only hantavirus with documented person-to-person transmission and historically carries a high fatality rate, so any active cluster warrants close, confirmed tracking rather than a passing mention.

Angola: Measles and Cholera (unconfirmed currency)

Status:

● WHO AFRO’s outbreak page listed measles activity in Cuanza Sul (dated July 29, 2025) and a cholera response with mass vaccination in the same region (dated July 14, 2025).

● Those dates are more than a year old relative to today and may reflect stale or pinned content on WHO’s page rather than new developments — flagged as unconfirmed rather than reported as current news.

Severity: Unconfirmed

Trend: Unconfirmed

Why it matters now: Worth a direct WHO AFRO data-portal check next cycle to determine whether either outbreak is still active before this item is dropped or elevated.

Watchlist (Pathogens to Monitor Closely)

● ★ SARS-CoV-2 — standing watch for new variants and any resurgence in acute activity.

● ★ Measles — active US outbreak with the year’s first deaths and rising exemption rates going into the school year.

● ★ Ebola (DR Congo) — historic case-fatality rate with transmission reportedly outpacing the response; top-priority item.

● ★ Avian flu (H5N1/H9N2) — continued mammalian spillover and first-ever spread into a new continent’s wild birds.

● ★ Mpox — regional spread to a new country plus likely substantial underdiagnosis.

● ★ Andes hantavirus — flagged by ECDC as an emerging threat; details unconfirmed and need direct follow-up.

References

CIDRAP — Home / News Roundup

CIDRAP — Measles

CIDRAP — Avian Influenza (Bird Flu)

CIDRAP — COVID-19

CIDRAP — Ebola

CIDRAP — Ebola: “DR Congo suffers deadliest week in its Ebola outbreak”

CIDRAP — RSV

CIDRAP — Influenza (General)

CIDRAP — Mpox

WHO AFRO — Health Topics: Disease Outbreaks

WHO AFRO — DR Congo Country News

ECDC — Newsroom

PAHO — News

Watch Items for Next Briefing

● 1. Confirm current diphtheria case data and outbreak status (CDC and CIDRAP diphtheria pages were unreachable this cycle).

● 2. Confirm current pertussis case data and outbreak status (CIDRAP topic page returned no results this cycle).

● 3. Track the DR Congo Ebola case/death trajectory and confirm whether it has become the largest Ebola outbreak on record in DR Congo or Africa.

● 4. Confirm the current SARS-CoV-2 variant landscape and wastewater/test-positivity trend.

● 5. Confirm Influenza A/B strain predominance and Southern Hemisphere season severity ahead of the Northern Hemisphere season.

● 6. Verify the Andes hantavirus item flagged by ECDC — location, case count, and whether it is truly active.

● 7. Re-check whether the Angola measles and cholera items on WHO AFRO’s page are current or stale legacy content.

A gentle reminder as always: a little kindness goes a long way — wearing a mask in crowded indoor spaces, staying current on your boosters, and pushing for cleaner indoor air are small acts that can spare someone a case of Long COVID or another lingering respiratory illness.

Take care,

Joe

Here is the current wastewater analysis through August 2nd, with a graph of the New Daily Infections (NDIs) by variant and the total NDIs. The biggest surprise is in the surge of XFG. XFG* has had the “pole” position for 13 months! This reminds me of BA.5 and XBB.1.5. I believe the recent surge in XFG* is related to the fact that the immunity it imparts wanes rather quickly. I will have more on this in the future.

Here is the same through August 11th that can be view on the WHN website. You can also view individual states there. We only release states that pass quality controls so there are a total of 27.

Clearly, we are experiencing a likely wave. The values in the preliminary estimate will likely fill in more. As of today, I would estimate we are probably over 600,000 NDIs. So what does the new version of MAPS say? You can view the last operational forecast below and see that it indicates we are at around 650-700k NDIs. It also predicts the peak will be near 870,000 on September 4/5th. What is concerning is that the tail-off does not drop dramatically. The environment appears ripe for a new saltation, perhaps PJ.2.1, which has not yet reached the 2% threshold at the national level. The holidays are not looking great given the level of SARS-CoV-2 in circulation.

I should have a new forecast out by this weekend. I have made several needed changes to the new model since the last forecast and hope to have Influenza A/B, RSV, and measles ready integrated into the model in the near future. In the meantime, stay in clean air, avoid large gatherings, mask up with an N95 or better, and get this year’s newly formulated vaccine, which is based on XFG. It should be quite effective for the coming months.

Executive Summary

• DR Congo’s Ebola outbreak is now the deadliest ever recorded in that country — over 4,000 cases, 1,600+ deaths, a 46% case-fatality rate, and roughly 100 new cases a day, with 60-70% of deaths still occurring outside health facilities. Two vaccine candidates have entered Phase 1 trials, but response is not keeping pace with spread.

• US measles cases have topped 2,500 (101 new in the latest count, concentrated in Pennsylvania and Ohio), the outbreak has run 20+ consecutive months, and a CDC-linked expert panel is reviewing whether the US has lost its 26-year measles elimination status. A new executive order separating the MMR vaccine and expanding exemption deference has drawn criticism from public health groups.

• Mpox clade 1b continues geographic diversification: Republic of Congo reported its first cases, Berlin is seeing a rapid rise in locally-acquired (non-travel) infections, and New Hampshire, Denmark, Missouri, and New York have logged clade 1b detections — while DRC’s outbreak has now caused 600+ deaths.

• A new multistate Cyclospora outbreak linked to iceberg lettuce is under CDC/FDA investigation across at least 5 states (first flagged mid-July, updated August 13); detailed case and hospitalization counts are not yet public — flagging as a data gap this cycle.

Pathogen-by-Pathogen Briefing

1. SARS-CoV-2 / COVID-19

Status:

● No acute surge or new variant-of-concern signal surfaced in today’s authoritative sources — this cycle’s coverage skewed toward long-term outcomes research rather than real-time case/variant tracking.

● New research: a Washington county analysis estimates the original vaccine rollout averted 20,000+ severe outcomes and 4,000+ deaths; a separate study found no increase in adverse infant outcomes from vaccination during pregnancy.

● Long COVID data continues to accumulate: most patients still have symptoms into their second year; night-shift workers show an 88% higher long-COVID risk than day-shift workers; up to 5% of hospital healthcare workers may be affected; post-exertional malaise appears in roughly 36% of long-COVID cases.

● Severe acute infection has also been linked to accelerated arterial plaque growth (elevated cardiovascular risk for up to a year afterward) and possible reactivation of dormant viruses.

● Data gap this cycle: current wastewater/case-trend levels and dominant variant lineage were not confirmed from available sources.

Severity: Low-Moderate

Trend: Stable, monitoring long-term sequelae

Why it matters now: Long COVID’s cumulative toll — on shift workers, healthcare staff, and cardiovascular health — remains the pathogen’s biggest ongoing burden even absent an acute wave; layered protection (masks, clean air, boosters) still meaningfully reduces both infection and downstream Long COVID risk.

2. Measles

Status:

● US measles cases have exceeded 2,500, with 101 new cases in the latest reporting period; Pennsylvania and Ohio account for most new infections.

● The outbreak has now persisted at least 20 consecutive months; a CDC-linked expert panel is actively reviewing whether the US has lost its measles elimination status (held since 2000).

● Rising kindergarten vaccine exemptions are widening the susceptible population as the school year begins; research also confirms vaccinated individuals can still transmit measles, though illness is typically milder and shorter.

● Policy development: an executive order signed in August 2026 directs separation of the combined MMR vaccine and greater state deference to religious/parental exemptions — a move public health organizations have criticized as likely to further erode coverage.

Severity: High

Trend: Worsening — expanding with school reopening and falling coverage

Why it matters now: Loss of US elimination status would be a historic public-health reversal; combined with new policy pushing toward vaccine fragmentation and looser exemptions, this is the clearest example this cycle of policy directly shaping outbreak trajectory.

3. Diphtheria

Status:

● Africa: roughly 29,000 suspected cases and 1,420 deaths reported across 8 nations since January 2025 — WHO characterizes this as a moderate risk to the continent.

● A separate alert flags diphtheria risk in Europe; specific current case figures were not available from today’s sources — data gap this cycle.

● No update found on Southeast Asia/Indonesia case trends, historically a hotspot; treat as unchanged pending next cycle’s check.

Severity: Moderate

Trend: Elevated, sustained in Africa; magnitude elsewhere unconfirmed

Why it matters now: Diphtheria’s high case-fatality rate in under-immunized populations makes the African case/death tally worth tracking as a bellwether for broader routine-immunization erosion, alongside measles.

4. Avian Flu (H5N1 / H9N2)

Status:

● H9N2 (China): 16-20 human detections reported in the past 6 months, including a 1-year-old girl and at least four other recent cases — sporadic, low-severity zoonotic spillover continues.

● H5N1 in US livestock: Idaho and Utah dairy cattle newly infected; roughly 54 dairy herds infected with H5N1 so far this year and 72 cumulative H5N1 detections in dairy cows nationally; Utah egg-laying poultry operations also affected.

● H5N1 geographic expansion: Australia recorded its first-ever H5N1 detection in wild birds — the last continent to report the virus, closing a major remaining gap in global spread.

● H5N1 human case: Cambodia confirmed an H5N1 infection in an infant.

Severity: Moderate

Trend: Expanding geographically and across species; human cases remain sporadic

Why it matters now: Two avian flu subtypes are now independently generating human spillover cases on different continents while H5N1 achieves near-global geographic coverage in birds — the ingredients public-health officials watch for pandemic risk (reassortment opportunity, sustained mammalian circulation) are accumulating even without evidence of human-to-human spread.

5. Pertussis (Whooping Cough)

Status:

● No current outbreak-specific case data was retrievable from today’s sources — CIDRAP’s dedicated pertussis tracking page returned no content this cycle. Data gap this cycle; will re-check next briefing.

● Background context (unchanged from prior known trend, not a new data point): pertussis has been resurging across multiple countries in recent years amid waning adolescent/adult immunity and reduced maternal Tdap uptake in some regions.

Severity: Moderate

Trend: Unknown this cycle — data gap

Why it matters now: Pertussis is highly contagious and most dangerous to unvaccinated infants; maternal Tdap remains the single highest-leverage intervention, so any confirmed uptick would warrant fast follow-up.

6. Ebola

Status:

● The Democratic Republic of Congo outbreak (began February 2026) has surpassed 4,000 cases and 1,600 deaths, a 46% case-fatality rate — making it the deadliest Ebola outbreak in DRC’s history and the second-deadliest globally on record.

● Approximately 100 new cases are being reported daily, and the outbreak is described by responders as “outpacing response efforts,” with WHO warning it is on track to become the largest Ebola outbreak in history.

● 60-70% of deaths are still occurring in the community rather than in health facilities, indicating major gaps in case-finding and care access.

● Two vaccine candidates have entered Phase 1 trials, with the first volunteer already vaccinated; officials stress there is “no magical solution” and are calling urgently for more funding and healthcare workers.

Severity: High

Trend: Worsening — outpacing containment efforts

Why it matters now: This is currently the single most acute crisis in this briefing: a historically high case-fatality rate, accelerating daily case counts, and response capacity that is by responders’ own account falling behind. Watch for updated WHO case/death totals and any shift in the community-death share as a leading indicator of whether containment is gaining ground.

7. RSV

Status:

● Off-season in the Northern Hemisphere; no acute surveillance signal this cycle. Recent coverage instead focused on immunization-program research.

● Real-world data show maternal RSV vaccination during pregnancy reduces infant RSV hospitalizations by roughly 70%; an international 8-country survey found pregnant women prefer maternal vaccination over direct infant antibody shots.

● A separate study found infant RSV immunization was associated with a 36% reduction in invasive pneumococcal disease risk, suggesting possible cross-protective benefit.

● New research flags that adults under 50 with asthma, chronic kidney disease, or other chronic conditions face nearly double the RSV severity risk yet currently fall outside CDC vaccination recommendations — a possible guidance gap.

Severity: Low

Trend: Seasonally quiet; watch for the guidance-gap discussion ahead of fall season

Why it matters now: With the fall RSV season approaching in the Northern Hemisphere, the under-50/chronic-condition guidance gap is worth watching — it could shape whether high-risk younger adults get protected before activity picks up.

8. Influenza A

Status:

● Data gap this cycle: CDC FluView surveillance data was not retrievable, and CIDRAP’s general influenza page did not include current strain-predominance or activity-level figures. Northern Hemisphere is in its typical off-season (August); Southern Hemisphere winter-season activity was not independently confirmed today.

● Related research: 2024-25 season flu vaccines are estimated to have prevented meaningful numbers of US hospitalizations and emergency/urgent-care visits; oseltamivir was shown to reduce ICU admissions and length of stay in pediatric patients.

Severity: Low

Trend: Unknown this cycle — data gap; expected seasonal lull in the Northern Hemisphere

Why it matters now: No actionable signal today, but flagging the FluView access gap so it can be rechecked before Northern Hemisphere flu season ramps up this fall.

9. Influenza B

Status:

● Same data gap as Influenza A — no current strain-specific surveillance figures were retrievable this cycle.

● Notable co-infection finding: concurrent COVID-19 and influenza infection significantly raises the risk of severe outcomes versus either infection alone, reinforcing the value of avoiding both simultaneously (masking, ventilation, staggered boosters).

Severity: Low

Trend: Unknown this cycle — data gap

Why it matters now: The COVID+flu co-infection severity finding is a practical, actionable reminder heading into respiratory season: layered precautions matter most when multiple pathogens are circulating at once.

Other Outbreaks of Interest

Mpox (Clade 1b and related)

Status:

● DRC’s ongoing outbreak has now caused over 600 deaths; neighboring Republic of Congo has reported its first cases, extending the region’s geographic footprint.

● Clade 1b is diversifying geographically outside Africa: a New Hampshire case exposed 17 people across two group homes; Berlin is seeing a “rapid rise” in locally-acquired (non-travel-linked) cases; Denmark, Missouri, and New York have all logged clade 1b detections.

● The CDC’s clade I test is reportedly “most likely not reliable” for detecting certain substrains, a potential under-ascertainment risk.

● European regulators have advised against using tecovirimat (Tpoxx) for mpox treatment after studies showed no benefit over placebo; separately, research suggests nonsexual and air-travel transmission risk are both low, though undiagnosed infections may substantially outnumber confirmed cases.

Severity: Moderate

Trend: Expanding geographically via local transmission chains outside Africa

Why it matters now: Locally-acquired clade 1b cases in Berlin and sustained US detections outside travel-linked chains are the signal to watch — that pattern, not the Africa case count alone, is what would indicate sustained community transmission establishing outside the outbreak’s origin region.

Cholera

Status:

● Sudan’s 18-month outbreak has concluded with more than 100,000 cases and an estimated 2,408 deaths nationwide.

● DRC’s outbreak is intensifying: over 58,000 cases and 1,700 deaths reported over the past 9 months.

● Chad is seeing surge activity; a vaccination campaign targeting nearly 2 million people has launched in the neighboring Darfur region of Sudan.

● WHO reports five African nations currently facing acute outbreaks with elevated mortality rates; preventive vaccination campaigns are resuming globally as supply improves, with Mozambique the first country to restart a campaign suspended since 2022.

Severity: Moderate-High

Trend: Intensifying in DRC and Chad; improving in Sudan post-outbreak

Why it matters now: Multiple concurrent African cholera outbreaks with elevated case-fatality rates reflect strained water/sanitation infrastructure and vaccine-supply constraints — the resumption of preventive campaigns (Mozambique) is a hopeful but early signal.

Dengue

Status:

● Sri Lanka has reported over 80,000 cases so far this year.

● US dengue cases rose 359% in 2024 amid a global surge, though most US infections were travel-related; competent mosquito vectors are present across much of the country.

● A Brazil dengue vaccination campaign was halted amid broader global-health funding pressures; Samoa has also reported cases.

● Research continues to link warmer temperatures to higher mosquito-bite rates and longer transmission seasons, tying dengue’s expansion to climate trends, particularly in lower- and middle-income countries.

Severity: Moderate

Trend: Rising globally, particularly in South/Southeast Asia

Why it matters now: The halted Brazil vaccination campaign amid funding cuts is worth watching — reduced prevention capacity arriving alongside climate-driven range expansion is an unfavorable combination.

Cyclosporiasis (new addition this cycle)

Status:

● CDC has an active multistate Cyclospora investigation linked to iceberg lettuce, spanning at least 5 US states; the outbreak was first flagged around July 18, 2026 and the CDC page was updated August 13, 2026.

● Case counts, hospitalization figures, and the specific distributor/grower have not yet been published in the sources checked this cycle — data gap; will follow up next briefing as CDC/FDA release fuller details.

Severity: Low-Moderate

Trend: Active investigation, scope not yet fully characterized

Why it matters now: Added to the briefing at Joe’s request — Cyclospora outbreaks linked to leafy greens have repeatedly grown larger than initial state counts suggest, so this is worth tracking until CDC publishes a case count and traceback source.

Watchlist (Pathogens to Monitor Closely)

★ SARS-CoV-2 — watch for updated variant/wastewater signals; long-COVID burden data continues to accumulate.

★ Measles — US elimination-status review and the new MMR-related executive order could both shift outbreak trajectory within weeks.

★ Ebola (DRC) — highest-severity item in this briefing; case-fatality rate, daily case count, and community-death share are the key indicators to track.

★ Mpox clade 1b — locally-acquired cases in Berlin and continued US state detections outside travel chains.

★ H5N1/H9N2 avian influenza — continued mammalian spillover (dairy cattle) and sporadic human cases across multiple countries.

★ Cholera (DRC/Chad) — intensifying case counts amid constrained vaccine supply.

★ Cyclosporiasis — newly tracked; awaiting CDC case count and traceback source.

References

● CIDRAP — Homepage / News Roundup

● CIDRAP — Ebola

● CIDRAP — Measles

● CIDRAP — Avian Influenza / Bird Flu

● CIDRAP — COVID-19

● CIDRAP — Mpox

● CIDRAP — RSV

● CIDRAP — Diphtheria

● CIDRAP — Influenza (General)

● CIDRAP — Cholera

● CIDRAP — Dengue

● CDC — Cyclosporiasis Outbreaks

● WHO — Disease Outbreak News (no new items returned this cycle)

Watch Items for Next Briefing

1. Confirm updated DRC Ebola case/death totals and whether the community-death share (currently 60-70%) is improving or worsening.

2. Check whether the US measles elimination-status review has concluded, and track any state-level response to the new MMR-separation executive order.

3. Follow up on the CDC/FDA Cyclospora-iceberg lettuce investigation for confirmed case counts, hospitalizations, and traceback source.

4. Re-check CDC FluView and WHO FluNet for current influenza A/B activity levels and strain predominance, given today’s data gap.

5. Look for pertussis-specific case data, since CIDRAP’s dedicated tracking page returned no content this cycle.

6. Track whether Berlin’s locally-acquired mpox clade 1b cases represent sustained community transmission or a contained cluster.

7. Monitor DRC and Chad cholera case trajectories and whether additional African countries resume suspended vaccination campaigns.

A gentle reminder as always: a little kindness, a well-fitted mask in crowded or high-risk indoor spaces, staying current on boosters, and pushing for cleaner indoor air go a long way toward preventing infection in the first place — and toward easing the burden of Long COVID and other lingering respiratory illness for the people around you.

Take care,

Joe

Daily Global Pathogen Briefing

Daily Update | August 17, 2026

Executive Summary

● DR Congo’s Ebola outbreak is on track to be the largest in history: cases have surpassed 4,000 and deaths are approaching/exceeding 2,000 (~40% case fatality rate), with WHO and Africa CDC warning the r…

Read more

• DR Congo’s Ebola outbreak has reached 4,449 confirmed cases and 2,061 deaths (WHO figures reported Aug. 12) and is now, per WHO Director-General Tedros Adhanom Ghebreyesus, on track to become the largest Ebola outbreak in history, surpassing the 2014-16 West African epidemic.

• The US measles outbreak…

Read more

MAPS Forecast

I just looked at our wastewater site, and basically every state that meets our data control criteria is increasing; California drives the majority of it. 27 states. 2 are flat, including Minnesota. Based on the data through 8-4-2026, it appears MAPS is slightly higher, with a predicted value of 269,000 vs. 241,000 shown in the data. I expec…

Read more

Daily Global Pathogen Briefing

Daily Update | August 7, 2026

Executive Summary

• DRC’s Ebola (Bundibugyo virus) outbreak is now the second-deadliest Ebola outbreak in history (4,053 cases / 1,850 deaths, ~44% CFR) and is outpacing containment efforts — WHO and Africa CDC leadership visited the region Aug 5–6 to urge an urgent scale-up. It remains a WHO Public Health Emergency of International Concern (declared May 17, 2026).

• US measles activity continues to climb (2,371 cases in 2026, 94% outbreak-associated), with a new outbreak just declared in Delaware; falling MMR coverage (92.5% among kindergartners) is the underlying driver.

• Avian influenza continues to diversify and spread geographically: new human H9N2 cases in China, a reported H5N1 case in an infant in Cambodia (unconfirmed detail), continued US dairy-cattle/poultry H5N1 activity, and Australia’s first-ever H5N1 detection in wild birds.

Pathogen-by-Pathogen Briefing

1. SARS-CoV-2 / COVID-19

Status: No major update today. ECDC’s most recent detailed regional assessment (May 29, 2026) describes ongoing endemic circulation with no acute signal; COVID is now managed through routine respiratory-virus surveillance alongside flu and RSV.

• Recent literature coverage has focused on updated vaccine effectiveness (2025–26 boosters reduced urgent-care visits by ~50% and symptomatic disease by 59%) and long-COVID sequelae rather than new outbreak activity.

• No specific dominant-variant name could be confirmed from available sources as of this briefing — flagged as a data gap, not an assumption.

Severity: Low

Trend: Stable

Why it matters now: Baseline surveillance shows no emerging variant-of-concern signal, but the Northern Hemisphere summer reporting lull limits visibility; re-check as autumn surveillance ramps up.

2. Measles

Status: US measles activity remains substantially elevated. CDC reports 2,371 confirmed cases in 2026 as of July 30 (2,355 domestic + 16 among international travelers), across 45 jurisdictions, with 37 outbreaks declared and 94% of cases outbreak-associated.

• Delaware just declared its first outbreak in over a decade (4 cases) after an unvaccinated Kent County resident tested positive.

• CIDRAP coverage referenced a UK measles death; case details/date could not be independently verified and are flagged as unconfirmed.

Severity: High

Trend: Worsening

Why it matters now: Kindergarten MMR coverage has fallen to 92.5% nationally — below the 95% herd-immunity threshold — leaving an estimated 286,000 young US children vulnerable. New states reporting first outbreaks in years signals continued geographic spread rather than containment.

3. Diphtheria

Status: No major update today. Background: ECDC’s most recent formal risk assessment (July 2025) documented the C. diphtheriae ST574 strain circulating in at least five EU/EEA countries plus Switzerland (82 cases, 2023–2025), concentrated among homeless populations, people who use drugs, and unvaccinated/older adults.

• General-population risk in highly vaccinated countries remains “very low.” No newer authoritative update was found.

Severity: Low

Trend: Stable

Why it matters now: Persistent low-level circulation in vulnerable populations, combined with reported global diphtheria antitoxin shortages, keeps this on the monitoring list even without new acute activity.

4. Avian Flu (H5N1 / H9N2 / other H*N*)

Status: Multiple concurrent threads are active across several countries:

• H9N2 (China): WHO reported 3 new human cases (July 10–16, 2026) — two 4-year-old boys (recovered) and a 44-year-old man (hospitalized in ICU at last report). China has recorded 170 of 173 human H9N2 infections documented globally since 2015 (2 deaths cumulative).

• H5N1 (Cambodia): A case reported in an infant per headline coverage; additional case details or an exact date could not be confirmed from a primary source — flagged as preliminary.

• H5N1 (United States): Continued detections in dairy cattle (Idaho, ~54 herd-level cases YTD) and egg-laying poultry (Utah). Cumulative US human H5 cases since Feb 2024: 71, almost entirely among dairy/poultry workers with direct animal exposure. CDC assesses general public health risk as low.

• H5N1 (Australia): First-ever detection in wild birds on a continent that had remained H5N1-free — a notable geographic milestone.

Severity: Moderate

Trend: Worsening (geographic spread) / Unclear (human severity)

Why it matters now: Continued mammalian spillover, an ICU-level human H9N2 case, and H5N1’s arrival in a previously unaffected continent all raise the reassortment/adaptation watch level, even though population-level risk assessments remain “low” for now.

5. Pertussis (Whooping Cough)

Status: No major new development dated to today, but the underlying trend remains notable. The US recorded 28,783 confirmed/probable cases in the most recently completed full year — the highest in the Americas region — and 2025 case counts (>25,000) marked a second consecutive high-activity year, including three infant deaths in Kentucky.

• PAHO has warned of a region-wide first-dose vaccination coverage gap (87%, down from pre-pandemic levels).

Severity: Moderate

Trend: Stable-to-elevated (multi-year resurgence)

Why it matters now: Sustained above-baseline circulation with vaccination gaps in the pediatric/maternal population increases risk of infant morbidity and mortality; maternal Tdap vaccination cuts infant hospitalization/ED visits by 70–89% where uptake is adequate.

6. Ebola (Bundibugyo virus disease — DRC / Uganda)

Status: This is the most significant global event in today’s briefing.

• Declared a WHO Public Health Emergency of International Concern on May 17, 2026.

• 4,053 confirmed cases and 1,850 deaths as of the most recent WHO/Africa CDC reporting (early August 2026) — the second-deadliest Ebola outbreak in history and the largest ever recorded in DRC. Crude case-fatality rate is running roughly 44%.

• Ituri province accounts for the large majority of cases and deaths (estimates range 88–90% across recent reports); the outbreak is adding ~75 new cases per day on average.

• Africa CDC Director-General Jean Kaseya reported that more than 70% of new cases and 67% of deaths are now originating in the community rather than from traced contacts — a strong signal that transmission is outpacing contact-tracing capacity.

• WHO Director-General Tedros Adhanom Ghebreyesus and Kaseya visited affected areas Aug 5–6, 2026 to press for a substantial scale-up of the response; Kaseya has publicly stated there is “no magical solution.”

• Healthcare-worker cases are significant (151 cases, 44 deaths, ~29% CFR among responders).

• Secondary impact: rising maternal mortality (an estimated six women per week dying of childbirth complications as women avoid facilities), compounded by reported aid cuts that have reduced sanitation-funding capacity by more than half between 2024 and 2025.

• Uganda’s linked, smaller outbreak has been declared over (20 cases, 2 deaths).

• Vaccines: WHO recommends prioritizing the licensed Ervebo vaccine in a phase 3 trial for this strain; Bundibugyo-specific candidates from Moderna and Oxford Vaccine Group have entered phase 1 trials; preliminary research suggests existing vaccine stockpiles may generate some cross-reactive antibody response.

Severity: High

Trend: Worsening

Why it matters now: This is a PHEIC-level event with a historically high case count, a rising share of untraceable community transmission, and compounding health-system and humanitarian-funding pressures. It warrants top-line attention for cross-border spread risk, vaccine/therapeutic deployment decisions, and international response coordination.

7. RSV

Status: No major update today. The Northern Hemisphere is in its off-season lull; CDC surveillance confirms circulation has returned to pre-pandemic seasonal patterns but shows no current elevated-activity signal.

• Maternal RSV vaccination during pregnancy has been associated with a ~70% reduction in infant hospitalizations.

• A separate study found a 36% lower risk of invasive pneumococcal disease among RSV-immunized newborns.

Severity: Low

Trend: Stable (seasonal lull)

Why it matters now: These vaccine-effectiveness findings are useful ahead of the fall/winter RSV season ramp-up and maternal-vaccination counseling.

8. Influenza A

Status: No major update today, and current-week strain-level surveillance data could not be confirmed from accessible sources — flagged as a data gap rather than an assumption of no activity. The Northern Hemisphere is in its typical summer seasonal lull.

• 2025–26 season context: 149 pediatric flu deaths were reported, the large majority in unvaccinated children; some analyses suggested influenza posed a greater hospitalization risk than COVID-19 last winter.

• The first mRNA-platform flu vaccine received FDA approval, which may improve vaccine effectiveness in future seasons.

Severity: Low (seasonal lull); vaccine news is Moderate-relevance

Trend: Unclear (insufficient current surveillance data accessed)

Why it matters now: The mRNA flu vaccine approval is a meaningful vaccination-implications development to track ahead of Southern Hemisphere season close-out and Northern Hemisphere fall planning.

9. Influenza B

Status: No major update today. Northern Hemisphere activity remains in its seasonal lull; no current elevated-activity signal identified.

Severity: Low

Trend: Stable

Why it matters now: Low absolute burden currently, but B-lineage predominance patterns remain relevant to Southern Hemisphere surveillance and planning for the next Northern Hemisphere season.

Other Outbreaks of Interest

Cyclospora (multistate US, foodborne parasitic illness)

• At least two concurrent outbreak threads are active. Michigan alone has confirmed over 2,600 cyclosporiasis cases, with the outbreak reported to have expanded to at least 9 states (including Illinois, Kansas, Oklahoma, and Pennsylvania).

• A separate, unrelated multistate outbreak has been linked to iceberg lettuce from Mexican suppliers served at Taco Bell locations in 5 states.

• Headline coverage referenced deaths in the Michigan cluster; an exact death count could not be independently confirmed from a primary source — flagged as preliminary.

Severity: Moderate

Trend: Improving in Michigan specifically (“worst is behind us” per state officials) but still expanding nationally overall.

Cholera (sub-Saharan Africa)

• Recent (non-dated-to-today) coverage indicates Sudan’s 18-month outbreak has ended (cumulative >100,000 cases, ~2,408 deaths), while DR Congo, Chad, and the Republic of Congo have reported ongoing/rising case counts (DRC cited at roughly 58,000 cases and 1,700 deaths over a recent 9-month period).

• Could not confirm whether these figures reflect August 2026 conditions specifically — included as background regional context; recommend independent verification via WHO AFRO or Africa CDC before decision-use.

US public health leadership

• The US Senate has confirmed a new CDC Director — an organizational/response-capacity development rather than a disease signal, noted here given its relevance to future US outbreak-response coordination.

Watchlist (Pathogens to Monitor Closely)

★ SARS-CoV-2 — standing watchlist item; monitor for autumn variant signal

★ Measles — standing watchlist item; US trajectory still climbing, new states affected

★ Ebola (DRC/Uganda, Bundibugyo virus) — active PHEIC, worsening trajectory, outpacing response capacity

★ Avian influenza (H5N1/H9N2) — geographic spread (Australia) and severe human H9N2 case; mammalian spillover continuing in US

★ Pertussis — multi-year US/Americas resurgence with vaccination coverage gaps

★ Cyclospora (US, multistate foodborne) — active, evolving, healthcare and public-communication impact

References

• WHO Disease Outbreak News (archive/index)

• WHO Ebola disease fact sheet

• CDC bird flu (H5) situation summary

• CDC measles data & research

• CDC RSV surveillance

• ECDC diphtheria overview

• ECDC rapid risk assessment, diphtheria ST574 (EU/EEA), Jul 8 2025

• ECDC COVID-19 page (communicable disease threats report, week 22, 2026)

• ECDC seasonal influenza

• CIDRAP — Ebola outbreak now second-deadliest in history

• CIDRAP — WHO/Africa CDC urge scale-up of Ebola response (Aug 6, 2026)

• CIDRAP — Ebola outbreak outpaces response efforts

• CIDRAP — Africa CDC chief “no magical solution”

• CIDRAP — Ebola deaths top 1,000 / measles Delaware / H9N2 China

• CIDRAP — avian influenza/bird flu topic page

• CIDRAP — cholera topic coverage

• CIDRAP — pertussis/whooping cough coverage

• CIDRAP — RSV coverage

• CIDRAP — COVID-19 coverage

• CIDRAP — homepage / top headlines

Watch Items for Next Briefing

1. DRC/Uganda Ebola: updated case/death counts, whether community-transmission share continues rising, and any cross-border spread beyond Uganda.

2. Ebola vaccine trial progress (Ervebo phase 3; Moderna/Oxford Bundibugyo-specific candidates) and any stockpile deployment decisions.

3. US measles: whether Delaware’s outbreak grows beyond 4 cases and whether any additional states report first-in-years outbreaks.

4. Avian flu: confirmation/details on the reported Cambodia H5N1 infant case; status of the hospitalized H9N2 adult patient in China; any further H5N1 spread within Australia.

5. Verification of the reported UK measles death (details currently unconfirmed).

6. Cyclospora: updated multistate case counts and confirmed death toll, and resolution status of the two concurrent US outbreak threads.

7. Confirm current-week influenza A/B and RSV surveillance data once accessible, ahead of Southern Hemisphere season close-out.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

A new MAPS forecast will be ready by tomorrow. Here is this week's update of GISAID+Wastewater-Derived NDIs. Is this the last hurrah for XGF? It appears to have driven the last increase at the national level, from 18% to 31%. Meanwhile, XFJ.3 has climbed to 2nd. Swapping places with PY.1. NB.1.8.1 has increased slightly and s topped by PQ.2 now. We are all keeping our eye on PJ.2.1, which has shown rapid spread in other parts of the globe and has been detected in 10 states as well as Ontario, Canada.

@LongDesertTrain did a deep dive and showed the samples match extremely closely. It spells trouble.

This is the output from the MAPS Initial Condition Builder displaying the current variant status and transmission strengths.

Daily Global Pathogen and Outbreak Briefing - 2026-08-05

Executive Summary

- Bundibugyo Ebola in eastern Democratic Republic of the Congo (DRC) remains the leading global outbreak emergency. New reporting on 4 August described approximately 1,700 deaths, up from more than 1,500 in reporting available a day earlier. WHO’s latest formal situation report, with data through 26 July, documented intensifying transmission, rising mortality, and geographic expansion. The exact totals are fast-moving and provisional.

- Measles remains High and worsening. The United States has recorded more than 2,300 cases in 2026, already exceeding all of 2025. A new analysis estimated that New Mexico’s 2025 outbreak alone cost $5.4 million, underscoring the operational and economic burden of preventable transmission.

- SARS-CoV-2 activity remains low globally, but a U.S. summer increase is under way. WHO has added PQ.16.1.1 to its variants-under-monitoring list; this indicates a surveillance signal, not evidence of increased severity.

- Seasonal influenza and RSV remain low in most temperate regions. Zoonotic influenza A deserves closer attention: China reported four additional human H9N2 infections, bringing the reported six-month total to 20, while Australia continues to detect H5N1 in wild birds.

- Other continuing priorities are multi-country cholera, the large and fragmented U.S. Cyclospora outbreak situation, mpox, and seasonal vector-borne threats in Europe.

Pathogen-by-Pathogen Briefing

1. SARS-CoV-2

Status: Low global burden, with a developing U.S. summer increase.

Notable countries/regions:

- United States: Low but rising activity has been reported across all four regions. Severe illness remains low, but regional growth warrants attention.

- Global: WHO’s latest available respiratory-virus update showed low activity overall, with localized higher positivity in tropical settings.

- Variant surveillance: WHO added PQ.16.1.1 as a variant under monitoring as of 27 July, alongside NB.1.8.1, XFG, and BA.3.2. Monitoring status alone does not establish greater severity or immune escape.

- EU/EEA: Activity remains low and inter-seasonal.

Severity: Moderate watch in the United States; Low globally.

Trend: Worsening in the United States; stable or unclear elsewhere.

Why it matters now: Broad U.S. growth can precede increased hospital burden, while the new variant designation highlights the importance of genomic and severity surveillance.

2. Measles

Status: Sustained high-significance transmission driven by immunity gaps.

Notable countries/regions:

- United States: More than 2,300 cases have been reported in 2026, already above the full-year 2025 total and the highest annual burden since the early 1990s. Most cases are outbreak-associated.

- New Mexico: A newly reported analysis estimated that the state’s 2025 outbreak cost $5.4 million in medical care, lost productivity, and public-health response.

- Florida: 155 cases have been reported against a historical annual average of roughly 3 to 4.

- Canada: Prolonged continuous transmission has resulted in loss of elimination status.

- Global: Large recent outbreaks in Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan continue to create importation pressure.

Severity: High.

Trend: Worsening.

Why it matters now: Persistent transmission, hospitalizations, school-level coverage gaps, and high response costs show that the problem extends well beyond the formal question of elimination status.

3. Pertussis

Status: Continued circulation, but no major new global escalation identified today.

Notable countries/regions:

- United States: Preliminary 2026 activity remains below the same period in 2025 and below the recent post-pandemic peak.

- No new late-July or early-August cross-border surge was verified in the available reporting.

Severity: Low to Moderate.

Trend: Stable to improving in the United States; unclear globally.

Why it matters now: Young infants remain at highest risk of severe disease, and local outbreaks can accelerate where maternal vaccination or childhood coverage is weak.

4. Ebola

Status: Rapidly worsening Bundibugyo Ebola virus disease outbreak in eastern DRC.

Notable countries/regions:

- DRC: Reporting published 4 August described approximately 1,700 deaths. WHO’s latest formal report, with data through 26 July, documented intensifying transmission, increasing mortality, and geographic expansion. The outbreak is the largest recorded Bundibugyo virus outbreak.

- Response indicators: Recent specialist reporting estimated that about 80% of cases were not linked to known contacts and roughly 60% of deaths occurred in the community, indicating that surveillance and referral systems are being outpaced.

- Operational constraints: Armed-group activity and healthcare-worker strikes in North Kivu and Ituri continue to impede contact tracing, treatment access, safe burial, and community engagement.

- Uganda: The incursion appears contained at about 20 cases, with the country progressing through its 42-day end-of-outbreak countdown. Reporting differs on the exact start date of that period.

- Regional risk: No new country was reported affected overnight, but population movement and incomplete transmission-chain visibility keep neighboring countries on high alert.

Severity: High.

Trend: Worsening rapidly in DRC; improving in Uganda; regional risk remains elevated.

Why it matters now: Rapid growth, community deaths, unlinked transmission, insecurity, and the absence of a licensed Bundibugyo-specific vaccine or treatment make continued expansion likely without major operational improvement.

Uncertainty note: Current totals are changing quickly. The approximately 1,700-death figure comes from recent medical reporting; WHO’s formal situation reports remain the preferred source for consolidated counts.

5. Diphtheria

Status: Significant Australian outbreak continues; no verified new acceleration today.

Notable countries/regions:

- Australia: The Australian CDC reported 429 notifications as of 6 July, concentrated in the Northern Territory and Western Australia. Most cases occurred among Aboriginal and Torres Strait Islander people in remote and very remote communities. About one-third were respiratory, and one death was considered probably diphtheria-associated.

- Genomic evidence links cases across Western Australia, Northern Territory, South Australia, and Queensland within the 2026 outbreak group.

Severity: Moderate.

Trend: Stable to possibly improving; recent-week data remain incomplete.

Why it matters now: Locally acquired respiratory diphtheria is unusual in Australia and exposes vaccination, booster, healthcare-access, contact-management, and antitoxin-logistics gaps.

6. RSV

Status: Low overall; no major update worth elevating today.

Notable countries/regions:

- United States and EU/EEA: Activity remains very low or inter-seasonal.

- Tropical and southern settings: Localized higher positivity persists in parts of Central and South America and isolated areas of Africa and Southern Asia.

Severity: Low globally; Moderate local pediatric watch where positivity is elevated.

Trend: Stable overall; localized increases.

Why it matters now: Infants remain the main severe-disease group, and localized activity can pressure pediatric services outside the usual temperate peak.

7. Influenza A

Status: Seasonal activity is low; zoonotic influenza signals merit attention.

Notable countries/regions:

- China: Four additional human H9N2 infections were reported, bringing the total reported over the past six months to 20. H9N2 infections are generally sporadic and linked to poultry exposure, but the frequency warrants continued investigation.

- Australia: Additional H5N1 detections have been reported in wild birds.

- United States: H5 viruses remain a concern in wild birds, poultry, and dairy cattle, with occupational-exposure monitoring continuing.

- Seasonal influenza A: Activity remains low in the United States and EU/EEA. A(H3N2) has predominated in parts of Central America/Caribbean and Middle Africa, while A(H1N1)pdm09 has been prominent in Southern Asia.

- No evidence of sustained human-to-human transmission of H5 or H9N2 was identified in the reporting reviewed.

Severity: Low for seasonal influenza A; Moderate for zoonotic influenza watch.

Trend: Seasonal activity stable/low; animal and sporadic human detections remain geographically dynamic.

Why it matters now: Repeated human H9N2 infections and continued H5N1 animal spread increase opportunities for viral adaptation and require rapid investigation of clusters or unexplained severe respiratory illness.

8. Influenza B

Status: Low global activity; no major update worth elevating today.

Notable countries/regions:

- Influenza B remains predominant among low-level global detections, including in Tropical South America and Western Africa.

- United States and EU/EEA activity remains low/inter-seasonal.

Severity: Low.

Trend: Stable.

Why it matters now: The absolute burden is low, but B-virus predominance remains relevant to southern-hemisphere surveillance and planning for the next northern-hemisphere season.

Other Outbreaks of Interest

1. Cholera

Status: Broad multi-country increase continues.

- WHO’s latest consolidated update reported 29,610 new cholera or acute watery diarrhoea cases from 16 countries during May, 43% more than the previous month.

- Reported deaths rose 30% to 271, with the largest burden in the Eastern Mediterranean and African regions.

Severity: High.

Trend: Worsening in the latest consolidated interval.

Why it matters now: Conflict, displacement, flooding, and damaged water and sanitation systems are increasing incidence and delaying access to life-saving rehydration.

2. Cyclospora, United States

Status: Very large, fragmented foodborne outbreak situation.

- Recent specialist reporting described about 11,000 cases and two deaths, likely representing four to six distinct outbreaks.

- Taylor Farms-linked lettuce may account for part of the burden, but other clusters may involve cilantro, parsley, travel, or unresolved sources.

Severity: Moderate.

Trend: Worsening or unclear while clusters and food vehicles are separated.

Why it matters now: The scale, multiple suspected vehicles, delayed traceability, and fragmented communication prolong exposure uncertainty.

3. Mpox

Status: Ongoing multi-country transmission without a major new early-August escalation identified.

Severity: Moderate.

Trend: Stable or unclear globally.

Why it matters now: Continued transmission requires sustained case detection, vaccination, and clinical vigilance, particularly in affected African settings and travel networks.

4. European vector-borne threats

Status: Seasonal activity is established.

- West Nile virus activity has been reported in Italy, Greece, Romania, North Macedonia, Spain, and France.

- Spain has reported two locally acquired Crimean-Congo haemorrhagic fever cases in 2026.

- A rare cluster of airport-associated Plasmodium falciparum malaria linked to Frankfurt Airport exposure remains under investigation.

Severity: Moderate.

Trend: Seasonal increase for West Nile virus; limited or unclear for CCHF and airport malaria.

Why it matters now: Peak vector season increases the likelihood of geographic expansion and severe neuroinvasive or haemorrhagic disease in vulnerable people.

Watchlist

- SARS-CoV-2: Always monitor. Watch U.S. hospitalizations, wastewater, emergency-department visits, and the epidemiology of PQ.16.1.1.

- Measles: Always monitor. Watch U.S. outbreak duration, hospitalizations, local vaccine gaps, importations, and elimination-status implications.

- Ebola Bundibugyo: Watch formal WHO case/death totals, unlinked cases, community deaths, geographic expansion, healthcare-worker strike resolution, border alerts, and Uganda’s clearance countdown.

- Influenza A(H9N2/H5N1): Watch additional human H9N2 cases in China, Australian H5N1 wildlife detections, U.S. mammalian outbreaks, exposed-worker infections, and any human cluster.

- Diphtheria: Watch Australia’s Northern Territory and Western Australia for respiratory cases, deaths, and sustained decline.

- Cholera: Watch mortality in the Eastern Mediterranean and African regions.

- Cyclospora: Watch for clear separation of outbreaks, identified food vehicles, recalls, and updated severe-outcome totals.

- West Nile virus/CCHF: Watch geographic expansion during the European vector season.

References

- WHO Ebola Bundibugyo virus disease outbreak report, DRC: https://www.afro.who.int/countries/democratic-republic-of-congo/publication/ebola-bundibugyo-virus-disease-outbreak-3

- WHO SARS-CoV-2 variant tracking: https://www.who.int/activities/tracking-SARS-CoV-2-variants/

- WHO Global Respiratory Virus Activity Weekly Update No. 587: https://www.who.int/publications/m/item/global-respiratory-virus-activity-weekly-update-n-587

- WHO COVID-19 dashboard: https://data.who.int/dashboards/covid19/summary

- CDC Respiratory Illnesses Data Channel: https://www.cdc.gov/respiratory-viruses/data/index.html

- CDC Measles Cases and Outbreaks: https://www.cdc.gov/measles/data-research/index.html

- CDC Global Measles Outbreaks: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- CDC Pertussis Surveillance and Trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

- CDC A(H5) Bird Flu Current Situation: https://www.cdc.gov/bird-flu/situation-summary/index.html

- WHO Cholera Epidemiological Update No. 38: https://www.who.int/publications/m/item/multi-country-outbreak-of-cholera-epidemiological-update-38-30-june-2026

- ECDC Communicable Disease Threats Reports: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report

- Australian CDC diphtheria epidemiological update: https://www.cdc.gov.au/sites/default/files/2026-07/20260707-diphtheria_epi_summary_-_web.pdf

- CIDRAP, 4 August 2026 daily reporting, including H9N2/H5N1 and measles-response costs: https://www.cidrap.umn.edu/news

- MedPage Today, 4 August 2026, Ebola mortality update: https://www.medpagetoday.com/infectiousdisease/ebola/122474

Source note: The general web-search service was unavailable during this run. This briefing uses directly accessible authoritative surveillance baselines, current public-health and medical reporting in the connected mailbox, and the prior briefing’s verified source trail. Fast-moving Ebola and Cyclospora figures are labeled provisional.

What to Monitor Next

- WHO’s next consolidated DRC Ebola count and whether transmission-chain visibility improves.

- Whether Uganda completes its Ebola clearance period without a new case.

- The next CDC measles update and any new sustained U.S. transmission chains.

- Whether the U.S. COVID increase translates into higher hospital or emergency-department burden.

- Additional H9N2 human infections in China or H5N1 detections in mammals and exposed people.

- The next WHO respiratory-virus update for southern-hemisphere influenza and RSV movement.

- Australia’s next diphtheria report and Cyclospora source attribution or recalls.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

... the long XFG* domination and subsequent immunity to it build up. I will have several new automated outputs out tomorrow. BTW, you can see in the US graphs when the model starts school, creating the humps during the week. So mask up, boost, and stay safe.

Selected active variants:

XFG share= 17.990% beta0_guess=0.17446386

PY.1 share= 15.842% beta0_guess=0.25946579

XFJ.3 share= 14.417% beta0_guess=0.26689971

PQ.2 share= 13.915% beta0_guess=0.25552717

NB.1.8.1 share= 8.844% beta0_guess=0.32564109

LF.7 share= 5.832% beta0_guess=0.24685718

XFG.1 share= 5.706% beta0_guess=0.19361494

BA.3.2.2 share= 5.376% beta0_guess=0.19904550

MC.10.1.7 share= 3.637% beta0_guess=0.20532365

XFG.3 share= 3.223% beta0_guess=0.23051626

OTHER share= 5.218% beta0_guess=0.17446386

Wrote: MAPS_FORECASTS/initial_conditions/maps_active_variants_07-12-2026.csv

Wrote: MAPS_FORECASTS/initial_conditions/maps_variant_fragment_07-12-2026.nml

Wrote: MAPS_FORECASTS/initial_conditions/maps_IC_07_12_2026.nc

Init date: 2026-07-12

History days: 500

Daily Global Pathogen and Outbreak Briefing - 2026-07-28

Executive Summary

- Highest-priority signal: the Bundibugyo Ebola outbreak in eastern Democratic Republic of the Congo remains the most consequential acute event. ECDC reported 2,905 confirmed DRC cases and 1,269 confirmed deaths as of 23 July, with 97 new confirmed cases and 62 deaths added from the previous day. Uganda has reported no new cases since 21 June and has begun its end-of-outbreak countdown, but regional spread risk remains elevated because of cross-border movement, insecurity, and incomplete transmission-chain visibility.

- Measles remains a major vaccine-preventable disease concern. CDC reported 2,318 confirmed U.S. cases as of 23 July, already exceeding the full-year 2025 total, with 93% of 2026 cases outbreak-associated. Globally, CDC/WHO data show large recent outbreaks across South Asia, the Middle East, the Americas, and Africa.

- Respiratory viruses remain mostly quiet globally and in the EU/EEA, with low SARS-CoV-2, RSV, and influenza activity overall. The main nuance is early COVID-19 growth signals in parts of the United States and pockets of elevated SARS-CoV-2, RSV, and influenza positivity in tropical and southern-hemisphere settings.

- Diphtheria in Australia remains notable because of its scale and local transmission in remote communities. Australian CDC reported 429 cases in 2026 as of 6 July, concentrated in the Northern Territory and Western Australia, with one probable diphtheria-associated death; recent national notifications appear to be slowing but recent weeks are incomplete.

- Other events worth monitoring: global cholera activity remains high with substantial new deaths; avian influenza A(H5) continues to pose a low but persistent zoonotic risk and is newly prominent in Australian wild seabirds; Europe has early-season West Nile virus activity, two CCHF cases in Spain, and a cluster of airport-associated malaria linked to Frankfurt Airport exposure.

Pathogen-by-Pathogen Briefing

1. SARS-CoV-2

Status: Low global activity overall, with regional pockets and early U.S. summer growth signals.

Notable countries/regions:

- Global: WHO reported SARS-CoV-2 positivity low and stable across most reporting countries in week 28, with elevated positivity above 10% in countries in Central America and the Caribbean and single countries in Tropical South America, Western Asia, and South-East Asia.

- EU/EEA: ECDC reported SARS-CoV-2 activity low across all age groups in primary and secondary care settings in week 29.

- United States: CDC reported national COVID-19 activity low and stable as of 24 July, but with early signs of increase in the West and South. CDC modeling estimated infections growing or likely growing in 37 states as of 22 July.

Severity: Low globally; Moderate watch in U.S. regions with growth signals.

Trend: Stable globally; worsening/early increase in parts of the United States.

Why it matters now: The current burden is low, but growth signals can precede healthcare impacts, especially for older adults and immunocompromised people.

2. Measles

Status: High public-health significance due to sustained outbreak activity and vaccination-gap implications.

Notable countries/regions:

- United States: CDC reported 2,318 confirmed measles cases in 2026 as of 23 July, including cases reported by 45 jurisdictions and 16 cases among international visitors. CDC reported 35 new outbreaks in 2026, with 93% of confirmed cases outbreak-associated. The 2026 count has already exceeded the 2,289 confirmed U.S. cases reported for all of 2025.

- Global: CDC/WHO monthly data covering December 2025-May 2026 listed the largest outbreak totals in Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan.

Severity: High.

Trend: Worsening.

Why it matters now: The scale and geographic breadth of measles transmission point to immunity gaps and cross-border seeding risk; the U.S. surge is especially important because elimination status depends on interruption of endemic transmission.

3. Pertussis

Status: No major new global escalation identified today; continued circulation at lower levels than recent post-pandemic peaks.

Notable countries/regions:

- United States: CDC’s pertussis surveillance page says preliminary 2026 case counts are lower than the same period in 2025, and CDC’s respiratory data channel notes whooping cough continues to circulate below post-pandemic peaks.

- Americas: PAHO’s March update remains relevant background for elevated regional attention, but no new late-July regional escalation was identified in today’s scan.

Severity: Low to Moderate, depending on local infant vulnerability and vaccination coverage.

Trend: Stable to improving in the United States; unclear globally.

Why it matters now: Pertussis can produce severe disease in infants, and waning immunity plus under-vaccination can drive local rebounds even when national signals are quieter.

4. Ebola

Status: Active high-severity Bundibugyo Ebola outbreak centered in eastern DRC; Uganda appears to be moving toward outbreak closure if no further transmission occurs.

Notable countries/regions:

- Democratic Republic of the Congo: ECDC reported 2,905 confirmed cases and 1,269 confirmed deaths as of 23 July, based on data through 22 July. Ituri remains the main focus, with additional affected health zones in North Kivu, South Kivu, Haut-Uele, and Tshopo.

- Uganda: 20 confirmed cases and two deaths have been reported; no new cases since 21 June. Uganda discharged its last patient on 16 July and began the 42-day countdown toward declaring the outbreak over.

- International evacuations: ECDC noted medically evacuated or precautionary cases/contacts involving Germany, France, Czechia, and the United Kingdom in connection with humanitarian/healthcare exposure in DRC.

Severity: High.

Trend: Worsening in DRC; improving in Uganda; regional risk remains high.

Why it matters now: Bundibugyo virus has no licensed vaccine or specific treatment, response is complicated by insecurity and humanitarian conditions, and neighboring countries remain at risk through population movement and uncertain transmission chains.

5. Diphtheria

Status: Significant ongoing outbreak in Australia, with evidence of recent plateau/slowing but continued transmission in remote and very remote communities.

Notable countries/regions:

- Australia: Australian CDC reported 429 diphtheria notifications in 2026 as of 6 July, including 426 confirmed and three probable cases. Most cases were in the Northern Territory and Western Australia, with smaller numbers in South Australia and Queensland. About 65% were cutaneous and 32.4% respiratory; one 2026 death was probably diphtheria-associated.

- Northern Territory and Western Australia: These remain the main affected jurisdictions. The outbreak is concentrated among Aboriginal and Torres Strait Islander people and remote/very remote communities. Genomic analysis indicates recent cases across WA, NT, SA, and Queensland are linked in the AU-2026 outbreak group.

Severity: Moderate.

Trend: Stable to improving, with caution because recent-week data are incomplete.

Why it matters now: Locally acquired respiratory diphtheria is rare in Australia, and the outbreak highlights booster timing, remote-community access, contact tracing, and vaccination response needs.

6. RSV

Status: Low globally overall, with localized elevated positivity in some tropical/southern settings.

Notable countries/regions:

- Global: WHO reported RSV positivity low globally in week 28, but elevated above 10% in a few countries in Central America and the Caribbean and in Tropical and Temperate South America; positivity exceeded 30% in single countries in Eastern Africa and Southern Asia.

- EU/EEA: ECDC reported RSV activity low and at inter-seasonal levels in week 29.

- United States: CDC reported RSV activity very low in most areas as of 24 July, with low emergency department visits and hospitalizations; infants and children younger than 4 remain the highest-burden group.

Severity: Low globally, with Moderate local pediatric watch where positivity is elevated.

Trend: Stable globally; localized increases.

Why it matters now: RSV is currently out of season in many temperate regions, but localized activity can still affect pediatric capacity and should be tracked ahead of seasonal transitions.

7. Influenza A

Status: Seasonal influenza A activity remains low globally, but zoonotic influenza A(H5) remains a watch item.

Notable countries/regions:

- Global seasonal influenza: WHO reported global influenza detections low in week 28, with influenza B predominant overall. In zones with elevated influenza positivity, influenza A(H3N2) predominated in Central America/Caribbean and Middle Africa, A(H1N1)pdm09 in Southern Asia, and A(H1N1)pdm09/A(H3N2) co-dominance in Western and South-East Asia.

- EU/EEA: ECDC reported influenza activity low and inter-seasonal in week 29.

- United States: CDC reported seasonal influenza activity low as of 24 July.

- Avian influenza A(H5): CDC continues to assess current U.S. public-health risk as low while monitoring exposed people. H5 remains widespread in wild birds worldwide and associated with poultry and U.S. dairy-cattle outbreaks plus sporadic worker infections. Recent reporting from Australia points to H5 detections in wild seabirds across multiple states, raising wildlife and poultry biosecurity watch concerns, though human risk is described as low and no poultry involvement was identified in the official summaries reviewed.

Severity: Low for seasonal influenza A; Moderate watch for zoonotic A(H5).

Trend: Seasonal influenza stable/low; A(H5) geographically dynamic in animals.

Why it matters now: Seasonal burden is low, but A(H5) remains important because animal spread can increase exposure opportunities and requires ongoing surveillance for mammalian adaptation or human clusters.

8. Influenza B

Status: Low global activity, but currently predominant among low-level global influenza detections.

Notable countries/regions:

- Global: WHO reported influenza B viruses were predominant among influenza detections in week 28, with influenza B predominating in Tropical South America and Western Africa among zones with elevated positivity. Influenza A and B were co-dominant in Temperate South America, Southern Africa, and Eastern Asia.

- EU/EEA and United States: Influenza activity remains low/inter-seasonal.

Severity: Low.

Trend: Stable.

Why it matters now: Influenza B is the leading type among current low-level detections globally, so it should stay on the respiratory-virus watchlist even while overall burden is low.

Other Outbreaks of Interest

1. Cholera

Status: Multi-country activity remains high.

Notable countries/regions:

- ECDC’s monthly update reported 19,659 new cholera cases and 261 deaths globally between 26 May and 22 June. The five countries reporting the most new cases were Nigeria, DRC, Angola, Malawi, and Burundi; the most new deaths were reported by DRC, Nigeria, Angola, Congo, and Mozambique.

- Since 1 January 2026 and as of 22 June, ECDC reported 105,813 cholera cases and 1,216 deaths worldwide.

Severity: High.

Trend: Worsening in the latest monthly interval compared with the prior reporting period.

Why it matters now: High death counts and multiple affected countries indicate water/sanitation stress, response-capacity pressure, and risk of cross-border or travel-associated spread.

2. Dengue

Status: Regionally active, with localized transmission signals in Europe and substantial burden in the Americas.

Notable countries/regions:

- EU/EEA: ECDC reported one locally acquired dengue case in France in 2026 as of 22 July, with one new case reported that week.

- Americas: PAHO reported more than 1.2 million suspected dengue cases in the Region of the Americas through epidemiological week 22 of 2026.

Severity: Moderate.

Trend: Seasonal/worsening in some areas; unclear globally.

Why it matters now: Dengue remains a large-burden arboviral threat, and locally acquired European cases are important early indicators during vector season.

3. West Nile Virus, Europe

Status: Seasonal activity underway.

Notable countries/regions:

- ECDC reported 35 affected areas across six European countries as of 22 July: Italy, Greece, Romania, North Macedonia, Spain, and France.

Severity: Moderate.

Trend: Seasonal increase.

Why it matters now: The transmission season is active, and older adults are at highest risk of neuroinvasive disease.

4. Crimean-Congo Haemorrhagic Fever, Europe

Status: Limited but important seasonal signal.

Notable countries/regions:

- ECDC reported two locally acquired CCHF cases in Spain in 2026 as of 22 July.

Severity: Moderate.

Trend: Stable/limited signal.

Why it matters now: CCHF has high severity potential and requires tick-exposure awareness, infection prevention, and rapid clinical recognition.

5. Airport-Associated Malaria, Germany

Status: Unusual cluster under investigation.

Notable countries/regions:

- ECDC reported four Plasmodium falciparum malaria cases among people who worked at Frankfurt International Airport before symptom onset between 4 and 6 July; none had travel to malaria-endemic areas. Investigations include risk communication, vector monitoring, genomic analyses, and case finding.

Severity: Moderate.

Trend: Unclear.

Why it matters now: Airport malaria is rare but clinically important; unexplained fever after relevant airport exposure should prompt consideration of malaria even without travel.

6. Mpox

Status: Ongoing global outbreak response, but no major new late-July escalation identified in today’s scan.

Notable countries/regions:

- WHO’s latest external situation report available in this scan covered global mpox epidemiology through 31 May and Africa through 14 June, with operational response updates through 17 June.

Severity: Moderate.

Trend: Unclear from today’s public updates.

Why it matters now: Mpox remains relevant because of ongoing multi-country transmission and risk during large gatherings, but today’s briefing did not identify a major new event requiring elevation beyond watch status.

Watchlist

- SARS-CoV-2: Watch for whether early U.S. growth signals in the West and South translate into increased hospitalizations or broader wastewater/test positivity increases.

- Measles: Watch U.S. outbreak-associated transmission, state-level acceleration, and global importation risk tied to large outbreaks in Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan.

- Ebola Bundibugyo: Watch DRC case growth, contact follow-up coverage, affected health-zone expansion, cross-border alerts, and Uganda’s 42-day countdown.

- Diphtheria: Watch Australia’s NT/WA trend, respiratory-case counts, hospitalization signals, vaccination/booster response, and spread outside remote outbreak areas.

- Cholera: Watch DRC, Nigeria, Angola, Congo, and Mozambique mortality trends and any sharp increases after the next WHO/ECDC monthly update.

- Avian influenza A(H5): Watch animal detections in Australia, U.S. dairy/poultry-linked exposure monitoring, human clusters, severity changes, and any evidence of sustained mammal-to-mammal or human-to-human transmission.

- Dengue/West Nile/CCHF: Watch seasonal vector-borne expansion in Europe and the Americas.

References

- WHO Global Respiratory Virus Activity Weekly Update No. 587, week 28 ending 12 July 2026: https://cdn.who.int/media/docs/default-source/influenza/influenza-updates/2026/202628_rvupdate_587.pdf

- WHO COVID-19 dashboard summary, week of 22-28 June 2026: https://data.who.int/dashboards/covid19/summary

- CDC Respiratory Illnesses Data Channel, updated 24 July 2026: https://www.cdc.gov/respiratory-viruses/data/index.html

- CDC Current Epidemic Trends based on Rt, updated 24 July 2026: https://www.cdc.gov/cfa-modeling-and-forecasting/rt-estimates/index.html

- CDC Measles Cases and Outbreaks, updated 24 July 2026: https://www.cdc.gov/measles/data-research/index.html

- CDC Global Measles Outbreaks, updated 14 July 2026: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- CDC Pertussis Surveillance and Trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

- WHO Ebola outbreak - DRC 2026 situation page: https://www.who.int/emergencies/situations/ebola-outbreak---drc-2026

- ECDC Communicable Disease Threats Report, Week 30, 18-24 July 2026: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-18-24-july-2026-week-30

- Australian Centre for Disease Control, Diphtheria in Australia epidemiological update as at 6 July 2026: https://www.cdc.gov.au/sites/default/files/2026-07/20260707-diphtheria_epi_summary_-_web.pdf

- CDC A(H5) Bird Flu Current Situation: https://www.cdc.gov/bird-flu/situation-summary/index.html

- WHO Western Pacific avian influenza surveillance page: https://www.who.int/westernpacific/wpro-emergencies/surveillance/avian-influenza

- ECDC Cholera worldwide overview, monthly update as of 22 June 2026: https://www.ecdc.europa.eu/en/all-topics-z/cholera/surveillance-and-disease-data/cholera-monthly

- WHO Multi-country outbreak of mpox, External Situation Report #67, 26 June 2026: https://www.who.int/publications/m/item/multi-country-outbreak-of-mpox--external-situation-report--67---26-june-2026

- PAHO Dengue epidemiological situation in the Region of the Americas, EW 22 2026: https://www.paho.org/en/documents/dengue-epidemiological-situation-region-americas-epidemiological-week-22-2026

Closing: What to Monitor Next

- Whether DRC Ebola daily additions remain near or above late-July levels, and whether the share of contacts under follow-up improves.

- Whether Uganda completes the 42-day Ebola clearance period without further cases.

- U.S. measles state dashboards for sustained transmission and any new large outbreaks.

- Next WHO respiratory-virus update for signs of increasing influenza, RSV, or SARS-CoV-2 activity in the southern hemisphere and tropics.

- Australia’s next diphtheria update for confirmation that notifications are continuing to slow and that respiratory cases are not increasing.

- Cholera mortality and case growth in DRC, Nigeria, Angola, Congo, Mozambique, and Malawi.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

These are MAPS-generated fields of New Daily Infections (NDIs).

These are the NDIs calculated on the WHN wastewater Website. There are also individual states at the site.

These are the NDIs by variant for the US made by combining the GISAID variant sequences with the WHN Wastewater data. The legend identifies the variants plotted and there color.

Shown above are the most up-to-date spatial, USA average total, and by variant plots of New Daily Infections (NDIs). The data runs through July 12, 2026. California is the hot spot right now, as indicated by the red, which indicates high NDIs. Other areas of interest are Georgia, Illinois, and Florida. Of interest is the rise of NB.1.8.1 and its child PQ.2. Back in January, I surmised that NB.1.8* would eventually take over for the leading variants XFG*. Overall, in the world we have seen these two fight for the leading with NB.1.8* leading globally. In many of the places they have flipped positions. Why? It is likely a build up of natural immunity for the dominating variant, thus the family has difficulty escape other family members immunity. In this country XFG* has now dominated for almost a year.

I am currently working on a new forecast that starts from 7-12-2026 and runs through 11-12-2026. I should have that ready tomorrow. MAPS is still predicting a peak in early September.

Daily Global Pathogen and Outbreak Briefing - 2026-07-27

Executive summary

- Highest concern: Ebola Bundibugyo virus disease in eastern Democratic Republic of the Congo remains the dominant global outbreak signal. Recent public counts differ by source because of rapid reporting changes, but all show fast growth, high fatality, and difficult response conditions. Uganda appears to be in enhanced surveillance after no new reported cases since 21 June, while internationally evacuated healthcare/humanitarian workers underscore cross-border response risk.

- Measles remains a high-momentum vaccine-preventable threat. The United States has now reported more confirmed cases in 2026 than in all of 2025, while WHO/CDC global data show large outbreaks across South Asia, the Middle East, Africa, and the Americas.

- Diphtheria remains notable because of geographically broad vaccine-preventable outbreaks, especially Australia’s largest recent outbreak, Haiti, and several sub-Saharan African countries.

- Respiratory viruses are comparatively quieter globally: WHO GISRS reports low global SARS-CoV-2, influenza, and RSV activity overall, with localized influenza and RSV positivity in parts of the Americas, Africa, and Asia.

- Other outbreak signals worth watching: U.S. multistate cyclosporiasis linked to recalled iceberg lettuce; European seasonal West Nile virus, CCHF, and locally acquired dengue signals; cholera’s continuing multi-country burden; and zoonotic/avian influenza A(H5) activity.

SARS-CoV-2 / COVID-19

Severity: Low globally, Moderate in localized areas

Trend: Stable globally; localized increases Status summary: WHO’s latest dashboard shows SARS-CoV-2 activity generally low and stable globally. For 22-28 June 2026, 57,509 sentinel/systematic surveillance samples were tested across 69 countries, with 1,327 positive, a 2.3% positivity rate. Reported 28-day cases rose modestly to 16,448 for 1-28 June, but WHO cautions that global testing and reporting are incomplete.

Notable countries/regions: Local elevated activity or increases were reported in parts of Central America and the Caribbean, Tropical South America, Northern Europe, multiple African subregions, and South-East Asia. ECDC and UKHSA/UKHSA-linked surveillance continue to show low baseline respiratory-virus activity in Europe/UK settings.

Why it matters now: COVID-19 is not the leading acute outbreak concern today, but SARS-CoV-2 should remain on the watchlist because surveillance is thinner than in earlier pandemic years and localized respiratory co-circulation can still stress healthcare systems.

Measles

Severity: High

Trend: Worsening

Status summary: Measles activity remains elevated globally and in the United States. CDC reported 2,318 confirmed U.S. measles cases as of 23 July 2026, surpassing the full-year 2025 total of 2,289. CDC reports 35 outbreaks in 2026 and 93% of U.S. confirmed cases are outbreak-associated.

Notable countries/regions: CDC’s global outbreak table based on WHO provisional data for December 2025-May 2026 lists the largest outbreak burdens in Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan. PAHO reports a multi-country measles outbreak in the Americas with nearly 15,000 confirmed cases and 29 deaths in its 2026 outbreak page. In the U.S., cases are spread across 45 jurisdictions plus international visitors.

Why it matters now: The combination of international travel, persistent immunity gaps, and large outbreaks threatens elimination status and creates repeated importation and outbreak-amplification risk.

Pertussis

Severity: Low to Moderate

Trend: Improving or below 2025 in some monitored settings; unclear globally Status summary: No new global high-severity pertussis signal stood out today. CDC’s U.S. surveillance page says preliminary 2026 U.S. pertussis cases are lower than the same period in 2025, after a post-pandemic peak in November 2024. Australia’s CDC similarly reported earlier in 2026 that national pertussis activity was far below the same period in 2025 and closer to inter-seasonal levels.

Notable countries/regions: United States and Australia are useful markers of the post-2024/2025 pertussis wave easing in some high-surveillance settings. PAHO’s March 2026 update still supports regional vigilance in the Americas because infants and under-immunized communities remain at highest risk.

Why it matters now: Pertussis remains a vaccine-timing and maternal/infant protection issue even when overall incidence is easing; macrolide resistance monitoring remains important internationally.

Ebola Bundibugyo Virus Disease

Severity: High

Trend: Worsening in DRC; improving/controlled signal in Uganda Status summary: The DRC outbreak is the most serious item today. WHO’s 17 July Disease Outbreak News reported 2,124 confirmed DRC cases and 828 deaths as of 15 July, with sustained transmission and substantial increases since the prior update. ECDC’s 24 July CDTR, using data through 22 July, reported a higher and more recent DRC total of 2,905 confirmed cases and 1,269 deaths, with 722 patients hospitalized in isolation. NaTHNaC, citing DRC Ministry of Health data as of 21 July, reported 2,536 confirmed cases and 1,033 deaths. These differences likely reflect fast-moving reporting and reconciliation rather than a resolved discrepancy.

Notable countries/regions: DRC provinces include Ituri, North Kivu, South Kivu, Tshopo, and Haut-Uele. Uganda has reported no new cases since 21 June and has begun the 42-day enhanced surveillance period after discharge of the most recent case. Germany has treated medically evacuated U.S. humanitarian workers; France previously notified a related case, reflecting international response exposures.

Why it matters now: Bundibugyo virus has no approved strain-specific vaccine or treatment, the case-fatality signal is high, and response work is occurring in areas with insecurity, population movement, and health-system stress.

Diphtheria

Severity: Moderate

Trend: Mixed; plateauing in Australia but active multi-country risk Status summary: Diphtheria remains a meaningful vaccine-preventable outbreak concern. Australia’s CDC reported 442 diphtheria notifications in 2026 as of 13 July, a substantial increase over historical levels. Most 2026 cases are in the Northern Territory and Western Australia, with smaller numbers in South Australia and Queensland; 32.8% were respiratory diphtheria and one 2026 death had diphtheria indicated as the probable cause. Recent Australian national trends appear to have plateaued or slowed, but recent data are incomplete.

Notable countries/regions: Australia’s outbreak is concentrated in remote and very remote areas and disproportionately affects Aboriginal and Torres Strait Islander people. CDC travel notices identify active diphtheria outbreaks in Haiti and in sub-Saharan African countries including Chad, Guinea, Niger, Nigeria, Mali, Mauritania, and Somalia. PAHO reported 163 confirmed cases and five deaths in the Americas during the first 21 epidemiological weeks of 2026, more than double the prior year-to-date level.

Why it matters now: Diphtheria is vaccine-preventable but can re-emerge where coverage, boosters, access to care, housing conditions, or outbreak control are insufficient. Respiratory diphtheria and antitoxin access are key severity concerns.

RSV

Severity: Low globally; Moderate in localized pediatric peaks

Trend: Stable globally, localized elevations Status summary: WHO GISRS reported RSV positivity low globally in week 28, ending 12 July 2026. However, RSV positivity was elevated above 10% in a few countries in Central America and the Caribbean and in Tropical and Temperate South America, and above 30% in single countries in Eastern Africa and Southern Asia.

Notable countries/regions: Central America/Caribbean, Tropical and Temperate South America, Eastern Africa, and Southern Asia have localized signals. ECDC reported EU/EEA respiratory virus activity at baseline levels in week 29.

Why it matters now: RSV is quiet globally but can create sharp pediatric and infant-care pressure when localized positivity rises, especially where access to preventive products or supportive care is limited.

Influenza A

Severity: Low globally; Moderate in localized seasonal/zoonotic settings

Trend: Stable low globally with localized activity Status summary: WHO’s week 28 global respiratory-virus update found influenza detections low globally, with overall positivity below 10%. Influenza A(H3N2) was predominant in Central America/Caribbean and Middle Africa; A(H1N1)pdm09 was predominant in Southern Asia; A(H1N1)pdm09 and A(H3N2) were codominant in Western and South-East Asia; and influenza A and B were codominant in Temperate South America, Southern Africa, and Eastern Asia.

Notable countries/regions: Local influenza positivity was elevated in parts of Temperate and Tropical South America, Southern and Eastern Africa, South-East Asia, Central America/Caribbean, Western/Middle Africa, Western/Eastern Asia, and Southern Asia. U.S. FluView for week 26 showed low seasonal influenza activity, with 0.6% clinical-lab positivity; influenza A represented 60% of clinical-lab positives that week.

Why it matters now: Seasonal influenza is not globally high today, but Southern Hemisphere and tropical activity warrants continued monitoring, and subtype mix matters for severity, vaccine match, and preparedness.

Influenza B

Severity: Low to Moderate

Trend: Stable low globally; locally predominant in some areas Status summary: WHO reported that influenza B viruses were predominant among global influenza detections in week 28, even as global influenza detections remained low overall. Influenza B predominated in Tropical South America and Western Africa, and codominated with influenza A in Temperate South America, Southern Africa, and Eastern Asia.

Notable countries/regions: Tropical South America, Western Africa, Temperate South America, Southern Africa, and Eastern Asia. In the U.S., influenza B accounted for 40% of clinical-lab positives in week 26, with low overall influenza activity.

Why it matters now: Influenza B can still contribute meaningfully to morbidity even when total influenza activity is low; localized predominance should guide clinical expectations and vaccine-performance review.

Other outbreaks of interest

- Cyclosporiasis, United States: Severity Moderate; trend worsening/ongoing. CDC/FDA updated a multistate outbreak linked to recalled iceberg lettuce from Taylor Farms de Mexico. As of the 24 July FDA update, 1,947 Taco Bell-exposed cases were reported from nine states, with at least 98 hospitalizations and no deaths. FDA says a false-positive sample does not change the epidemiologic basis for the recall and traceback investigation. This matters because cases may continue rising for weeks due to reporting and classification delays, and recalled product distribution involved multiple states and foodservice channels.

- Cholera, multi-country: Severity Moderate to High; trend unclear but persistent. WHO’s 30 June update reported 29,610 cholera/AWD cases from 16 countries in May 2026, a 43% rise from April, and 271 deaths, though May 2026 levels were lower than May 2025. ECDC’s June overview reported 105,813 cholera cases and 1,216 deaths worldwide as of 22 June 2026. This remains a sustained global water/sanitation and vaccine-supply concern.

- Dengue, Americas and Europe: Severity Moderate; trend seasonal/ongoing. PAHO reported 1,373,756 suspected dengue cases in the Americas by epidemiological week 26 of 2026. ECDC reported one locally acquired dengue case in France as of 22 July, highlighting seasonal vector risk in Europe.

- West Nile virus, Europe: Severity Moderate; trend seasonal/worsening as vector season advances. ECDC reported 35 affected areas in six European countries as of 22 July: Italy, Greece, Romania, North Macedonia, Spain, and France.

- Crimean-Congo haemorrhagic fever, Europe: Severity Moderate; trend stable/seasonal. ECDC reported two locally acquired CCHF cases in Spain in 2026 as of 22 July and will continue weekly monitoring through November.

- Airport-associated malaria, Germany: Severity Low to Moderate; trend unclear. ECDC reports four Plasmodium falciparum malaria cases among people who worked at Frankfurt International Airport before symptoms began 4-6 July. This is rare but operationally important for clinician awareness in unexplained fever after airport exposure.

- Avian influenza A(H5): Severity Moderate for zoonotic risk; trend stable. WHO Western Pacific reported no new human H5N1 or H5N6 cases from 17-23 July, but animal HPAI outbreaks were reported in Australia and New Zealand. WHO assesses sustained human-to-human transmission as unlikely, while zoonotic threat remains elevated where avian viruses circulate in birds.

- Mpox clade Ib, Thailand: Severity Moderate; trend unclear. NaTHNaC reported 88 confirmed clade Ib mpox cases in Thailand as of 24 July. Continue monitoring for international spread and clinical/community transmission patterns.

- Lassa fever, Nigeria: Severity Moderate; trend ongoing. NaTHNaC reported 963 confirmed cases and 229 deaths across 23 Nigerian states as of 12 July 2026.

Watchlist

- SARS-CoV-2: Watch for localized increases in the Americas, Africa, South-East Asia, and Northern Europe, and for any variant/severity signal amid reduced reporting.

- Measles: Watch U.S. state updates, PAHO Americas totals, and high-burden WHO-listed countries, especially Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan.

- Ebola Bundibugyo: Watch DRC daily/weekly updates, contact-tracing performance, healthcare-worker infections, Uganda’s 42-day surveillance countdown, international evacuations, and vaccine/therapeutic trial developments.

- Diphtheria: Watch Australia’s NT/WA/SA trends, Haiti, Nigeria and other sub-Saharan outbreaks, antitoxin availability, respiratory-case hospitalizations, and booster campaign uptake.

- Influenza A/B and RSV: Watch Southern Hemisphere and tropical-zone positivity, especially countries reporting simultaneous RSV and influenza elevation.

- Cyclosporiasis: Watch whether U.S. outbreak counts continue to rise after the lettuce recall and whether additional distribution channels or sources are identified.

- Cholera and dengue: Watch areas with water/sanitation disruption, conflict, flooding, vector expansion, or vaccine/logistics constraints.

References

- WHO COVID-19 dashboard, accessed 27 July 2026: https://data.who.int/dashboards/covid19/summary

- WHO Global Respiratory Virus Activity, Update No. 587, week 28 ending 12 July 2026: https://cdn.who.int/media/docs/default-source/influenza/influenza-updates/2026/202628_rvupdate_587.pdf

- WHO Disease Outbreak News, Ebola disease caused by Bundibugyo virus, DRC and Uganda, 17 July 2026: https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON613

- ECDC Communicable Disease Threats Report, week 30, 18-24 July 2026: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-18-24-july-2026-week-30

- CDC Measles Cases and Outbreaks, updated 24 July 2026: https://www.cdc.gov/measles/data-research/index.html

- CDC Global Measles Outbreaks, updated 14 July 2026: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- PAHO Measles Multi-Country Outbreak 2026: https://www.paho.org/en/measles-multi-country-outbreak-2026

- CDC Pertussis Surveillance and Trends, updated July 2026: https://www.cdc.gov/pertussis/php/surveillance/index.html

- Australian Centre for Disease Control, Diphtheria in Australia epidemiological update, 13 July 2026: https://www.cdc.gov.au/sites/default/files/2026-07/20260714-diphtheria_epi_summary_-_web.pdf

- PAHO diphtheria update/news release, 15 June 2026: https://www.paho.org/en/news/15-6-2026-paho-urges-countries-strengthen-vaccination-efforts-diphtheria-cases-rise-americas

- CDC Travel Health Notices, diphtheria and dengue notices, accessed 27 July 2026: https://wwwnc.cdc.gov/travel/notices

- FDA investigation of 9-state Cyclospora outbreak linked to iceberg lettuce, updated 24 July 2026: https://www.fda.gov/food/outbreaks-foodborne-illness/investigation-9-state-outbreak-cyclospora-illnesses-iceberg-lettuce-july-2026

- CDC newsroom, Cyclospora outbreak linked to iceberg lettuce expanded to four new states, 24 July 2026: https://www.cdc.gov/media/releases/2026/cyclospora-outbreak-linked-to-iceberg-lettuce-expanded-to-four-new-states.html

- WHO multi-country cholera outbreak epidemiological update #38, 30 June 2026: https://www.who.int/publications/m/item/multi-country-outbreak-of-cholera--epidemiological-update--38--30-june-2026

- PAHO dengue epidemiological situation, EW 26 2026: https://www.paho.org/en/documents/dengue-epidemiological-situation-region-americas-epidemiological-week-26-2026

- WHO Western Pacific Avian Influenza Weekly Update #1054, 24 July 2026: https://www.who.int/westernpacific/publications/m/item/avian-influenza-weekly-update---1054--24-july-2026

- NaTHNaC Outbreak Surveillance, accessed 27 July 2026: https://travelhealthpro.org.uk/outbreaks

Closing watch items for next briefing

- Reconcile the latest DRC Ebola case/death counts across DRC Ministry of Health, WHO, Africa CDC, ECDC, and NaTHNaC.

- Check whether Uganda completes additional days of enhanced surveillance without new Ebola cases.

- Track U.S. measles updates after the 24 July CDC total and any PAHO Americas revisions.

- Watch for any new human avian influenza A(H5) cases or evidence of mammal/poultry expansion.

- Review whether post-recall cyclosporiasis cases continue rising and whether FDA/CDC identify additional implicated products.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-26

Executive summary

- Highest-concern development: Bundibugyo Ebola transmission remains intense in eastern Democratic Republic of the Congo (DRC), with ECDC citing 2,905 confirmed cases and 1,269 deaths reported by DRC as of 22 July, plus 722 patients hospitalized in isolation. Uganda is in its 42-day enhanced surveillance countdown after discharging its last patient, but the DRC outbreak is still worsening.

- Measles remains a major vaccine-preventable disease signal. The United States has reported 2,318 confirmed cases in 2026 as of 23 July, exceeding the full-year 2025 total and involving 35 new outbreaks. Global cross-border risk remains high because outbreaks are active in all WHO regions.

- Respiratory viruses remain generally low globally, but with pockets of activity. WHO’s week 28 global update says SARS-CoV-2 activity is low overall, influenza remains below 10% positivity globally with influenza B predominant among detections, and RSV is low globally but elevated in selected countries in the Americas, eastern Africa, and southern Asia.

- Other notable event: the U.S. Cyclospora outbreak linked to iceberg lettuce has expanded to 1,947 laboratory-confirmed illnesses across 9 states, with 98 hospitalizations and no deaths; recalled Taylor Farms de Mexico iceberg lettuce had broad foodservice and retail distribution.

Pathogen-by-pathogen briefing

SARS-CoV-2

- Status summary: Global SARS-CoV-2 activity remains low overall, but not absent. WHO reported stable, low positivity in most reporting countries in week 28, with elevated positivity above 10% in countries in Central America and the Caribbean and single countries in tropical South America, western Asia, and South-East Asia.

- Notable countries/regions: Central America and the Caribbean; tropical South America; western Asia; South-East Asia; United States; Australia.

- Severity: Low globally; Moderate watch in parts of the United States because early summer growth signals are accumulating.

- Trend: Stable globally; worsening/early increase in parts of the United States.

- Why it matters now: CDC estimates, as of 22 July, that COVID-19 infections are growing or likely growing in 37 U.S. states, while CDC’s respiratory illness summary still describes national activity as low and stable with early increases in the West and South. WHO’s variant dashboard for 24 May-21 June shows NB.1.8.1 rising to 50% of submitted global sequences; WHO states available evidence does not indicate additional public-health risk from NB.1.8.1, XFG, or BA.3.2 relative to other circulating variants.

Measles

- Status summary: Measles remains one of the most important global vaccine-preventable threats today. The U.S. has now exceeded its full-year 2025 case total, and international import/export risk remains material because outbreaks are occurring in every WHO region.

- Notable countries/regions: United States; Canada; United Kingdom; Israel; EU/EEA; global travel corridors.

- Severity: High.

- Trend: Worsening in the United States; variable globally but still high-risk because of sustained outbreaks and immunity gaps.

- Why it matters now: CDC reports 2,318 confirmed U.S. measles cases as of 23 July 2026, with 93% outbreak-associated and 35 new outbreaks reported in 2026. CDC’s global measles page notes that outbreaks are happening in every region of the world. Recent CDC Emerging Infectious Diseases reporting on Israel’s 2025-2026 outbreak highlights the public-health importance of genomic surveillance and rapid response in preventing sustained transmission.

Pertussis

- Status summary: No major new global escalation found today, but pertussis continues to circulate after the post-pandemic resurgence.

- Notable countries/regions: United States; Australia; EU/EEA; Americas Region.

- Severity: Moderate for infants and under-immunized communities; Low-to-Moderate for general population situational awareness today.

- Trend: Improving compared with 2025 in the United States and Australia, but ongoing circulation persists.

- Why it matters now: CDC says preliminary U.S. pertussis reports in 2026 are lower than at the same point in 2025, after a November 2024 peak. Australia similarly reported in February that early-2026 pertussis activity was about 80% lower than the same period in 2025. Risk remains concentrated in infants too young to be fully vaccinated and in communities with delayed boosters.

Ebola disease, Bundibugyo virus

- Status summary: The DRC outbreak remains the highest-severity item in today’s briefing. Transmission is sustained and still expanding in affected eastern provinces.

- Notable countries/regions: DRC, especially Ituri, North Kivu, Haut-Uele, South Kivu, and Tshopo; Uganda; imported/medically evacuated cases treated in Germany and France.

- Severity: High.

- Trend: Worsening in DRC; improving in Uganda if no further cases emerge.

- Why it matters now: ECDC’s 24 July update cites 2,905 confirmed DRC cases and 1,269 deaths reported up to 22 July, including 97 new confirmed cases and 62 deaths since the previous day. Ituri remains the epicenter, with 2,595 cases and 1,077 deaths, and 47 of 140 health zones affected across five provinces. Uganda reported 20 confirmed cases and 2 deaths as of 17 July, with no new cases since 21 June and its final patient discharged on 16 July, starting the 42-day countdown toward declaring the outbreak over.

Diphtheria

- Status summary: Diphtheria remains a notable vaccine-preventable disease concern, with current public-health focus on Australia, the Americas, and parts of Africa.

- Notable countries/regions: Australia, especially Northern Territory and Western Australia; Americas Region; African Region including Nigeria, Niger, Mali, Mauritania, Guinea, Chad, Algeria, and South Africa.

- Severity: Moderate.

- Trend: Mixed. Australia shows plateauing/slowing after increases; the Americas and parts of Africa remain concerning because of under-immunization and recurrent outbreaks.

- Why it matters now: Australia’s 6 July epidemiological update reported 426 confirmed 2026 cases as of 6 July, with 55% in the Northern Territory and 41.3% in Western Australia; the past fortnight had 30 notifications versus 67 in the previous fortnight. PAHO reported 163 confirmed cases and 5 deaths in the Americas during epidemiological weeks 1-21 of 2026, more than double the comparable period cited in its alert. WHO’s July diphtheria factsheet underscores that recent outbreaks reflect gaps in multi-dose and booster coverage.

RSV

- Status summary: RSV is low globally but elevated in selected regions and seasonally active in parts of the Southern Hemisphere.

- Notable countries/regions: Central America and the Caribbean; tropical and temperate South America; eastern Africa; southern Asia; Australia.

- Severity: Moderate for infants, older adults, pregnant people, and high-risk groups; Low globally today.

- Trend: Stable/low globally; increasing in some localized areas.

- Why it matters now: WHO’s week 28 update says RSV positivity remains low globally, but is elevated above 10% in a few countries in Central America and the Caribbean and tropical/temperate South America, and above 30% in single countries in eastern Africa and southern Asia. Australia reported RSV cases increased 6.0% in the 29 June-12 July fortnight, with 85,002 RSV notifications year-to-date and increased sentinel hospital admissions driven partly by RSV.

Influenza A

- Status summary: Influenza activity remains low globally, but some tropical and Southern Hemisphere areas have elevated positivity and mixed subtype patterns.

- Notable countries/regions: Central America and the Caribbean; Middle Africa; southern Asia; western and South-East Asia; temperate South America; southern Africa; eastern Asia; Australia.

- Severity: Low globally; Moderate in localized seasonal settings and for high-risk groups.

- Trend: Mostly stable/low globally; increasing in Australia and selected tropical/Southern Hemisphere countries.

- Why it matters now: WHO reports global influenza positivity below 10% in week 28. In zones with elevated positivity, A(H3N2) predominated in Central America/Caribbean and Middle Africa; A(H1N1)pdm09 predominated in southern Asia; A(H1N1)pdm09 and A(H3N2) were codominant in western and South-East Asia. Australia reported a 47.1% fortnightly increase in influenza notifications, driven by New South Wales and Western Australia, though activity remains lower than the same period in previous years.

Influenza B

- Status summary: Influenza B is proportionally important among current global influenza detections despite overall low global activity.

- Notable countries/regions: Tropical South America; western Africa; temperate South America; southern Africa; eastern Asia; Australia.

- Severity: Low globally; Moderate in localized seasonal settings and vulnerable groups.

- Trend: Stable/low globally; localized elevation.

- Why it matters now: WHO reports influenza B viruses were predominant among global influenza detections in week 28. Influenza B was predominant in tropical South America and western Africa, and influenza A and B were codominant in temperate South America, southern Africa, and eastern Asia. This matters for vaccine-match monitoring and clinical testing, because influenza B can still drive morbidity even when overall influenza positivity is below seasonal peaks.

Other outbreaks of interest

Cyclospora, United States

- Status summary: Large multistate foodborne outbreak linked to iceberg lettuce.

- Notable countries/regions: United States; cases with Taco Bell exposure in Illinois, Indiana, Kansas, Kentucky, Michigan, Ohio, Oklahoma, Pennsylvania, and West Virginia; recalled product distribution across many additional states.

- Severity: Moderate.

- Trend: Worsening/expanding by case count and states affected, though recall and product removal are active controls.

- Why it matters now: CDC reports 1,947 laboratory-confirmed illnesses, 98 hospitalizations, and no deaths as of the July 24 update, with illness onsets through 20 July. FDA says recalled Taylor Fresh Foods iceberg lettuce products were distributed to foodservice and retail channels across numerous states, and advises consumers, restaurants, and retailers to discard recalled products.

Avian influenza A(H5N1)

- Status summary: Ongoing animal panzootic with sporadic human infections; no current evidence of sustained human-to-human spread in the sources reviewed today.

- Notable countries/regions: United States dairy and poultry settings; global wild bird and poultry systems.

- Severity: Moderate watch item.

- Trend: Ongoing/unclear.

- Why it matters now: CDC continues to describe A(H5) as widespread in wild birds globally, causing poultry outbreaks and U.S. dairy cow infections, with sporadic human cases in exposed workers; CDC states current public-health risk remains low. WHO’s 7 July H5N1 update continues monthly reporting of confirmed human cases under IHR obligations.

Mpox

- Status summary: Continues as a multi-country outbreak with clade I and clade II circulation, but no sharper escalation found in today’s scan than the Ebola, measles, and Cyclospora signals.

- Notable countries/regions: Africa, including countries with clade I transmission; countries outside Africa reporting travel-linked and non-travel-linked clade I cases.

- Severity: Moderate watch item.

- Trend: Ongoing/unclear.

- Why it matters now: WHO’s 26 June external situation report provides the latest global situation through 31 May and Africa data through 14 June. ECDC notes that clade I and II MPXV are circulating in multiple countries globally, including clade I cases outside Africa with and without travel history to countries with ongoing transmission.

Watchlist

- SARS-CoV-2: Watch U.S. West/South increases, CDC Rt estimates, wastewater signals, and whether NB.1.8.1 growth changes severity or healthcare pressure.

- Measles: Watch U.S. outbreak-associated transmission, Canada/UK/Israel and EU/EEA signals, cross-border importations, and MMR coverage response.

- Ebola Bundibugyo: Watch DRC daily case growth, contact follow-up completeness, spread outside Ituri/North Kivu, Uganda’s 42-day countdown, and any additional international medical evacuations or exportations.

- Diphtheria: Watch Australian Northern Territory/Western Australia trends, PAHO follow-up updates, and African Region outbreak persistence.

- RSV/influenza: Watch Southern Hemisphere winter activity, especially Australia, temperate South America, southern Africa, and countries where RSV and influenza are simultaneously elevated.

- Cyclospora: Watch whether U.S. case counts continue rising because of reporting delays and whether traceback identifies broader distribution beyond known recall channels.

- Avian influenza A(H5N1): Watch for human cases outside known exposure groups, mammal outbreaks, and any evidence of adaptation or sustained human transmission.

References

- WHO, Global Respiratory Virus Activity: Weekly Update No. 587, week 28 ending 12 July 2026: https://www.who.int/publications/m/item/global-respiratory-virus-activity--weekly-update-n--587

- WHO COVID-19 dashboard, variant circulation 24 May-21 June 2026: https://data.who.int/dashboards/covid19/summary

- CDC Respiratory Illnesses Data Channel, updated 24 July 2026: https://www.cdc.gov/respiratory-viruses/data/index.html

- CDC Current Epidemic Trends, COVID-19 Rt estimates, 22 July 2026: https://www.cdc.gov/cfa-modeling-and-forecasting/rt-estimates/index.html

- CDC Measles Cases and Outbreaks, updated 24 July 2026: https://www.cdc.gov/measles/data-research/index.html

- CDC Global Measles Outbreaks: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- CDC Emerging Infectious Diseases, Israel measles outbreak genomic/epidemiologic report, published 24 July 2026: https://wwwnc.cdc.gov/eid/article/32/9/26-0625_article

- CDC Pertussis Surveillance and Trends, updated 10 July 2026: https://www.cdc.gov/pertussis/php/surveillance/index.html

- ECDC Ebola disease outbreak in DRC and Uganda, updated 24 July 2026: https://www.ecdc.europa.eu/en/ebola-outbreak-democratic-republic-congo-and-uganda

- WHO Disease Outbreak News, Ebola disease caused by Bundibugyo virus, DRC and Uganda, 17 July 2026: https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON613

- Australian Centre for Disease Control, Diphtheria in Australia epidemiological update, 6 July 2026: https://www.cdc.gov.au/sites/default/files/2026-07/20260707-diphtheria_epi_summary_-_web.pdf

- PAHO, Diphtheria cases rise in the Americas, 15 June 2026: https://www.paho.org/en/news/15-6-2026-paho-urges-countries-strengthen-vaccination-efforts-diphtheria-cases-rise-americas

- WHO Diphtheria factsheet, updated 15 July 2026: https://www.who.int/news-room/fact-sheets/detail/diphtheria

- Australian Respiratory Surveillance Report, 29 June-12 July 2026: https://www.cdc.gov.au/resources/publications/australian-respiratory-surveillance-report-29-june-2026-12-july-2026

- CDC Cyclospora outbreak investigation update, July 2026: https://www.cdc.gov/cyclosporiasis/outbreaks/07-26/investigation.html

- FDA Cyclospora outbreak investigation, iceberg lettuce, July 2026: https://www.fda.gov/food/outbreaks-foodborne-illness/investigation-9-state-outbreak-cyclospora-illnesses-iceberg-lettuce-july-2026

- CDC A(H5) Bird Flu Current Situation: https://www.cdc.gov/bird-flu/situation-summary/index.html

- WHO cumulative confirmed human A(H5N1) cases, 7 July 2026: https://www.who.int/publications/m/item/cumulative-number-of-confirmed-human-cases-for-avian-influenza-a%28h5n1%29-reported-to-who--2003-2026--7-july-2026

- WHO mpox external situation report No. 67, 26 June 2026: https://www.who.int/publications/m/item/multi-country-outbreak-of-mpox--external-situation-report--67---26-june-2026

Next items to monitor

- DRC Ebola daily reporting for whether new cases remain concentrated in Ituri/North Kivu or continue spreading across health zones.

- CDC’s next measles update for new outbreaks and whether U.S. case growth accelerates before the autumn school term.

- U.S. COVID wastewater/Rt updates for confirmation of a summer increase.

- FDA/CDC Cyclospora updates for additional states, hospitalizations, or revised traceback findings.

- Southern Hemisphere respiratory-virus reports for RSV/influenza pressure on hospitals through winter.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-23

Executive summary

- Ebola Bundibugyo virus disease remains today’s highest-significance event. WHO’s latest detailed Disease Outbreak News reported sustained transmission in the Democratic Republic of the Congo, 2,124 confirmed DRC cases and 828 deaths as of 15 July, plus 20 cases in Uganda and one imported case in France. Uganda has begun the 42-day enhanced surveillance period after the most recent case was discharged, but DRC transmission remains active.

- Measles remains a major global and cross-border vaccine-preventable threat. The United States has reported 2,260 confirmed cases as of 16 July, with 93% outbreak-associated; England reported 933 laboratory-confirmed cases between 1 January and 20 July, with London accounting for just over half. PAHO has also reported sustained regional resurgence in the Americas.

- Global respiratory-virus activity is comparatively quiet. WHO’s week 28 update reported low global SARS-CoV-2 activity, influenza positivity below 10% globally, influenza B predominance among detections, and low RSV activity overall, with localized elevations in parts of the Americas, Africa, South-East Asia and Asia.

- Other items worth watching: multi-country cholera increased in May; CDC updated chikungunya outbreak areas for travelers on 22 July; Nigeria continues to report diphtheria cases, though latest weekly confirmed incidence was low compared with the large year-to-date burden.

SARS-CoV-2

Severity: Low

Trend: Stable to low globally

Notable countries/regions: Central America and the Caribbean; single countries in Tropical South America, Western Asia and South-East Asia

Status: WHO’s global respiratory-virus update for week 28, ending 12 July, found SARS-CoV-2 positivity stable and low across most reporting countries. Elevated positivity above 10% was reported in countries in Central America and the Caribbean and in single countries in Tropical South America, Western Asia and South-East Asia, with small increases in a few of these areas.

Why it matters now: SARS-CoV-2 is not currently a leading global outbreak signal, but localized increases can still affect healthcare capacity and should be monitored alongside influenza and RSV as seasonal patterns vary by hemisphere.

Measles

Severity: High

Trend: Worsening / sustained high activity Notable countries/regions: United States; England; Americas Region; Canada remains notable after loss of elimination status in 2025

Status: The United States reported 2,260 confirmed measles cases in 2026 as of 16 July across 44 jurisdictions, with 34 outbreaks reported and 93% of cases outbreak-associated. CDC also notes 2025 had 2,289 confirmed cases, meaning 2026 is already close to matching last year’s total by mid-July. England reported 933 laboratory-confirmed cases between 1 January and 20 July, with 51% in London, 16% in the West Midlands and 10% in the North West. The Americas continue to report multi-country resurgence, with PAHO situation reporting noting ongoing regional transmission.

Why it matters now: Measles is a highly contagious indicator of immunity gaps. Sustained outbreaks threaten elimination status, create heavy contact-tracing demands, and expose unvaccinated children and immunocompromised people to severe complications.

Pertussis

Severity: Moderate

Trend: Improving in some settings, but underlying risk persists Notable countries/regions: United States; Americas Region; Europe as a post-pandemic resurgence context

Status: CDC’s pertussis surveillance page indicates preliminary 2026 U.S. pertussis case counts are below the same period in 2025, after a recent peak in reported cases in November 2024. WHO notes that more than 264,000 pertussis cases were reported globally in 2025 and that DTP3 coverage was 85% globally in 2025.

Why it matters now: Current U.S. momentum appears lower than 2025, but pertussis remains a serious infant-risk pathogen. Countries should keep maternal vaccination, infant-series completion and outbreak detection high on the routine-immunization agenda.

Ebola Bundibugyo virus disease

Severity: High

Trend: Worsening in DRC; improving/stabilizing in Uganda Notable countries/regions: Democratic Republic of the Congo; Uganda; Germany and France as treatment/importation locations

Status: WHO reported on 17 July that the Bundibugyo virus disease outbreak remains active in DRC, with sustained transmission driving increases in cases and deaths. As of 15 July, DRC had reported 2,124 confirmed cases and 828 deaths. Overall, WHO reported 2,145 confirmed cases: 2,124 in DRC, 20 in Uganda and one in France, with 830 total deaths. A U.S. humanitarian worker medically evacuated from DRC to Germany was laboratory-confirmed on 13 July; this was the second U.S. citizen treated in Germany. Uganda has reported no new cases since 21 June and began the 42-day enhanced surveillance period after the latest patient was discharged.

Why it matters now: DRC transmission is occurring in a difficult operating environment marked by humanitarian stress, insecurity, population movement and the absence of an approved Bundibugyo-specific vaccine or treatment. Regional preparedness and contact tracing remain decisive.

Diphtheria

Severity: Moderate

Trend: Persistent, with mixed country-level patterns Notable countries/regions: Nigeria; Chad; Guinea; Niger; Mali; Mauritania; Somalia; wider African Region

Status: CDC maintains a travel notice for diphtheria outbreaks in parts of Sub-Saharan Africa, including Chad, Guinea, Niger, Nigeria, Mali, Mauritania and Somalia. WHO’s African Region risk assessment described a broad regional resurgence, with outbreaks reported across multiple countries since 2025. Nigeria’s latest Week 27 epidemiological report recorded four suspected diphtheria cases, one confirmed case and no deaths for the week, but a substantial year-to-date burden of 10,345 suspected cases, 8,604 confirmed cases and 237 deaths in 2026.

Why it matters now: Diphtheria is vaccine-preventable but can be severe and fatal without rapid antitoxin and antibiotics. Persistent outbreaks point to immunity gaps, supply constraints and surveillance challenges.

RSV

Severity: Low globally; Moderate in localized hot spots

Trend: Stable/low globally, localized elevations Notable countries/regions: Central America and the Caribbean; Tropical and Temperate South America; single countries in Eastern Africa and Southern Asia

Status: WHO reported RSV positivity remained low globally in week 28. However, RSV positivity exceeded 10% in a few countries in Central America and the Caribbean and Tropical and Temperate South America, and exceeded 30% in single countries in Eastern Africa and Southern Asia. A small increase was observed in one Central American country.

Why it matters now: RSV is not broadly elevated globally, but localized high positivity can affect pediatric and older-adult care capacity, especially where RSV and influenza are both elevated.

Influenza A

Severity: Low globally; Moderate in localized settings

Trend: Mostly low, localized elevated activity Notable countries/regions: Central America and the Caribbean; Middle Africa; Southern Asia; Western Asia; South-East Asia; Eastern Asia; Temperate South America; Southern Africa

Status: WHO reported global influenza detections remained low in week 28, with influenza positivity below 10% globally. Influenza A(H3N2) predominated in Central America and the Caribbean and Middle Africa; A(H1N1)pdm09 predominated in Southern Asia; A(H1N1)pdm09 and A(H3N2) were codominant in Western and South-East Asia; and influenza A and B were codominant in Temperate South America, Southern Africa and Eastern Asia. Separately, CDC continues to assess the current public-health risk from A(H5) bird flu as low, while noting widespread animal outbreaks and sporadic human infections associated with exposure.

Why it matters now: Seasonal influenza A is not driving a broad global surge, but localized activity and zoonotic A(H5) surveillance both warrant continued monitoring.

Influenza B

Severity: Low to Moderate

Trend: Stable globally; locally elevated in some areas Notable countries/regions: Tropical South America; Western Africa; Temperate South America; Southern Africa; Eastern Asia

Status: WHO reported that influenza B viruses were predominant among global influenza detections in week 28. Influenza B predominated in Tropical South America and Western Africa, while influenza A and B were codominant in Temperate South America, Southern Africa and Eastern Asia.

Why it matters now: Influenza B predominance is notable for vaccine-match and clinical planning, but overall global influenza activity remains low.

Other outbreaks of interest

Cholera

Severity: Moderate to High

Trend: Worsening in latest WHO monthly update Notable countries/regions: Eastern Mediterranean Region; African Region; South-East Asia Region; Region of the Americas

Status: WHO’s 30 June multi-country cholera update reported 29,610 new cholera/AWD cases in May 2026 across 16 countries in four WHO regions, a 43% increase from the previous month. Deaths also increased, with 271 cholera-related deaths reported in May, up 30% from the previous month.

Why it matters now: The combination of increasing cases and deaths across multiple regions signals continuing gaps in water, sanitation, access to care and oral cholera vaccine availability.

Chikungunya

Severity: Moderate

Trend: Worsening / geographically active for travelers Notable countries/regions: Bolivia; Costa Rica; French Guiana; Mauritius; Seychelles; Suriname; elevated traveler risk in Brazil, Colombia, India, Indonesia, Mexico, Nigeria, Pakistan, Peru, Philippines and Thailand

Status: CDC updated its chikungunya risk page on 22 July. Current outbreak travel notices include Bolivia, Costa Rica, French Guiana, Mauritius, Seychelles and Suriname. CDC also lists several countries with elevated risk for U.S. travelers based on recent traveler-associated cases.

Why it matters now: Multiple outbreak locations and traveler risk signal expanding Aedes-borne transmission risk. Prevention depends heavily on mosquito-bite avoidance and targeted vaccination considerations for eligible travelers.

Cyclosporiasis, United States

Severity: Moderate

Trend: Worsening / under investigation

Notable countries/regions: United States, especially multi-state foodborne investigation signals

Status: Public reporting indicates a large U.S. cyclosporiasis season with federal and state investigations into produce-linked clusters. Source attribution has been contested and some product-test findings have been revised, so this should be treated as an active investigation with uncertainty.

Why it matters now: The event is notable for its size, food-safety implications, and surveillance complexity; avoid over-interpreting source claims until agencies finalize findings.

Mpox

Severity: Low to Moderate

Trend: Ongoing monitoring

Notable countries/regions: Nigeria; EU/EEA monitoring; broader clade-related international surveillance

Status: ECDC’s latest communicable disease threats report included mpox among monitored threats, and Nigeria’s Week 27 epidemiological report recorded one confirmed mpox case with no deaths that week. No major new global escalation was identified in today’s scan.

Why it matters now: Continued genomic and regional surveillance remains important, but no major new signal was strong enough to elevate above other threats today.

Watchlist

- SARS-CoV-2: Watch localized increases in Central America/Caribbean, Tropical South America, Western Asia and South-East Asia as integrated respiratory surveillance continues.

- Measles: Watch U.S. outbreak-associated spread, England’s London/West Midlands/North West activity, and Americas regional transmission. School reopening periods could amplify spread where MMR coverage is low.

- Ebola Bundibugyo: Watch DRC transmission intensity, contact-tracing performance, healthcare-worker infections, cross-border movement, Uganda’s 42-day surveillance clock, and any further medical evacuations/importations.

- Diphtheria: Watch Nigeria’s weekly confirmed cases and mortality, plus broader African Region immunity-gap indicators and antitoxin availability.

- Chikungunya: Watch whether additional CDC travel notices are added and whether Costa Rica/northwest Pacific coastal transmission expands.

- Cholera: Watch the next WHO update for whether the May increase continues into June/July and whether deaths rise disproportionately.

- Influenza A(H5): Watch for additional human cases, evidence of human-to-human transmission, and animal outbreak expansion affecting occupational exposure groups.

References

- WHO. Global Respiratory Virus Activity: Weekly Update No. 587, week 28 ending 12 July 2026, published 22 July 2026. https://www.who.int/publications/m/item/global-respiratory-virus-activity--weekly-update-n--587

- WHO. Ebola disease caused by Bundibugyo virus, Democratic Republic of the Congo & Uganda, Disease Outbreak News, 17 July 2026. https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON613

- WHO. Ebola outbreak - DRC 2026 situation page and daily epidemiological update. https://www.who.int/emergencies/situations/ebola-outbreak---drc-2026

- ECDC. Communicable Disease Threats Report, 13-17 July 2026, week 29. https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-13-17-july-2026-week-29

- CDC. Measles Cases and Outbreaks, updated 17 July 2026. https://www.cdc.gov/measles/data-research/index.html

- CDC. Global Measles Outbreaks, updated 14 July 2026. https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- UKHSA. Measles data dashboard, updated 23 July 2026. https://ukhsa-dashboard.data.gov.uk/vaccine-preventable-diseases/measles

- PAHO/WHO. Measles multi-country outbreak 2026 and regional situation reporting. https://www.paho.org/en/measles-multi-country-outbreak-2026

- WHO. Diphtheria fact sheet, updated 15 July 2026. https://www.who.int/news-room/fact-sheets/detail/diphtheria

- WHO African Region. Rapid risk assessment: Diphtheria, African Region, version 2, 2026. https://cdn.who.int/media/docs/default-source/_sage-2026/who-rapid-risk-assessment---diphtheria---african-region-v.2.pdf

- CDC Travelers’ Health. Diphtheria in Sub-Saharan Africa travel notice. https://wwwnc.cdc.gov/travel/notices/level1/diphtheria-sub-saharan-africa

- Nigeria Centre for Disease Control and Prevention. Weekly Epidemiological Report, Week 27, 2026. https://ncdc.gov.ng/reports/weekly

- CDC. Pertussis Surveillance and Trends. https://www.cdc.gov/pertussis/php/surveillance/index.html

- WHO. Pertussis health topic page. https://www.who.int/health-topics/pertussis

- WHO. Multi-country outbreak of cholera, Epidemiological Update No. 38, 30 June 2026. https://www.who.int/publications/m/item/multi-country-outbreak-of-cholera--epidemiological-update--38--30-june-2026

- CDC. Areas at Risk for Chikungunya, updated 22 July 2026. https://www.cdc.gov/chikungunya/data-maps/index.html

- CDC. A(H5) Bird Flu: Current Situation. https://www.cdc.gov/bird-flu/situation-summary/index.html

- CDC. A(H5) Bird Flu Surveillance and Human Monitoring, situation through 27 June 2026. https://www.cdc.gov/bird-flu/h5-monitoring/index.html

Closing watch items for the next briefing

- Confirm whether WHO or DRC daily Ebola counts show continued acceleration after the 17 July DON.

- Check the next CDC measles update for whether U.S. 2026 cases exceed the full-year 2025 total.

- Monitor UKHSA’s next measles update due 6 August, with attention to London and West Midlands spread.

- Re-check WHO respiratory-virus update for any shift in influenza B predominance or SARS-CoV-2 localized increases.

- Look for new official updates on cyclosporiasis source attribution and any further chikungunya travel notices.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-21

Executive summary

- Ebola remains the most consequential global outbreak signal today. WHO reports 2,145 confirmed Bundibugyo Ebola cases across DRC, Uganda, and one case diagnosed in France, with 830 deaths reported overall. DRC continues to worsen, while Uganda has had no new case since 21 June and has begun its 42-day countdown toward declaring the outbreak over.

- Global respiratory-virus activity is generally low, but there are regional exceptions. WHO reports low global SARS-CoV-2, influenza, and RSV activity overall, with elevated pockets in parts of the Americas, Africa, Asia, and the southern hemisphere. Australia is seeing RSV and influenza activity increase in winter surveillance.

- Measles remains a major vaccine-preventable threat. The Americas continue to report multi-country transmission, the United States is near its full-year 2025 case total, and Bangladesh’s large nationwide outbreak remains important because of high pediatric burden and immunity gaps.

- Zoonotic influenza warrants continued watch: recent human avian influenza A(H5N1) in Cambodia, avian influenza A(H5) in Bangladesh, and swine-origin influenza A(H3N2)v in Brazil were all reported without detected onward spread among contacts.

- Other notable developments: a U.S. multistate Cyclospora outbreak linked to recalled iceberg lettuce has more than 1,644 cases in the five-state linked cluster; ECDC reports stable but ongoing mpox clade I transmission in the EU/EEA; WHO considers the cruise-linked Andes hantavirus outbreak contained.

SARS-CoV-2

Status: Low globally; mostly stable, with localized increases.

Notable countries/regions:

- WHO’s latest global respiratory-virus update for week 26 reported SARS-CoV-2 positivity stable and low across most reporting countries, with elevated positivity in countries in Central America and the Caribbean, Tropical South America, Middle Africa, Western Asia, and South-East Asia.

- United States: CDC reported very low and stable national COVID-19 activity as of 17 July, but early signs of increase mainly in the South.

- Australia: the Australian Respiratory Surveillance Report for 29 June-12 July recorded 3,824 COVID-19 notifications in the fortnight, down 10.2% from the prior fortnight, and 51,998 year-to-date notifications, 56.5% below the same period in 2025. NB.1.8.1 was the most common variant under monitoring.

Direction: Stable to mildly increasing in selected regions.

Why it matters now: SARS-CoV-2 is not the dominant respiratory threat globally today, but summer/winter regional increases and variant monitoring remain relevant for healthcare demand and vaccination strategy.

Measles

Status: Worsening in several regions; high-risk where immunity gaps persist.

Notable countries/regions:

- United States: CDC reported 2,260 confirmed measles cases as of 16 July 2026, with 34 outbreaks reported in 2026 and 93% of confirmed cases outbreak-associated. This is already close to the full-year 2025 total of 2,289 confirmed cases.

- Americas: PAHO’s regional situation reporting has continued to document multi-country transmission in 2026, with a May report showing Mexico, Guatemala, the United States, and Canada accounting for most confirmed cases at that point. PAHO’s later 2 July situation report noted 479 new confirmed cases across seven countries/territories during epidemiological weeks 23-24.

- Bangladesh: WHO’s May DON remains a significant signal. Bangladesh reported a nationwide increase across 58 of 64 districts, with 19,161 suspected cases and 2,973 laboratory-confirmed cases from 15 March to 14 April, plus 166 suspected measles-related deaths. Children under 5 accounted for 79% of reported cases.

Direction: Worsening in the United States and still active across the Americas; Bangladesh remains high risk though today’s search did not identify a newer WHO DON.

Why it matters now: Measles is a direct marker of under-immunization. Imported and outbreak-linked cases continue to threaten elimination status and can rapidly strain public-health response capacity.

Pertussis

Status: Elevated post-pandemic baseline, but no major new global escalation found today.

Notable countries/regions:

- United States: CDC says preliminary 2026 data show fewer reported pertussis cases than at the same time in 2025; the last major peak was in November 2024.

- Australia: after record high 2024-2025 activity, Australian CDC reporting earlier in 2026 indicated activity had fallen substantially compared with 2025. Current Australian respiratory surveillance still includes pertussis among monitored respiratory pathogens, but no new national pertussis surge was identified today.

- Global immunization context: WHO/UNICEF’s 15 July coverage update reported 2025 DTP1 coverage of 90% and DTP3 coverage of 85%, with 13.5 million zero-dose children. These gaps sustain pertussis risk, particularly for infants.

Direction: Stable to improving compared with 2024-2025 peaks, with persistent vulnerability.

Why it matters now: The main current concern is infant protection and delayed recovery of routine immunization, not a newly detected international surge.

Ebola

Status: DRC worsening; Uganda improving; international risk management active.

Notable countries/regions:

- Democratic Republic of the Congo: WHO reported 2,124 confirmed cases and 828 deaths in DRC as of 15 July, with 390 recoveries. WHO also reported 664 additional confirmed cases and 376 confirmed deaths in DRC since its prior 3 July DON. ECDC’s week 29 report says five DRC provinces have been affected: Ituri, North Kivu, South Kivu, Tshopo, and Haut-Uele, with Ituri most affected.

- Uganda: 20 confirmed cases and two deaths have been reported; no new case since 21 June. The last Ebola patient was discharged on 16 July and Uganda began the 42-day countdown toward declaring the outbreak over.

- International/cross-border: WHO reports one case in France and two DRC cases later treated in Germany. CDC has continued U.S. entry restrictions and traveler measures for people recently in DRC, Uganda, or South Sudan, with the July 13 order in effect for 30 days.

Direction: Worsening in DRC, improving in Uganda, unclear overall because surveillance scale-up and insecurity complicate interpretation.

Why it matters now: This is a PHEIC involving Bundibugyo virus disease, for which there are no licensed vaccines or specific treatments. Community deaths, affected health workers, insecurity, and population movement raise the risk of under-detection and regional spread.

RSV

Status: Low globally overall, but active in several seasonal or regional pockets.

Notable countries/regions:

- WHO: RSV positivity remained low globally in week 26, but was elevated in a few countries in Central America and the Caribbean, Tropical and Temperate South America, and above 30% in single countries in Eastern Africa and Southern Asia.

- United States: CDC reported RSV activity very low in most areas, with ED visits and hospitalizations low but still highest among infants and children under 4.

- EU/EEA: ECDC reported RSV activity low and inter-seasonal in week 27.

- Australia: RSV is an important winter signal. The 29 June-12 July Australian report recorded 12,475 RSV notifications in the fortnight, up 6.0% from the prior fortnight, and 85,002 year-to-date notifications. RSV admissions contributed to increased sentinel severe acute respiratory infection admissions in the previous severity reporting period.

- South Africa: NICD week 28 surveillance found RSV in 17 of 103 samples tested, with RSV activity currently at low level after an earlier season start in week 11.

Direction: Stable/low globally; increasing in Australia and selected countries.

Why it matters now: RSV is currently a bigger operational issue in some southern hemisphere settings than in the U.S. or EU/EEA, especially for infants and older adults.

Influenza A

Status: Seasonal influenza A remains low globally overall, with important regional increases and zoonotic A events.

Notable countries/regions:

- WHO: global influenza detections remained low in week 26, with influenza A and B detected in fairly similar proportions. Elevated positivity was noted in parts of Temperate South America, Central America and the Caribbean, Southern Asia, Western/Southern Asia, Southern Africa, and South-East Asia. In elevated zones, A(H3N2) predominated in Central America/Caribbean, Temperate South America, Southern Africa, and South-East Asia; A(H1N1)pdm09 predominated in Western and Southern Asia.

- United States: CDC FluView week 27 reported seasonal influenza activity low. Clinical lab positivity was 0.6%; of positive clinical specimens, 67.2% were influenza A.

- Australia: influenza notifications increased 47.1% in the 29 June-12 July fortnight, driven largely by NSW and WA, but activity remained lower than the same time in previous years.

- Zoonotic influenza: ECDC’s week 29 report highlighted a Cambodian infant hospitalized with avian influenza A(H5N1), a Bangladesh child with avian influenza A(H5), and a Brazil child with swine-origin influenza A(H3N2)v. No additional cases were detected among identified contacts in these reported events.

Direction: Low overall but increasing in parts of the southern hemisphere; zoonotic risk remains sporadic but consequential.

Why it matters now: The seasonal signal is not globally severe, but increasing southern hemisphere activity and sporadic human A(H5)/A(H3N2)v infections are important for vaccine-match, exposure-control, and pandemic-risk monitoring.

Influenza B

Status: Low to moderate contribution depending on region; no major standalone influenza B escalation found today.

Notable countries/regions:

- WHO: influenza A and B detections were reported in fairly similar proportions globally in week 26, and influenza B predominated in Western Africa among zones with elevated positivity.

- United States: CDC week 27 clinical lab data showed influenza B accounted for 44 of 134 positive clinical specimens, or 32.8%; cumulative 2025-26 clinical positives were 29.6% influenza B.

- EU/EEA: ECDC reported overall influenza activity low and inter-seasonal.

Direction: Stable/low globally, with localized predominance in Western Africa per WHO.

Why it matters now: Influenza B is not the top global respiratory signal today, but its substantial share of detections means it remains relevant for surveillance and vaccine performance.

Other outbreaks of interest

Avian and swine-origin influenza events

- Cambodia: A nine-month-old child with A(H5N1) was reported on 11 July and remained hospitalized receiving intensive care; contact investigation and antiviral prophylaxis were underway.

- Bangladesh: A child in Sylhet Division had A(H5) detected in June, recovered, and no additional cases were detected among contacts. ECDC notes this was Bangladesh’s third laboratory-confirmed human A(H5) case in 2026.

- Brazil: WHO reported one swine-origin A(H3N2)v infection in a child in Santa Catarina state, with likely swine exposure through a household contact. No additional cases were found among identified contacts.

- Assessment: Sporadic zoonotic infections remain the pattern; no sustained human-to-human transmission reported in these events.

Mpox

- EU/EEA, Western Balkans, Türkiye: ECDC reported 129 mpox clade I cases in June 2026 across nine EU/EEA countries, describing transmission as relatively stable after earlier increases. Twenty-two clade II cases were reported by six countries, continuing a decreasing trend. Transmission remains concentrated in sexual networks, most cases are among unvaccinated people, and summer travel/mass gatherings could support further spread.

- Direction: Stable for clade I in the EU/EEA after prior increases; clade II decreasing.

Cyclosporiasis - United States

- CDC is investigating a multistate Cyclospora outbreak linked to shredded iceberg lettuce in five states. As of the 18 July CDC alert, the linked outbreak had more than 1,644 cases, 94 hospitalizations, and no deaths. Taylor Farms de Mexico recalled all iceberg lettuce sourced from central Mexico on 17 July. CDC separately noted 1,645 confirmed domestically acquired cases nationally since 1 May and awareness of more than 5,100 additional cases requiring confirmation or classification.

- Direction: Worsening/active investigation.

- Why it matters: The national burden is substantially higher than the same point in 2025, the outbreak involves widely distributed produce/food-service supply chains, and diagnostic under-detection is likely.

Hantavirus - cruise-linked Andes virus

- WHO’s 2 July DON reported 13 cases, including three deaths, linked to the M/V Hondius cruise ship. All identified contacts completed follow-up without additional secondary cases. WHO assessed the outbreak as contained and no longer posing a public-health risk.

- Direction: Improving/contained.

- Why it matters: It was a notable international contact-tracing event across multiple countries, but it is now primarily a lessons-learned watch item.

Watch items for the next 24-72 hours

- DRC Ebola: daily case and death growth, new affected health zones or provinces, healthcare worker infections, community deaths, and cross-border signals involving Uganda, South Sudan, Rwanda, or air travel.

- Uganda Ebola: completion of the 42-day countdown without new cases.

- Measles: updated PAHO situation reporting, U.S. weekly CDC update, and any new deaths or healthcare-facility exposures.

- Southern hemisphere respiratory season: Australia, South Africa, and South America for influenza A(H3N2), RSV hospitalization pressure, and SARS-CoV-2 variant shifts.

- Zoonotic influenza: any new human A(H5), A(H5N1), or swine-origin infections and whether contact follow-up remains negative.

- U.S. cyclosporiasis: CDC/FDA traceback updates, additional recalls, and whether the outbreak remains limited to iceberg lettuce or expands to other produce vehicles.

Key sources consulted

WHO Global Respiratory Virus Activity Weekly Update No. 585, 9 July 2026: https://www.who.int/publications/m/item/global-respiratory-virus-activity--weekly-update-n--584

WHO Ebola Disease Outbreak News, 17 July 2026: https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON613

ECDC Communicable Disease Threats Report, week 29, 17 July 2026: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-13-17-july-2026-week-29

CDC Respiratory Illnesses Data Channel, 17 July 2026: https://www.cdc.gov/respiratory-viruses/data/index.html

CDC Measles Cases and Outbreaks, 17 July 2026: https://www.cdc.gov/measles/data-research/index.html

CDC Pertussis Surveillance and Trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

WHO/UNICEF immunization coverage release, 15 July 2026: https://www.who.int/news/item/15-07-2026-global-childhood-immunization-coverage-inches-forward-despite-conflict-and-hesitancy---unicef--who

Australian Respiratory Surveillance Report, 29 June-12 July 2026: https://www.cdc.gov.au/resources/publications/australian-respiratory-surveillance-report-29-june-2026-12-july-2026

South Africa NICD Weekly Respiratory Pathogens Surveillance Report, week 28: https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/weekly-respiratory-pathogens-surveillance-report-week/

CDC Cyclosporiasis outbreak alert, 18 July 2026: https://www.cdc.gov/cyclosporiasis/outbreaks/07-26/index.html

CDC HAN: Domestically Acquired Cyclosporiasis Cases in Multiple U.S. States, 14 July 2026: https://www.cdc.gov/han/php/notices/han00531.html

WHO Hantavirus Disease Outbreak News, 2 July 2026: https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON611

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-20

Executive summary

- Ebola disease caused by Bundibugyo virus remains the most consequential global outbreak signal today. WHO reported 2,124 confirmed cases and 828 deaths in DRC as of 15 July, with substantial growth since 3 July and active transmission across 38 health zones. Uganda has reported no new cases since 21 June and has begun the 42-day enhanced-surveillance countdown, but cross-border risk remains because the DRC outbreak is still expanding.

- Measles remains elevated globally and in the United States. CDC reported 2,260 confirmed U.S. cases in 2026 as of 16 July, just below the full-year 2025 total of 2,289, with 93% outbreak-associated. WHO/UNICEF’s latest immunization estimates continue to show measles coverage below the 95% outbreak-prevention threshold.

- Global SARS-CoV-2, RSV, and seasonal influenza activity remains generally low, though WHO reports pockets of elevated SARS-CoV-2, RSV, and influenza positivity in parts of the Americas, Africa, and Asia. In the EU/EEA, respiratory virus activity is at baseline/inter-seasonal levels.

- Zoonotic influenza A remains a watch item: WHO/ECDC reported recent human avian influenza detections in Cambodia and Bangladesh, and WHO Western Pacific reported three new human A(H9N2) cases in China. No sustained human-to-human transmission has been identified.

- Other notable events: cholera increased globally in May; a large multistate U.S. cyclosporiasis outbreak linked to shredded iceberg lettuce prompted a Taylor Farms recall; dengue activity is above epidemic thresholds or increasing in parts of the Western Pacific; the Andes hantavirus cruise-linked outbreak is considered contained.

SARS-CoV-2

Status: Stable to low globally, with localized elevated positivity.

Notable countries/regions:

- WHO’s global respiratory virus update for week 27, ending 5 July, reported SARS-CoV-2 activity as low globally and stable across most reporting countries.

- Elevated positivity above 10% was reported in countries in Central America and the Caribbean, Tropical South America, Northern and Middle Africa, and Western and South-East Asia.

- ECDC reported SARS-CoV-2 activity low in all age groups in EU/EEA primary and secondary care for week 27.

- CDC reported U.S. COVID-19 activity as very low and stable nationally as of 17 July, with early signs of increase mainly in the South.

Trend assessment: Mostly stable/low, with early localized upward signals.

Why it matters now: Current burden is low, but summer increases in parts of the U.S. and elevated test positivity in several WHO regions warrant continued surveillance for variant-driven or regional rebounds.

Measles

Status: Worsening/elevated globally and in the United States.

Notable countries/regions:

- CDC’s global measles outbreak table, based on provisional WHO data for December 2025-May 2026, lists the largest outbreaks in Bangladesh (42,174), India (26,607), Yemen (14,521), Mexico (12,495), Pakistan (11,037), Cameroon (9,653), Kazakhstan (7,730), Guatemala (6,832), Angola (6,815), and Sudan (5,766).

- United States: CDC reported 2,260 confirmed measles cases in 2026 as of 16 July across 44 jurisdictions plus 15 cases among international visitors. There have been 34 outbreaks in 2026, and 93% of confirmed cases are outbreak-associated.

- The U.S. 2026 total is close to the full-year 2025 total of 2,289 cases, indicating sustained high activity.

- WHO/UNICEF reported on 15 July that global first-dose measles vaccine coverage was 84% and second-dose coverage 77% in 2025, both far below the 95% threshold needed to prevent outbreaks. They reported 57 countries with large or disruptive measles outbreaks in 2025.

Trend assessment: Worsening/elevated.

Why it matters now: The combination of international outbreaks, suboptimal vaccine coverage, and outbreak-associated U.S. transmission increases importation and domestic spread risk, especially in undervaccinated communities.

Pertussis

Status: No major new global escalation identified today; ongoing circulation with vaccination relevance.

Notable countries/regions:

- United States: CDC’s July 2026 surveillance update says preliminary 2026 pertussis reports are lower than the same period in 2025, after the last peak in November 2024. CDC’s respiratory dashboard also says whooping cough continues at lower levels than post-pandemic peaks.

- Global context: WHO notes more than 264,000 pertussis cases globally in 2025. WHO/UNICEF estimated 2025 global DTP1 coverage at 90% and DTP3 coverage at 85%, with 13.5 million zero-dose children.

Trend assessment: Improving or stable in the U.S.; unclear globally because timely country-level reporting is uneven.

Why it matters now: Pertussis remains most dangerous for infants. Coverage gaps and incomplete DTP series keep outbreak risk elevated even where current reported incidence is below recent peaks.

Ebola Disease - Bundibugyo Virus

Status: Worsening in DRC; improving but still watchful in Uganda; international response implications.

Notable countries/regions:

- Democratic Republic of the Congo: WHO reported 2,124 confirmed cases and 828 deaths as of 15 July, with 664 additional confirmed cases and 376 confirmed deaths since 3 July. Cases have been reported across 46 health zones in five provinces: Ituri, North Kivu, South Kivu, Haut-Uele, and Tshopo. Thirty-eight health zones reported cases in the past 21 days.

- Ituri remains the center of gravity, accounting for about 90% of DRC confirmed cases. WHO reported 119 confirmed infections among health workers, including 36 deaths.

- Uganda: 20 confirmed cases and two deaths; no new cases since 21 June. The most recent case was discharged on 16 July after two negative tests, starting the 42-day enhanced surveillance countdown.

- International links: WHO reported an imported case in France earlier in the outbreak with no secondary transmission, and a U.S. humanitarian worker medically evacuated from DRC to Germany in July. ECDC also noted the Germany evacuation and continues to assess EU/EEA public risk as very low.

- WHO’s Director-General described the DRC outbreak on 16 July as the third-largest Ebola outbreak on record and said it has expanded faster in the past month than any previous outbreak.

Trend assessment: Worsening in DRC; improving in Uganda; regional risk remains high around cross-border corridors.

Why it matters now: The DRC outbreak is expanding in conflict-affected, high-mobility areas with missed transmission chains, community deaths, health-worker infections, and no approved vaccine or specific treatment for Bundibugyo virus disease. This is the highest-priority watch item.

RSV

Status: Low globally and in the EU/EEA and U.S., with localized elevated positivity.

Notable countries/regions:

- WHO reported RSV positivity low globally in week 27.

- Elevated RSV positivity above 10% was reported in a few countries in Central America and the Caribbean and Tropical and Temperate South America. Positivity exceeded 30% in single countries in Eastern Africa and Southern Asia.

- ECDC reported RSV activity at inter-seasonal levels in the EU/EEA.

- CDC reported very low RSV activity in most U.S. areas, with ED visits and hospitalizations low but still highest among infants and children younger than 4 years.

Trend assessment: Stable/low overall; localized increases.

Why it matters now: Global burden is low, but regional increases can affect pediatric capacity where RSV and influenza are co-elevated.

Influenza A

Status: Seasonal influenza A remains low overall; zoonotic influenza A requires close monitoring.

Notable countries/regions:

- Seasonal influenza: WHO reported global influenza detections remained low in week 27, with influenza A and B in similar proportions. Influenza A(H3N2) predominated in elevated zones in Central America and the Caribbean, Temperate South America, and South-East Asia. Influenza A(H1N1)pdm09 predominated in Southern Asia.

- EU/EEA: ECDC reported influenza activity at inter-seasonal levels.

- United States: CDC reported seasonal influenza activity low nationally.

- Zoonotic A(H5N1): WHO Western Pacific reported one new human H5N1 case from Phnom Penh, Cambodia, with repeated poultry exposure; the child was reported stable. ECDC noted Cambodia’s Ministry of Health reported the case on 11 July.

- Zoonotic A(H5): ECDC reported a laboratory-confirmed human A(H5) infection in a child in Bangladesh’s Sylhet Division, with no additional cases among contacts.

- Zoonotic A(H9N2): WHO Western Pacific reported three new human A(H9N2) cases in China from 10-16 July; all had live-poultry exposure, two mild cases recovered, and one adult with comorbidities was in intensive care.

Trend assessment: Seasonal influenza A stable/low; zoonotic spillover risk persistent but no evidence of sustained human transmission.

Why it matters now: Sporadic severe avian influenza infections in children and poultry-exposed people remain a pandemic-preparedness signal, even when seasonal flu activity is low.

Influenza B

Status: Low overall; co-circulating with influenza A.

Notable countries/regions:

- WHO reported influenza A and B detections in similar proportions globally in week 27.

- Influenza B predominated in elevated zones in Western Africa and Eastern Asia; influenza A and B were codominant in Tropical South America.

- ECDC reported overall influenza activity low in the EU/EEA.

Trend assessment: Stable/low overall, with localized activity.

Why it matters now: Influenza B is not the dominant global risk today, but codominance with influenza A in some regions can complicate sentinel interpretation and vaccine-impact assessments.

Other Outbreaks of Interest

Cholera

- WHO’s 30 June epidemiological update reported 29,610 new cholera/AWD cases from 16 countries across four WHO regions in May 2026, a 43% increase from April. Cholera-related deaths also increased 30% to 271.

- The Eastern Mediterranean Region reported the highest number of cases, followed by the African Region, South-East Asia Region, and Region of the Americas.

- Trend: Worsening in the latest monthly global update.

- Why it matters now: The monthly increase, multi-region spread, and mortality rise point to sustained water/sanitation and response-capacity stress.

Mpox

- WHO’s latest multi-country mpox situation report (#67, 26 June) covers global data through 31 May and Africa through 14 June.

- ECDC reported that in June 2026, nine EU/EEA countries reported 129 mpox cases caused by clade I, suggesting relatively stable transmission after increases earlier in 2026. ECDC also reported 22 clade II cases from six countries, continuing a decreasing trend.

- ECDC notes ongoing circulation, mainly in networks of men who have sex with men, with most cases among unvaccinated individuals and generally mild disease, but summer travel and mass gatherings could support further spread.

- Trend: Stable in the EU/EEA after earlier increases; still a global watch item because of clade I/IB international spread.

- Why it matters now: Clade I circulation outside historically affected areas and mass-gathering season sustain importation and targeted vaccination/communication needs.

Cyclosporiasis - United States

- CDC, FDA, and state partners are investigating a multistate Cyclospora outbreak linked to shredded iceberg lettuce in five states. CDC reported more than 1,644 cases, 94 hospitalizations, and no deaths.

- Taylor Farms de Mexico recalled all iceberg lettuce sourced from central Mexico on 17 July; CDC advised consumers, restaurants, and retailers not to eat recalled lettuce.

- Michigan’s health department reported 6,148 cyclosporiasis cases and 102 hospitalizations as of 16 July, updated 20 July; not all Michigan cases are necessarily confirmed as part of the same CDC-defined multistate outbreak.

- Trend: Worsening/active investigation.

- Why it matters now: This is a large foodborne outbreak with a recalled product, multistate distribution, and substantial case volume; attribution and case classification remain in flux.

Dengue

- WHO Western Pacific’s 9 July dengue update reported above-threshold or increasing activity in multiple places. Cambodia’s weekly cases have remained above the epidemic threshold for much of 2026 with an increasing trend since week 19.

- Indonesia reported 58,357 cases and 150 deaths from January-June 2026, though monthly cases have decreased since January. Malaysia’s trend has been increasing since week 13, with 33,697 cases and 24 deaths reported in 2026 as of the latest cited reporting week. Viet Nam reported 41,684 cases and eight deaths from January-June, with June cases up 55% from May.

- PAHO reported 1,215,584 suspected dengue cases in the Americas through epidemiological week 22 of 2026.

- Trend: Mixed by country, but materially active in parts of Asia and the Americas.

- Why it matters now: Seasonal vector conditions plus simultaneous circulation in multiple regions keep severe dengue and health-system burden risks elevated.

Hantavirus - Cruise-linked Andes Virus Outbreak

- WHO’s 2 July update reported 13 cases, including three deaths, linked to the M/V Hondius Andes hantavirus outbreak. All confirmed cases were among travelers onboard.

- WHO stated that all identified contacts completed 42-day follow-up with no additional secondary cases and that the outbreak no longer poses a public-health risk.

- Trend: Improving/contained.

- Why it matters now: No immediate action signal, but the event remains notable as a cross-border, travel-associated outbreak that tested international contact tracing and port-health coordination.

Watch items for the next briefing

- DRC Bundibugyo Ebola: daily case growth, health-zone expansion, health-worker infections, contact follow-up, community deaths, security disruptions, and candidate vaccine/therapeutic trial updates.

- Uganda Ebola: continuation of the 42-day enhanced-surveillance countdown without new cases.

- Measles: U.S. case count relative to the 2025 full-year total; new state outbreaks; global outbreak-table changes for Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan.

- SARS-CoV-2: early U.S. South signal and elevated positivity pockets in WHO regions.

- Zoonotic influenza: new H5/H9 detections, any contact infections, or evidence of mammal or human-to-human transmission.

- Cyclosporiasis: updated CDC/FDA case counts, product tracing, and whether the Michigan case surge aligns with or diverges from the multistate lettuce-linked outbreak.

- Cholera and dengue: next WHO/PAHO monthly updates, especially mortality and country expansion.

Key sources reviewed: WHO Global Respiratory Virus Activity Update #586 (15 July); WHO Disease Outbreak News on Bundibugyo Ebola (17 July) and hantavirus (2 July); ECDC CDTR Week 29 (17 July); CDC measles, pertussis, respiratory virus, bird flu, and cyclosporiasis updates; WHO/UNICEF WUENIC immunization release (15 July); WHO cholera epidemiological update #38; WHO Western Pacific avian influenza and dengue updates.

It appears the model could be correct; wastewater-derived NDIs are rising.

Here is the last forecast, with the new school algorithm working. Currently, all schools start September 1. I am still tinkering with some settings, so please be patient. More tomorrow; it is my birthday, and I am going to enjoy family time.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

It appears the model could be correct; wastewater-derived NDIs are rising.

Here is the last forecast, there will be a new one tomorrow.

So, do we need to provide safer school conditions in terms of air quality? Here is an example using the MAPS system for the current forecast. In MAPS, there is a school algorithm available to examine this. This example assumes schools have had few updates to improve air quality (or require masking). I can turn that part of the algorithm on and investigate the effect of clean air in schools, and I will do so in a future study. Below are plotted the integrated NDIs for the current forecast with/without the school algorithm turned on. At first glance, it seems to have a minor effect; the lines themselves are quite close, but the total difference is ~700,000 NDIs. Remember, the schools were only in session for seven weeks. We have been sending out children for nearly 7 years! This means school children have caught over 25 million infections, and that is a very conservative estimate. And what about the rest of the family? And right now, we have a variant known as Cicada, BA.3.2*, that has been shown to preferentially infect those under the age of 10. Good grief, people, let’s get our shit together and provide them a safe environment. SARS-CoV-2 has likely caused orders of magnitude more school-age deaths than active shooters. Let that sink in.

Daily Global Pathogen and Outbreak Briefing - 2026-07-18

Executive summary

- Highest-priority development: the Bundibugyo Ebola outbreak in DRC continues to worsen rapidly. ECDC reported 2,124 confirmed DRC cases and 828 confirmed deaths as of 16 July, with five provinces affected; Uganda has reported no new cases since 21 June after 20 confirmed cases and two deaths.

- Respiratory viruses remain generally low globally and in the EU/EEA and United States, but Southern Hemisphere winter activity is uneven. Australia reported rising influenza and RSV notifications in the latest fortnight, with RSV possibly nearing a national peak and influenza rising sharply from a lower-than-usual base.

- Measles remains a major global vaccine-preventable disease signal. CDC/WHO provisional data show outbreaks in every world region, with the largest recent country totals in Bangladesh, India, Yemen, Mexico, Pakistan, Cameroon, Kazakhstan, Guatemala, Angola, and Sudan.

- Pertussis remains elevated compared with pre-pandemic baselines in several settings but is lower than recent post-pandemic peaks in the United States and Australia. The key operational issue remains infant protection and vaccination coverage.

- Other notable developments: a U.S. multistate cyclosporiasis outbreak is now linked by CDC/FDA to shredded iceberg lettuce served at Taco Bell in five states; sporadic zoonotic influenza A events were reported in Cambodia, Bangladesh, and Brazil; mpox clade I transmission remains stable but established in parts of Europe; and seasonal vector-borne risks in Europe are active.

SARS-CoV-2

Status summary: Globally low, with localized increases.

Notable countries/regions:

- WHO GISRS reported SARS-CoV-2 positivity stable and low across most reporting countries in week 27, with elevated positivity above 10% in some countries in Central America and the Caribbean, Tropical South America, Northern and Middle Africa, and Western and South-East Asia.

- EU/EEA: ECDC reported SARS-CoV-2 activity low in all age groups in primary and secondary care for week 27.

- United States: CDC reported very low and stable national COVID-19 activity as of 17 July, with early signs of increase mainly in the South.

- Australia: latest national report for 29 June-12 July found COVID-19 notifications decreased 10.2% versus the previous fortnight, with no clear winter peak so far in 2026; NB.1.8.1 was the most common circulating variant under monitoring.

Direction: Mostly stable/low globally; localized increases remain worth watching.

Why it matters now: Summer/winter regional increases can emerge from a low baseline, and variant-driven changes remain the main uncertainty.

Measles

Status summary: High global burden and continuing cross-border risk; no single newly dominant global event identified today, but the aggregate signal remains elevated.

Notable countries/regions:

- CDC’s global measles page, based on WHO provisional data covering December 2025-May 2026, lists the top outbreak case counts as Bangladesh (42,174), India (26,607), Yemen (14,521), Mexico (12,495), Pakistan (11,037), Cameroon (9,653), Kazakhstan (7,730), Guatemala (6,832), Angola (6,815), and Sudan (5,766).

- United States: CDC reports 2,260 confirmed measles cases in 2026 across 44 jurisdictions and 34 outbreaks; 93% of confirmed cases are outbreak-associated. The 2026 total is nearing the 2025 full-year total of 2,289 confirmed cases.

Direction: Worsening/continued high activity globally; U.S. outbreak activity remains high.

Why it matters now: Measles remains a sensitive marker of immunity gaps and importation risk; travel-linked introductions can seed outbreaks in under-immunized communities.

Pertussis

Status summary: No major new global escalation identified today, but post-pandemic pertussis activity remains a vaccination and infant-risk concern.

Notable countries/regions:

- United States: CDC’s 10 July update says preliminary 2026 case reports are lower than the same time in 2025, after a post-pandemic peak in November 2024; pertussis continues to circulate below recent peaks.

- Americas: PAHO’s March update noted a major regional resurgence, with Americas cases rising from 11,202 in 2023 to 66,184 in 2024, then declining moderately to 46,870 in 2025. Early 2026 country-level signals in the Americas included infant deaths in some countries, underscoring under-vaccinated infant risk.

- Australia: the Australian CDC reports just over 1,300 cases so far in 2026 as of its latest contextual update, about 80% lower than the same period in 2025, following record/high activity in 2024-2025.

Direction: Improving from recent peaks in the U.S. and Australia; global/regional risk remains uneven.

Why it matters now: Severe disease concentrates in infants too young or insufficiently protected by vaccination; maternal and childhood DTP/DTaP coverage remains the decisive control lever.

Ebola

Status summary: Major worsening outbreak of Ebola disease caused by Bundibugyo virus in DRC, with Uganda currently contained but still in the monitoring period.

Notable countries/regions:

- Democratic Republic of the Congo: ECDC reported 2,124 confirmed cases and 828 confirmed deaths as of 16 July, based on data through 15 July. Five provinces have been affected: Ituri, North Kivu, South Kivu, Tshopo, and Haut-Uele. The latest ECDC report noted an increase of 51 confirmed cases and 32 deaths since the prior report.

- Uganda: no new cases since 21 June; cumulative total remains 20 confirmed cases and two deaths. Continued 42-day monitoring is required before declaring the event over.

- Cross-border/response: WHO notes the outbreak is in a difficult setting with humanitarian crisis, insecurity, high population movement, and no licensed vaccine or specific treatment for Bundibugyo virus disease, though diagnostic and therapeutic work is underway. A U.S. humanitarian worker was medically evacuated to Germany, highlighting responder risk.

Direction: Worsening in DRC; stable/improving in Uganda but not over.

Why it matters now: High fatality, rapidly expanding DRC case counts, contact-tracing challenges, cross-border movement, and limited Bundibugyo-specific countermeasures make this the top global outbreak watch item.

RSV

Status summary: Low globally in WHO and EU/EEA summaries, but active Southern Hemisphere winter transmission, especially Australia.

Notable countries/regions:

- WHO GISRS reported RSV positivity low globally in week 27, but elevated in a few countries in Central America and the Caribbean and Tropical/Temperate South America, with positivity above 30% in single countries in Eastern Africa and Southern Asia.

- EU/EEA: ECDC reported RSV activity at inter-seasonal levels.

- United States: CDC reported RSV activity very low in most areas, with ED visits and hospitalizations low but still highest among infants and children under 4.

- Australia: for 29 June-12 July, the Australian CDC reported 12,475 RSV cases, a 6.0% increase from the prior fortnight, and 85,002 year-to-date notifications. It noted the national RSV peak may be approaching, but this is uncertain because some jurisdictions are still increasing and Tasmania data were incomplete from 10 July.

Direction: Stable/low globally; Australia elevated but possibly nearing peak.

Why it matters now: RSV is driving pediatric and older-adult respiratory burden in winter settings; vaccination and infant monoclonal programs are central to reducing severe disease.

Influenza A

Status summary: Low globally overall, but Southern Hemisphere winter activity is rising in some countries and zoonotic influenza A events require monitoring.

Notable countries/regions:

- WHO GISRS reported influenza detections low globally in week 27, with influenza A and B detected in similar proportions. Influenza A(H3N2) predominated in elevated zones in Central America/Caribbean, Temperate South America, and South-East Asia; A(H1N1)pdm09 predominated in Southern Asia.

- Australia: 8,105 influenza cases were reported in the latest fortnight, up 47.1%; 7,530 were influenza A, up 53.9%. NSW and Western Australia drove much of the increase. Influenza remains lower than the same period in previous years.

- EU/EEA and United States: seasonal influenza activity remains low/inter-seasonal.

- Zoonotic influenza A events: ECDC reported a new human A(H5N1) case in Cambodia in a hospitalized nine-month-old child, one human A(H5) case in Bangladesh, and one swine-origin A(H3N2)v infection in Brazil. No sustained human-to-human transmission has been detected in these events.

Direction: Seasonal influenza A is increasing in parts of the Southern Hemisphere but remains low globally; zoonotic events are sporadic.

Why it matters now: Australia may be entering a later winter influenza rise, while sporadic H5/H3N2v infections keep human-animal interface surveillance relevant.

Influenza B

Status summary: Low globally overall; present in several regions, with some predominance in specific zones.

Notable countries/regions:

- WHO GISRS reported influenza A and B detected in similar proportions globally in week 27. Influenza B predominated in Western Africa and Eastern Asia; influenza A and B were codominant in Tropical South America.

- Australia: influenza B notifications decreased 11.1% in the latest fortnight, from 597 to 531, while influenza A rose. Australian CDC noted influenza B had declined in recent weeks, especially in ages 5-19, though subtype trends are affected by testing and typing practices.

- EU/EEA and United States: overall seasonal influenza activity remains low, with no major influenza B-specific escalation identified.

Direction: Stable/low globally; decreasing recently in Australia.

Why it matters now: Influenza B remains a contributor to seasonal burden and vaccine-match monitoring, but today’s sharper movement is in influenza A.

Other outbreaks of interest

- Cyclosporiasis, United States: CDC reported an open multistate outbreak linked to shredded iceberg lettuce served at Taco Bell locations in Indiana, Kentucky, Michigan, Ohio, and West Virginia. Fast facts as of 17 July: more than 1,644 cases, 94 hospitalizations, no deaths, five states for this linked outbreak. CDC also states it is investigating other national cyclosporiasis outbreaks/illnesses unrelated to this specific outbreak. Direction: worsening/active. Why it matters: actionable food-source control, specialized testing needs, and additional suspected/unrelated cases mean the public-health footprint may grow.

- Mpox: ECDC reports mpox clade I and II continuing in the EU/EEA, Western Balkans and Turkiye. In June, nine EU/EEA countries reported 129 clade I cases, while six countries reported 22 clade II cases; clade I appears relatively stable after earlier increases, and clade II is decreasing. Direction: stable for clade I, improving for clade II. Why it matters: summer travel and mass gatherings may increase spread among higher-risk sexual networks, and vaccination uptake remains important.

- Avian/swine influenza human cases: Cambodia’s A(H5N1) case, Bangladesh’s A(H5) case, and Brazil’s A(H3N2)v case are notable but remain sporadic with no sustained human-to-human transmission reported. Direction: unclear/sporadic. Why it matters: these events test surveillance at the human-animal interface and may require rapid characterization of unsubtypable influenza A samples.

- West Nile virus, Europe: ECDC reported that, as of 15 July, 28 areas affected by WNV had been identified in five countries: Italy, Greece, North Macedonia, Romania, and Spain. Direction: seasonal increase expected/active. Why it matters: mosquito-borne risk is entering the high season in Europe.

- Crimean-Congo haemorrhagic fever, Europe: ECDC reported two locally acquired 2026 CCHF cases in Spain as of 15 July. Direction: limited but active. Why it matters: severe tick-borne viral hemorrhagic fever risk is seasonal and requires clinician awareness in affected areas.

- Diphtheria, Northern Territory, Australia: NT Health continues to list an active diphtheria outbreak across the Northern Territory, with health-professional alerts and vaccination recommendations in place. Direction: active; exact latest official case totals were not available on the NT Health page reviewed today. Why it matters: respiratory diphtheria is vaccine-preventable and potentially severe; outbreak control depends on rapid diagnosis, contact management, and booster uptake.

Watch items for the next 24-72 hours

- DRC Ebola: new confirmed cases/deaths, geographic expansion, contact tracing performance, healthcare-worker infections, responder evacuations, and trial/diagnostic updates.

- Uganda Ebola: whether the 42-day countdown remains uninterrupted with no new cases.

- Australia respiratory season: whether RSV peaks nationally and whether the influenza A rise in NSW and WA accelerates.

- SARS-CoV-2: early U.S. South and West increases, plus any variant shift around NB.1.8.1 or other emerging lineages.

- Measles: U.S. outbreak growth toward/exceeding the 2025 annual total, and new international importation-linked clusters.

- Cyclosporiasis: whether CDC/FDA expand the implicated food source beyond the Taco Bell-linked shredded iceberg lettuce outbreak or update national case/hospitalization counts.

- Zoonotic influenza A: any additional human H5/H3N2v cases, evidence of clustering, or mammalian adaptation markers.

Key sources reviewed

- WHO Global Respiratory Virus Activity, week 27 ending 5 July 2026: https://cdn.who.int/media/docs/default-source/influenza/influenza-updates/2026/202627_rvupdate_586.pdf

- ECDC Communicable Disease Threats Report, week 29, 13-17 July 2026: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-13-17-july-2026-week-29

- WHO Ebola outbreak - DRC 2026 situation page: https://www.who.int/emergencies/situations/ebola-outbreak---drc-2026

- CDC Measles Cases and Outbreaks: https://www.cdc.gov/measles/data-research/index.html

- CDC Global Measles Outbreaks: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

- CDC Respiratory Illnesses Data Channel: https://www.cdc.gov/respiratory-viruses/data/index.html

- CDC Pertussis Surveillance and Trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

- PAHO Pertussis Epidemiological Update, 25 March 2026: https://www.paho.org/en/documents/epidemiological-update-pertussis-whooping-cough-americas-region-25-march-2026

- Australian Respiratory Surveillance Report, 29 June-12 July 2026: https://www.cdc.gov.au/resources/publications/australian-respiratory-surveillance-report-29-june-2026-12-july-2026

- CDC Cyclosporiasis outbreak linked to shredded iceberg lettuce, July 2026: https://www.cdc.gov/cyclosporiasis/outbreaks/07-26/index.html

- ECDC Mpox worldwide overview: https://www.ecdc.europa.eu/en/mpox-worldwide-overview

- ECDC West Nile virus seasonal surveillance: https://www.ecdc.europa.eu/en/west-nile-fever/surveillance-and-disease-data/disease-data-ecdc

- NT Health diphtheria information for health professionals: https://health.nt.gov.au/public-health-notifiable-diseases/diphtheria

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

It appears the model could be correct; wastewater-derived NDIs are rising.

Here is the last forecast, there will be a new one tomorrow.

Daily Global Pathogen and Outbreak Briefing - 2026-07-17

Executive summary

- Ebola Bundibugyo virus disease in DRC remains the most urgent global outbreak signal. WHO reported 2,073 cases and 796 deaths as of its 16 July media briefing, with intense transmission in Ituri, more than 80% of new cases outside known contact lists, and community deaths still high. Uganda appears to be moving toward containment, with the last confirmed case discharged on 16 July and the 42-day countdown beginning.

- Measles remains a major vaccine-gap and travel-linked threat. The U.S. has reported 2,260 confirmed cases in 2026 as of 16 July, close to the full-year 2025 total of 2,289. PAHO’s latest regional situation report reported 22,974 confirmed measles cases and 39 deaths across 17 countries and territories in the Americas as of 27 June, up 181% year over year.

- SARS-CoV-2, influenza, and RSV are generally low globally, but not quiet everywhere. WHO’s week 27 respiratory-virus update found low global SARS-CoV-2 and RSV activity and low global influenza detections, with elevated influenza positivity in parts of South America and Asia and elevated RSV in parts of the Americas, Eastern Africa, and Southern Asia.

- Pertussis remains a watch item because routine immunization gaps persist, although U.S. 2026 case reports are currently below the same period in 2025. WHO/UNICEF’s newly released 2025 immunization estimates show DTP3 coverage at 85% and 13.5 million zero-dose children globally.

- Other notable outbreak signals today: a large U.S. cyclosporiasis outbreak linked in part to shredded iceberg lettuce served at Taco Bell in five states; yellow fever activity in Africa and the Americas; new or ongoing travel notices for chikungunya, dengue, diphtheria, malaria, and mpox; and continued global avian influenza monitoring.

SARS-CoV-2

Status: Low globally, with localized increases. Situation appears mostly stable, with regional increases requiring watch.

Notable countries/regions:

- Global: WHO reported 57,509 SARS-CoV-2 samples tested across 69 countries for 22-28 June; 1,327 were positive, a 2.3% positivity rate. Activity was described as generally low and stable globally, with increases or elevated activity in some countries in Central America and the Caribbean, Tropical South America, Northern Europe, several African subregions, and South-East Asia.

- Reported cases: For 1-28 June, WHO received 16,448 reported confirmed cases from 58 countries, up from 13,564 in the prior 28-day period. WHO cautions that reported cases substantially undercount true infections because testing and reporting have declined.

- Variants: WHO is tracking JN.1 as a variant of interest and NB.1.8.1, XFG, and BA.3.2 as variants under monitoring. NB.1.8.1 rose to about 50% of submitted global sequences in the week ending 21 June; WHO says available evidence does not indicate additional public-health risk for XFG, NB.1.8.1, or BA.3.2 relative to other circulating variants.

- United States: CDC’s 10 July respiratory-virus update described COVID-19 as low and stable nationally, but beginning to increase from low in a few areas. CDC notes the South and West could see summer increases, especially if population immunity and variant dynamics shift.

Why it matters now: The current signal is not a severe global surge, but low surveillance intensity means trends can be missed. Summer increases in some regions and variant turnover warrant continued wastewater and sentinel surveillance.

Measles

Status: Worsening in the Americas and still a global vaccine-gap threat.

Notable countries/regions:

- United States: CDC reported 2,260 confirmed measles cases in 2026 as of 16 July, across 44 jurisdictions, plus 15 cases among international visitors. CDC reported 34 new outbreaks in 2026; 93% of confirmed cases are outbreak-associated. The 2026 total is approaching the full-year 2025 total of 2,289.

- Americas: PAHO’s 2 July situation report reported 22,974 confirmed cases across 17 countries and territories as of 27 June, a 181% increase compared with the same period in 2025, with 39 deaths.

- Global: WHO/UNICEF’s 15 July immunization release found first-dose measles vaccine coverage stalled at 84% and second-dose coverage at 77%, well below the 95% threshold needed to prevent outbreaks. WHO/UNICEF reported 57 countries had large or disruptive measles outbreaks in 2025.

Why it matters now: The combination of high transmissibility, sub-95% MCV coverage, regional outbreaks, and summer travel keeps importation and sustained local transmission risk elevated.

Pertussis

Status: Mixed. U.S. reports are down from 2025, but global and regional vaccination gaps keep infants at risk. Situation is unclear to stable in the U.S.; broader global risk remains elevated compared with pre-pandemic lows.

Notable countries/regions:

- United States: CDC says preliminary 2026 pertussis reports are lower than the same period in 2025. CDC also notes that pertussis peaked nationally in November 2024, remained elevated in 2025, and has trended down since that peak.

- Global immunization context: WHO/UNICEF reported 2025 DTP1 coverage of 90% and DTP3 coverage of 85%, both still below 2019 levels. A large pool of zero-dose and under-immunized children remains.

- Antibiotic resistance: CDC notes macrolide-resistant Bordetella pertussis remains rare in the United States but has been increasingly reported in Asia, Australia, Europe, and South America.

Why it matters now: Pertussis is most consequential for infants, and gaps in maternal, infant, and booster vaccination can convert endemic circulation into severe infant disease and hospital pressure.

Ebola

Status: Worsening in DRC; improving but still under observation in Uganda.

Notable countries/regions:

- Democratic Republic of the Congo: WHO’s 16 July media briefing reported 2,073 Ebola Bundibugyo cases and 796 deaths. WHO described this as the third-largest Ebola outbreak on record and said the past-month expansion has been faster than any previous outbreak. Ituri province remains the main concern.

- Response indicators: WHO reported treatment capacity above 800 beds, laboratory capacity expanded from one lab to 16, contact follow-up rates near 80%, and more than 21,000 community workers being trained. However, WHO also said transmission is outpacing the response, more than 80% of new cases are outside known contact lists, and about two-thirds of deaths are occurring in communities.

- Uganda: WHO said the last confirmed case was discharged from care on 16 July, beginning the 42-day countdown to the end of the outbreak. Uganda has reported 20 cases and two deaths.

- Travel risk: CDC updated travel notices on 15 July, recommending avoidance of nonessential travel to affected DRC provinces: Haut-Uele, Ituri, Nord-Kivu/North Kivu, and Tshopo. CDC recommends enhanced precautions for Uganda and other DRC provinces.

Why it matters now: Bundibugyo virus has no approved vaccine or specific treatment. Missed transmission chains, community deaths, insecurity, attacks on health facilities, and cross-border movement make this a high-risk outbreak despite scale-up of response capacity.

RSV

Status: Low globally overall, but elevated in selected countries and important in Australia. Global trend appears mostly stable; selected Southern Hemisphere settings are active.

Notable countries/regions:

- Global: WHO’s week 27 update reported RSV positivity low globally, but elevated above 10% in a few countries in Central America and the Caribbean and Tropical and Temperate South America. Positivity exceeded 30% in single countries in Eastern Africa and Southern Asia.

- United States: CDC’s 10 July update says RSV activity is very low in most areas, with ED visits and hospitalizations low, though remaining highest among infants and children under 4.

- Australia: Nationally reported RSV notifications remain high for the year; NNDSS-linked reporting cited 83,678 RSV notifications through 13 July. Queensland reported 737 RSV diagnoses in the week ending 12 July and 49 people hospitalized with RSV on 12 July, with children under 2 and older adults prominent among hospitalized cases.

Why it matters now: RSV is seasonally important in the Southern Hemisphere and remains high-impact for infants and older adults. Vaccine and maternal immunization uptake are operational watch points.

Influenza A

Status: Low globally but seasonally active in parts of the Southern Hemisphere and tropics. Situation is stable globally with regional elevations.

Notable countries/regions:

- Global: WHO reported global influenza detections remained low in week 27, with influenza A and B detected in similar proportions. Influenza positivity was above 10% in some countries in Temperate South America and in single countries in Tropical South America and South-East Asia; positivity exceeded 30% in some Temperate South America countries.

- Strain pattern: WHO reported A(H3N2) predominance in Central America and the Caribbean, Temperate South America, and South-East Asia; A(H1N1)pdm09 predominance in Southern Asia.

- Australia/Queensland: Queensland reported 271 influenza diagnoses in the week ending 12 July and 12 people hospitalized with influenza on 12 July.

- Avian influenza A: CDC says A(H5) remains widespread in wild birds globally and continues to cause poultry and U.S. dairy-cow outbreaks with sporadic human cases, but U.S. flu surveillance through late June showed no indicators of unusual influenza activity in people, including A(H5). WHO Western Pacific’s recent avian influenza update reported one new human A(H9N2) case in Guangdong Province, China, in a one-year-old with live poultry market exposure and no additional close-contact cases reported.

Why it matters now: Seasonal influenza A remains the main respiratory driver in several Southern Hemisphere/tropical settings, while avian influenza remains a zoonotic surveillance priority even without evidence of sustained human-to-human transmission.

Influenza B

Status: Low globally, but present in meaningful co-circulation.

Notable countries/regions:

- Global: WHO reported influenza A and B were detected in similar proportions globally in week 27.

- Regional pattern: Influenza B was predominant in Western Africa and Eastern Asia, and influenza A and B were codominant in Tropical South America.

Why it matters now: Influenza B can contribute substantially to school-age and young adult illness and complicates strain-specific expectations for Southern Hemisphere respiratory seasons.

Other outbreaks of interest

Cyclosporiasis - United States

- Status: Worsening/active investigation. CDC issued a 14 July HAN and a 16 July outbreak notice.

- CDC reported 1,645 confirmed domestically acquired cyclosporiasis cases since 1 May across 34 states, with more than 5,100 additional cases requiring analysis. Among confirmed cases with available information, 141 people, or 9%, were hospitalized; no deaths were reported.

- CDC/FDA linked one outbreak to shredded iceberg lettuce served at Taco Bell locations in Indiana, Kentucky, Michigan, Ohio, and West Virginia. More than 1,644 sick people in this outbreak reported eating at Taco Bell locations in those five states, and FDA traceback identified a single Mexico lettuce supplier for those locations. CDC says other cyclosporiasis outbreaks and illnesses nationally are also being investigated and may be unrelated.

- Why it matters now: This is a large, multistate foodborne outbreak with a specific consumer action and a broader unresolved national signal.

Yellow fever - Africa and the Americas

- Status: Active, geographically dispersed, vaccine-preventable risk.

- WHO reported that from January to May 2026, six countries in the Americas - Bolivia, Brazil, Colombia, Ecuador, Peru, and Venezuela - reported 79 confirmed cases, with Colombia most affected. In Africa, Burkina Faso, Central African Republic, and Cameroon reported 16 confirmed cases, with additional suspected cases under investigation in Angola, Cote d’Ivoire, Gabon, Ghana, and Nigeria.

- Why it matters now: WHO highlights uneven vaccination coverage, sylvatic spillover, competent vectors, urban expansion into forested areas, and cross-border spread risk.

Chikungunya and dengue travel-linked risk

- Status: Active regional outbreaks/travel notices.

- CDC posted a new Level 2 travel notice on 16 July for chikungunya in Guanacaste Province, Costa Rica, with most cases in Playa Langosta. CDC also lists active chikungunya notices for French Guiana, Mauritius, Mayotte, Suriname, Bolivia, and Seychelles. CDC’s global dengue notice remains active for multiple destinations including Bolivia, Cambodia, Colombia, Guyana, Maldives, Mali, New Caledonia, Samoa, Timor-Leste, Tonga, and Vietnam.

- Why it matters now: Vector-borne risk is seasonally and travel relevant, particularly for pregnant travelers and people with comorbidities.

Mpox

- Status: Ongoing but not the top escalation signal today.

- CDC reports the global clade IIb outbreak has exceeded 100,000 cases across 122 countries since 2022. Separately, clade I outbreaks have continued in Central and Eastern Africa since late 2023, with more than 55,000 confirmed cases globally and more than 150 deaths since January 2024. ECDC’s latest global overview notes recent African clade I activity has been concentrated in DRC, Uganda, Madagascar, Burundi, and Kenya.

- Why it matters now: Cross-border clade I spread and travel-associated cases remain a vaccination and surveillance issue, though today’s major acute signal is Ebola.

Diphtheria, malaria, and polio travel signals

- CDC travel notices include diphtheria in Haiti and several sub-Saharan African countries, increased malaria in Yemen and Mayotte, and global poliovirus circulation affecting multiple destinations. These are not today’s primary outbreak escalations, but they remain relevant for travel medicine and immunization checks.

Watch items for the next briefing

- Ebola: whether DRC case growth slows, whether unknown transmission chains fall, whether security incidents continue to disrupt care, and whether Uganda completes the 42-day countdown without new cases.

- Measles: U.S. case count versus the 2025 total; PAHO updates for the Americas; any new exportation/importation clusters linked to summer travel.

- SARS-CoV-2: whether low-level summer increases broaden in the U.S. South/West and in WHO regions reporting elevated positivity; variant changes in NB.1.8.1, XFG, BA.3.2, and JN.1.

- RSV/influenza: Southern Hemisphere hospital pressure, especially Australia and Temperate South America; influenza A(H3N2)/A(H1N1)pdm09/B mix changes.

- Cyclospora: whether FDA/CDC identify distribution beyond the five-state Taco Bell lettuce signal and how many of the >5,100 pending U.S. cases are confirmed.

- Avian influenza: any new human A(H5), A(H9N2), or other novel influenza detections; wild-bird/poultry spread in Australia/New Zealand and U.S. dairy/poultry surveillance.

Selected sources

WHO Global Respiratory Virus Activity, week 27: https://cdn.who.int/media/docs/default-source/influenza/influenza-updates/2026/202627_rvupdate_586.pdf

WHO COVID-19 dashboard summary: https://data.who.int/dashboards/covid19/summary

CDC Respiratory Illnesses Data Channel: https://www.cdc.gov/respiratory-viruses/data/index.html

CDC Measles Cases and Outbreaks: https://www.cdc.gov/measles/data-research/index.html

CDC Global Measles Outbreaks: https://www.cdc.gov/global-measles-vaccination/data-research/global-measles-outbreaks/index.html

WHO/UNICEF immunization coverage release: https://www.who.int/news/item/15-07-2026-global-childhood-immunization-coverage-inches-forward-despite-conflict-and-hesitancy---unicef--who

CDC Pertussis Surveillance and Trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

WHO Ebola DRC 2026 situation page: https://www.who.int/emergencies/situations/ebola-outbreak---drc-2026

WHO Director-General remarks, 16 July 2026: https://www.who.int/news-room/speeches/item/who-director-general-s-opening-remarks-at-the-media-briefing---16-july-2026

CDC Travel Health Notices: https://wwwnc.cdc.gov/travel/notices

CDC Cyclosporiasis HAN: https://www.cdc.gov/han/php/notices/han00531.html

CDC Cyclospora outbreak notice: https://www.cdc.gov/cyclosporiasis/outbreaks/07-26/index.html

WHO Yellow Fever Disease Outbreak News: https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON610

Queensland respiratory surveillance: https://www.health.qld.gov.au/clinical-practice/guidelines-procedures/diseases-infection/surveillance/reports/flu

CDC A(H5) Bird Flu Situation Summary: https://www.cdc.gov/bird-flu/situation-summary/index.html

WHO Western Pacific avian influenza updates: https://www.who.int/westernpacific/wpro-emergencies/surveillance/avian-influenza

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-16

Executive summary

- Highest-priority development: the Bundibugyo Ebola outbreak in DRC continues to expand. ECDC’s 16 July update, reflecting DRC data through 14 July, reports 2,073 confirmed cases and 796 deaths, with 62 new confirmed cases and 42 deaths since the prior daily report. Uganda has reported no new case since 21 June and discharged its last patient on 16 July, starting the 42-day countdown toward declaring the outbreak over if no further cases occur.

- Respiratory viruses: WHO’s week 27 global update says SARS-CoV-2 activity remains low globally, influenza detections remain low with influenza A and B detected in similar proportions, and RSV remains low globally, though some countries in the Americas, Africa, and Asia report elevated positivity.

- Measles remains a major vaccine-preventable risk, especially in the Americas. CDC reports 2,231 confirmed U.S. measles cases in 2026 as of 9 July, with 93% outbreak-associated. PAHO’s latest regional situation reporting also shows continuing confirmed cases across multiple countries.

- Other outbreak watch: global cholera/AWD increased in May, West Nile risk areas are expanding seasonally in Europe, and a new human avian influenza A(H9N2) case was reported in China.

SARS-CoV-2

Status: stable to low globally, with localized increases.

Notable countries/regions:

- WHO reports SARS-CoV-2 positivity remained stable and low across most reporting countries in week 27. Elevated positivity above 10% was reported in countries in Central America and the Caribbean, Tropical South America, Northern and Middle Africa, and Western and South-East Asia.

- EU/EEA: ECDC’s week 28 respiratory-virus overview says SARS-CoV-2 activity is low in all age groups in primary and secondary care.

- Variants: ECDC’s 26 June variant page lists no SARS-CoV-2 variant currently meeting variant-of-concern criteria. BA.2.86 remains a variant of interest; NB.1.8.1, XFG, and BA.3.2 are under monitoring, with XFG dominant in the EU/EEA but without assessed evidence of increased transmissibility, immune escape, or severity.

Assessment: stable/low overall. The issue matters now because localized increases and evolving monitored variants warrant continued sequencing and integrated respiratory surveillance, even while severe public-health signal remains muted.

Measles

Status: worsening or persistently elevated in the Americas; continued European transmission.

Notable countries/regions:

- United States: CDC reports 2,231 confirmed measles cases in 2026 as of 9 July, across 42 jurisdictions plus 13 international visitors. CDC reports 32 outbreaks in 2026 and 93% of confirmed cases outbreak-associated.

- Americas: PAHO Situation Report #6 says that during epidemiological weeks 23 and 24 of 2026, 479 new confirmed measles cases were reported across seven countries and territories.

- Canada: national surveillance reports 1,083 measles cases in 2026, including 1,002 confirmed and 81 probable cases, reported by seven jurisdictions.

- EU/EEA: ECDC’s measles-rubella monitoring indicates 2,928 measles cases reported by 30 EU/EEA Member States from 1 June 2025 to 31 May 2026.

Assessment: worsening/persistently elevated. This matters now because travel, mass gatherings, and sub-95% MMR coverage create sustained outbreak risk and threaten elimination status in parts of the Americas.

Pertussis

Status: no major new global escalation identified today; elevated post-pandemic baseline remains a concern.

Notable countries/regions:

- United States: CDC’s 10 July update says preliminary data show fewer pertussis cases in 2026 than during the same period in 2025, after the last peak in November 2024.

- Americas/global: PAHO’s March 2026 update notes WHO-reported global pertussis cases reached 941,582 in 2024, a 5.8-fold increase from 2023, with the largest shares in the Western Pacific and Europe.

Assessment: stable to improving in the U.S.; unclear globally because recent comparable 2026 global data are limited. The item matters because infants remain at highest risk and maternal/childhood vaccination coverage gaps can rapidly convert endemic circulation into severe outbreaks.

Ebola

Status: worsening in DRC; improving but not over in Uganda.

Notable countries/regions:

- DRC: ECDC reports 2,073 confirmed Bundibugyo Ebola cases and 796 deaths as of DRC data through 14 July. Forty-five of 140 health zones are affected across five provinces: Ituri, North Kivu, South Kivu, Haut-Uele, and Tshopo. Ituri remains the epicenter with 1,863 cases and 668 deaths.

- Uganda: 20 confirmed cases and two deaths have been reported, with no new case since 21 June. Uganda discharged its last Ebola patient on 16 July and began the 42-day countdown toward declaring the outbreak over.

- International movement: imported/medically evacuated cases linked to the DRC outbreak have been reported in Germany and France; a U.S. humanitarian worker was medically evacuated to Germany on 13 July after testing positive.

Assessment: DRC worsening; Uganda improving but watchful. This matters now because Bundibugyo virus has no licensed vaccine or specific treatment, surveillance gaps persist, community deaths suggest delayed detection, and cross-border movement keeps regional risk elevated.

RSV

Status: low globally, with seasonal or regional elevations.

Notable countries/regions:

- WHO reports RSV positivity remained low globally in week 27, but elevated positivity above 10% was seen in a few countries in Central America and the Caribbean and Tropical/Temperate South America. Positivity exceeded 30% in single countries in Eastern Africa and Southern Asia.

- EU/EEA: ECDC reports RSV activity at low, inter-seasonal levels.

- United States: CDC says RSV activity is very low in most areas, with low emergency department visits and hospitalizations, though burden remains highest in infants and children under 4.

- Australia: NNDSS-derived reporting compiled by the Immunisation Coalition shows 83,678 RSV notifications in 2026 through 13 July, with the largest totals in New South Wales, Queensland, and Victoria. This is a meaningful Southern Hemisphere winter signal.

Assessment: mostly stable/low globally, but regionally active in the Southern Hemisphere and tropics. It matters now because RSV burden is concentrated in infants, older adults, and people with comorbidities, and timing affects prophylaxis/vaccination campaigns.

Influenza A

Status: low globally for seasonal influenza A, with regional elevations; separate zoonotic A(H9N2) event in China.

Notable countries/regions:

- WHO reports global influenza detections remained low in week 27. In zones with elevated positivity, influenza A(H3N2) predominated in Central America and the Caribbean, Temperate South America, and South-East Asia; A(H1N1)pdm09 predominated in Southern Asia.

- EU/EEA and U.S.: both ECDC and CDC report low/inter-seasonal influenza activity.

- China: ECDC reports one new human avian influenza A(H9N2) case in Guangdong Province, in a one-year-old girl with symptom onset on 12 June. Thirteen human A(H9N2) cases have been reported in China over the last six months; ECDC notes no evidence of sustained human-to-human transmission.

Assessment: seasonal influenza A stable/low overall; zoonotic A(H9N2) remains a watch item. It matters because H3N2/H1N1 regional dominance informs vaccine-strain and clinical-readiness monitoring, while sporadic avian influenza infections require rapid exposure and cluster investigation.

Influenza B

Status: low globally, with localized predominance in some regions.

Notable countries/regions:

- WHO reports influenza A and B were detected in similar proportions globally in week 27.

- Influenza B was predominant in Western Africa and Eastern Asia among areas with elevated influenza positivity, and influenza A/B were codominant in Tropical South America.

- EU/EEA and U.S. remain at low/inter-seasonal influenza levels.

Assessment: stable/low overall. It matters now because influenza B can still contribute materially to late-season or tropical outbreaks even when global influenza activity is low.

Other outbreaks of interest

- Cholera/AWD: WHO’s 30 June multi-country update reports 29,610 new cholera/AWD cases from 16 countries in May 2026, a 43% increase from April, and 271 deaths, a 30% increase. The Eastern Mediterranean Region reported the highest number of cases, followed by Africa, South-East Asia, and the Americas. Situation: worsening. Why it matters: rising cases and deaths indicate continuing water/sanitation and health-system stress.

- West Nile virus, Europe: ECDC’s week 28 CDTR reports 11 WNV-affected areas in five European countries as of 8 July: Italy, North Macedonia, Romania, Greece, and Spain. Seasonal conditions favor further mosquito-borne transmission. Situation: worsening seasonally. Why it matters: public-health and blood-safety measures are time-sensitive.

- Crimean-Congo haemorrhagic fever, Spain: ECDC reports one locally acquired case in Spain in 2026 as of 8 July. Situation: localized/seasonal. Why it matters: tick exposure risk rises during outdoor activity season in areas where Hyalomma ticks and CCHF virus are established.

- Vibrio risk, Europe: ECDC identified high environmental suitability for Vibrio growth across 276 local administrative units in 11 European countries for the period ending 15 July. Situation: seasonal risk increasing. Why it matters: warm, brackish coastal waters raise risk for wound and seafood-associated infections.

- Dengue, Americas: PAHO’s EW22 2026 update reports 1,215,584 suspected dengue cases in the Region of the Americas. Situation: substantial but below the exceptional 2024 regional peak. Why it matters: dengue remains a high-volume arboviral burden with severe-dengue and health-system implications.

Watch items for the next 1-2 weeks

- DRC Ebola: pace of new cases/deaths, contact follow-up coverage, community-death share, and any additional international exportations.

- Uganda Ebola: whether the 42-day countdown proceeds without new cases.

- Measles: new PAHO situation reports and any evidence of sustained cross-border transmission or elimination-status implications in the Americas.

- Respiratory viruses: Southern Hemisphere influenza/RSV trends, especially Temperate South America and Australia.

- Arboviruses and summer bacterial risks: West Nile, CCHF, Vibrio, dengue, and yellow fever signals as vector and travel seasons continue.

Key sources consulted

- WHO Global Respiratory Virus Activity, Weekly Update No. 586, week 27 ending 5 July 2026: https://www.who.int/publications/m/item/global-respiratory-virus-activity--weekly-update-n--586

- ECDC Communicable Disease Threats Report, week 28, 6-10 July 2026: https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-6-10-july-2026-week-28

- ECDC Ebola outbreak page, updated 16 July 2026: https://www.ecdc.europa.eu/en/ebola-outbreak-democratic-republic-congo-and-uganda

- CDC Measles Cases and Outbreaks, updated 10 July 2026: https://www.cdc.gov/measles/data-research/index.html

- PAHO Situation Report #6: Measles in the Americas Region, 2 July 2026: https://www.paho.org/en/documents/situation-report-6-measles-americas-region-2-july-2026

- CDC Pertussis Surveillance and Trends, updated 10 July 2026: https://www.cdc.gov/pertussis/php/surveillance/index.html

- WHO Multi-country outbreak of cholera, epidemiological update #38, 30 June 2026: https://www.who.int/publications/m/item/multi-country-outbreak-of-cholera--epidemiological-update--38--30-june-2026

- PAHO Dengue epidemiological situation, EW22 2026: https://www.paho.org/en/documents/dengue-epidemiological-situation-region-americas-epidemiological-week-22-2026

- ECDC SARS-CoV-2 variants of concern page, as of 26 June 2026: https://www.ecdc.europa.eu/en/covid-19/variants-concern

- CDC Respiratory Illnesses Data Channel, updated 10 July 2026: https://www.cdc.gov/respiratory-viruses/data/index.html

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Daily Global Pathogen and Outbreak Briefing - 2026-07-15

Executive summary

- Ebola disease due to Bundibugyo virus in DRC/Uganda remains the highest-consequence global outbreak signal today. Confirmed cases in DRC are now reported across five provinces, with cross-border transmission to Uganda and response operations challenged by insecurity, community deaths, and incomplete contact tracing. Trend: worsening.

- Global respiratory virus activity remains comparatively low overall, but influenza and RSV are elevated in parts of the Southern Hemisphere and selected tropical/subtropical areas. Australia, especially New South Wales, remains notable for high RSV activity and rising influenza activity.

- Measles remains a sustained vaccine-preventable disease concern in multiple high-income settings, including the United States, England, and Canada/the Americas region more broadly. Transmission is still largely outbreak-associated and concentrated where immunity gaps persist.

- Pertussis remains above pre-pandemic concern levels in several regions, though U.S. preliminary 2026 reporting is below the same point in 2025. Infant risk and vaccination coverage gaps remain the key operational issues.

- Other watch items: cholera continues across multiple countries, especially Nigeria and DRC; mpox clade I continues to be monitored in Africa and through travel-linked detections; sporadic avian influenza A(H5N1) human cases remain a preparedness concern; recent Marburg, Crimean-Congo hemorrhagic fever, dengue, Legionnaires’, yellow fever, and shigellosis signals merit watch but are more localized.

SARS-CoV-2 / COVID-19

Status: Low globally, with localized increases.

Notable countries/regions:

- WHO’s global respiratory virus update for week 26 reported SARS-CoV-2 activity as low globally, with elevated positivity in countries in Central America and the Caribbean, tropical South America, Middle Africa, Western Asia, and South-East Asia.

- In the United States, CDC reported acute respiratory illness at very low levels as of July 10. COVID-19 activity was low and stable nationally, though beginning to increase from low levels in a few areas; CDC Rt estimates as of July 8 suggested infections growing or likely growing in 11 states.

- New South Wales, Australia, reported COVID-19 activity at a low level for the week ending July 4.

Trend: Stable globally, with localized early increases.

Why it matters now: COVID-19 is not the dominant acute global signal today, but low-level growth in selected areas and ongoing variant surveillance remain important ahead of seasonal shifts and travel-related mixing.

Measles

Status: Sustained outbreak activity, especially in the Americas and England.

Notable countries/regions:

- United States: CDC reported 2,231 confirmed measles cases in 2026 as of July 9, across 42 jurisdictions plus 13 international visitor cases. CDC reported 32 new outbreaks in 2026 and said 93% of confirmed cases were outbreak-associated.

- England: UKHSA reported 883 laboratory-confirmed measles cases from Jan. 1 to July 6, 2026, an increase of 82 since the June 22 report. London accounted for 52% of cases, and three measles-related deaths have been reported in 2026.

- Americas: PAHO’s multi-country measles outbreak page reports a broad 2025-2026 resurgence in the region, with the greatest operational concern where vaccination gaps and sustained transmission threaten elimination gains.

Trend: Worsening/ongoing in affected settings.

Why it matters now: Measles remains a sensitive indicator of immunity gaps. Continued summer travel and clustered under-immunization raise the risk of additional importations and outbreaks.

Pertussis / Whooping cough

Status: Elevated relative to pre-pandemic norms, but mixed recent trajectory.

Notable countries/regions:

- United States: CDC’s July 2026 surveillance page says preliminary 2026 cases are below the same point in 2025, after elevated 2024-2025 activity and a late-2024 peak.

- Americas: PAHO’s March 2026 update highlighted confirmed pertussis and deaths in several countries, including Bolivia, Honduras, Mexico, and Panama during early 2026, with infants under one year repeatedly the most affected group.

- Global note: CDC continues to flag that macrolide-resistant Bordetella pertussis remains rare in the United States but is increasingly reported in parts of Asia, Australia, Europe, and South America.

Trend: Unclear globally; improving in U.S. preliminary data, but still a vaccination and infant-protection concern.

Why it matters now: Severe outcomes concentrate in young infants, making maternal vaccination, infant series completion, and rapid prophylaxis around cases the key risk-reduction levers.

Ebola disease / Bundibugyo virus

Status: Major worsening outbreak in DRC with cross-border implications.

Notable countries/regions:

- Democratic Republic of the Congo: WHO confirms the outbreak involves Bundibugyo virus, with no licensed vaccine or specific approved treatment for this species, and is occurring amid insecurity, high population movement, and humanitarian strain.

- DRC provinces: CDC says cases have been confirmed in Haut-Uele, Ituri, North Kivu, South Kivu, and Tshopo. CDC describes this as the third-largest Ebola outbreak on record and notes it reached more than 1,000 confirmed cases within 40 days of response activation.

- Latest publicly reported count: NaTHNaC, citing DRC official data, reported 1,963 confirmed cases and 719 confirmed deaths as of July 12. AP, citing Congolese authorities and WHO briefing comments, reported at least 1,926 infections and 702 deaths as of July 14, with roughly 80% of new cases outside known contact lists.

- Uganda/Germany/U.S. relevance: WHO and CDC confirm spread to Uganda. German authorities reported medical evacuation of a second U.S. citizen infected in DRC; CDC says no U.S. cases have been confirmed domestically and the risk to the U.S. public remains low.

Trend: Worsening.

Why it matters now: The outbreak is outpacing response capacity, with unknown transmission chains, community deaths, disrupted care, and limited medical countermeasures for Bundibugyo virus. This is the main global outbreak watch item.

RSV

Status: Low globally overall, but elevated in selected countries/regions.

Notable countries/regions:

- WHO week 26 update: RSV positivity remained low globally, but was elevated in a few countries in Central America/Caribbean and tropical/temperate South America; positivity exceeded 30% in single countries in Eastern Africa and Southern Asia.

- Australia/New South Wales: NSW reported RSV activity at a high level for the week ending July 4, while COVID-19 remained low and influenza was rising. Public reporting from Australia also points to a heavy RSV season, with vaccination uptake among older adults and protection of infants as key response themes.

- United States: CDC reported RSV activity very low in most areas as of July 10, with emergency department visits and hospitalizations low but highest among infants and children under 4.

Trend: Stable/low globally; elevated or worsening in parts of the Southern Hemisphere and selected tropical areas.

Why it matters now: RSV is a pediatric and older-adult hospitalization risk. The current signal is most actionable for southern-hemisphere winter planning and immunization uptake.

Influenza A

Status: Generally low globally, with Southern Hemisphere and tropical pockets elevated.

Notable countries/regions:

- WHO week 26: Global influenza detections remained low, with influenza A and B detected in fairly similar proportions. In zones with elevated positivity, A(H3N2) predominated in Central America/Caribbean, temperate South America, Southern Africa, and South-East Asia; A(H1N1)pdm09 predominated in Western and Southern Asia.

- PAHO: On July 1, PAHO warned of rising influenza activity in several Southern Hemisphere countries and urged vaccination and early clinical management for high-risk groups.

- Australia/New South Wales: NSW reported influenza activity increased for the week ending July 4 and was listed as moderate in the latest summary, with vaccination recommended now.

- United States/EU-EEA: CDC and ECDC respiratory surveillance indicate seasonal influenza activity is low/inter-seasonal in the U.S. and Europe.

Trend: Worsening in some Southern Hemisphere/tropical areas; stable low in most Northern Hemisphere temperate areas.

Why it matters now: Influenza A is driving much of the elevated influenza signal where activity is rising, especially A(H3N2), which can pressure hospitals and affect vaccine-match monitoring.

Influenza B

Status: Present globally, not the dominant high-severity signal today.

Notable countries/regions:

- WHO week 26: Influenza A and B were detected in fairly similar proportions globally, and influenza B predominated in Western Africa among zones with elevated positivity.

- Northern Hemisphere temperate areas: Influenza activity is generally at baseline/inter-seasonal levels.

Trend: Stable to unclear; localized prominence in Western Africa.

Why it matters now: Influenza B deserves continued monitoring because it can contribute to late-season or regional burdens even when influenza A dominates broader attention. Current vaccine formulations include B/Victoria lineage coverage; B/Yamagata has not re-emerged as a major signal in current routine summaries.

Other outbreaks of interest

- Cholera: ECDC’s June 22 global cholera update reported 19,659 new cholera cases and 261 deaths worldwide from May 26 to June 22, with new cases in Afghanistan, Angola, Burundi, Congo, DRC, Haiti, India, Kenya, Malawi, Mozambique, Nigeria, Pakistan, Yemen, and Zambia. Nigeria and DRC reported the most new cases; DRC and Nigeria reported the most new deaths. Trend: ongoing, with major burden in Africa.

- Mpox: ECDC’s late-June overview says clade I and clade II mpox continue to circulate globally. In Africa, the most clade I cases since 2025 have been reported by DRC, Uganda, Madagascar, Burundi, and Kenya; Madagascar reported the most confirmed clade I cases in the prior six weeks as of June 14. ECDC assesses the clade I situation as broadly similar to previous weeks, with cases outside Africa not unexpected. Trend: ongoing, not sharply escalating globally.

- Avian influenza A(H5N1): CDC reported no indicators of unusual influenza activity in people, including A(H5), through June 27. Internationally, CDC summarized 12 H5N1 human cases since August 2025 in Bangladesh, Cambodia, and India, mostly linked to infected poultry exposure. Trend: sporadic human cases; pandemic risk still low but requires continued monitoring.

- Marburg virus disease: NaTHNaC reports a confirmed Marburg case in Uganda’s Western Region on June 30, citing WHO. Trend: localized, high-consequence watch.

- Crimean-Congo hemorrhagic fever: Local authorities reported a fatal case in Salamanca, Spain, associated with a tick bite as of July 10. Trend: localized.

- Legionnaires’ disease: New York City reported 46 confirmed cases on the Upper East Side between July 2 and July 9. Trend: localized cluster requiring environmental investigation.

- Dengue: PAHO’s latest Americas dengue situation report for epidemiological week 22 reported more than 1.2 million suspected cases in 2026, down from the exceptional 2025 level but still operationally significant. Pacific and Nigeria dengue signals remain localized watch items. Trend: regionally active, generally lower than 2025 in the Americas.

- Yellow fever: Liberia reported a confirmed case in Grand Gedeh County on June 21, per NaTHNaC/Africa CDC. Trend: localized but vaccine-preventable and high-consequence.

- Shigellosis: Northern Kerala, India reported 273 confirmed shigellosis cases and seven deaths in 2026 as of June 29, per WHO-cited reporting. Trend: localized.

Watch items for the next 24-72 hours

- Ebola: updated DRC/Uganda case counts, proportion of cases linked to known contacts, health-worker strike/resumption status, treatment-trial enrollment, cross-border spread, and any additional medical evacuations.

- Measles: new U.S. CDC weekly update, England reporting lag correction, and PAHO/Canada indicators of sustained transmission or elimination-status risk.

- Respiratory viruses: WHO week 27 respiratory-virus update; Australia/NSW RSV and influenza trajectory; any U.S. regional COVID-19 summer growth signal.

- Cholera and mpox: next WHO/ECDC/Africa CDC situation updates, especially DRC/Nigeria cholera burden and Madagascar/DRC/Uganda mpox clade I trends.

- High-consequence sporadic events: Marburg in Uganda, CCHF in Spain, H5N1 human case reporting, and any clusters tied to healthcare exposure or cross-border travel.

Key sources consulted

- WHO Global Respiratory Virus Activity, weekly update no. 585: https://www.who.int/publications/m/item/global-respiratory-virus-activity--weekly-update-n--584

- WHO Ebola outbreak - DRC 2026: https://www.who.int/emergencies/situations/ebola-outbreak---drc-2026

- CDC Ebola outbreak current situation: https://www.cdc.gov/ebola/situation-summary/index.html

- CDC respiratory virus data: https://www.cdc.gov/respiratory-viruses/data/index.html

- CDC measles cases and outbreaks: https://www.cdc.gov/measles/data-research/index.html

- CDC pertussis surveillance and trends: https://www.cdc.gov/pertussis/php/surveillance/index.html

- UKHSA England measles epidemiology 2026: https://www.gov.uk/government/publications/measles-epidemiology-2023-to-2026/confirmed-cases-of-measles-in-england-by-month-age-region-and-upper-tier-local-authority-2026

- NSW respiratory surveillance: https://www.health.nsw.gov.au/Infectious/covid-19/Pages/reports.aspx

- ECDC cholera worldwide overview: https://www.ecdc.europa.eu/en/all-topics-z/cholera/surveillance-and-disease-data/cholera-monthly

- ECDC mpox worldwide overview: https://www.ecdc.europa.eu/en/mpox-worldwide-overview

- CDC A(H5) bird flu surveillance and human monitoring: https://www.cdc.gov/bird-flu/h5-monitoring/index.html

- CDC global H5N1 human case summary: https://www.cdc.gov/bird-flu/spotlights/global-summary-06262026.html

- NaTHNaC outbreak surveillance: https://travelhealthpro.org.uk/outbreaks

- AP Ebola report, July 14, 2026: https://apnews.com/article/congo-ebola-outbreak-who-a9093ea39928bfa3f2f0e5aa13c506bb

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

A serious accident left me with multiple fractures to my femur, forcing me to spend months recovering. Like many people recovering from major injuries, I suddenly found myself with time that I hadn’t planned on having.

Instead of viewing those months as lost time, I decided to use them to rethink how we predict infectious diseases completely.

The result is a completely new version of MAPS—the Multi-Agent Pathogen Simulation and Forecasting System.

Over the past month, I have presented this work twice to my colleagues at the World Health Network. While the software is still under active development, it has reached the point where I can finally begin sharing the vision behind it.

MAPS Part I

MAPS Part 2

I believe this system has the potential to fundamentally change how we forecast epidemics.

The idea is actually very simple.

Learning from Weather Forecasting

Most people take weather forecasts for granted.

Every morning we can look at our phones and see a forecast for the next week. Sometimes it is wrong, but compared to forty years ago it is remarkably accurate.

That accuracy didn’t happen because meteorologists found one perfect equation.

Instead, modern weather forecasting combines several powerful ideas.

Scientists gather enormous amounts of observations from satellites, weather stations, aircraft, radar, balloons, and ships. Those observations are used to initialize sophisticated physics-based computer models. Multiple forecasts are run simultaneously, each with slightly different assumptions, and the results are continually compared with reality. The system learns from its mistakes and improves over time.

Disease forecasting has largely not followed this path.

Many epidemiological models are built for a specific outbreak, answer one research question, or estimate a handful of parameters. They are incredibly valuable scientific tools, but they often are not designed to become operational forecasting systems that continually learn from new observations.

MAPS was designed from the beginning to adopt the philosophy that transformed weather forecasting.

Instead of producing a single prediction, it creates an evolving forecasting system that continually compares itself against the real world and becomes better with experience.

Diseases Don’t Stand Still

One of the biggest lessons of the COVID pandemic is that pathogens evolve.

The virus we encountered in early 2020 is very different from the virus circulating today.

New variants appear. Old variants disappear. Some spread faster.

Others evade immunity more effectively.

Traditional epidemiological models often treat the disease as though it were one unchanging organism.

MAPS takes a different approach.

Each variant is treated as its own interacting population, with its own characteristics and its own competition with other variants. Instead of asking “What will COVID do next?” the model asks, “Which variants are likely to dominate next, and why?”

That makes the forecasts much more realistic because evolution itself becomes part of the simulation.

More Than One Forecast

If you’ve ever watched hurricane forecasts, you’ve probably seen what meteorologists call the “spaghetti plots.”

Those dozens of tracks aren’t a mistake. They’re one of the reasons modern weather forecasting works so well. Each line represents a slightly different forecast. Some perform better than others. Taken together, they provide both a prediction and an estimate of uncertainty.

MAPS follows the same philosophy.

Instead of relying on one simulation, it runs an ensemble of forecasts that explore different assumptions about transmission, immunity, and variant behavior.

The system then evaluates which forecasts most closely matched reality and gives greater weight to those that consistently perform well.

Rather than asking us to trust one model, MAPS lets the evidence decide which forecasts deserve the greatest confidence.

Teaching the Model to Learn

Perhaps the most exciting component of the new system is something called MEEWS—the MAPS Evaluation and Ensemble Weighting Software.

Think of it as the report card for every forecast the model makes. Every forecast is eventually compared with what actually happened. How accurately did it predict total infections? Did it correctly anticipate which variants became dominant? Did it predict the timing of the wave? The better a forecast performs, the more influence similar forecasts receive in the future.

In other words, the system doesn’t simply make predictions. It learns from its own successes and failures.

That is one of the defining characteristics of modern artificial intelligence, but here the learning is firmly grounded in observations and transparent scientific evaluation rather than a “black box.”

Building a Virtual Earth

Another major advance has been the development of MGPS—the MAPS Geographic Preprocessor System.

Every weather model first builds a digital description of the Earth. Where are the mountains? Where are the lakes? Where are the forests? Those features rarely change, so they are prepared once and reused over and over.

MGPS does something similar for disease modeling.

It creates detailed maps of population density, age structure, schools, land and water, and eventually hospitals, airports, transportation systems, and other important infrastructure.

This allows the disease model to understand not only how pathogens spread, but also where people actually live, work, travel, and interact.

Beyond COVID

Although COVID has been the primary development platform, MAPS was never intended to become “a COVID model.” The architecture is designed to simulate many infectious diseases. Influenza, RSV, Pertussis, Measles, Tuberculosis are few that are in the implementation phase. Even emerging pathogens that have not yet appeared can be added.

The long-term vision is a unified forecasting framework capable of helping researchers and public health officials understand multiple diseases simultaneously.

Just as modern weather centers forecast hurricanes, winter storms, and heat waves using one integrated modeling framework, I hope MAPS can eventually provide a similar capability for infectious diseases.

Still Under Construction

The project is far from finished.

Many important pieces are still being developed.

School interactions, vaccination dynamics, transportation improvements, additional pathogens, and global forecasting are all on the roadmap.

But after five months of intensive work, the foundation is finally in place.

For the first time, MAPS has become more than a research model. It is becoming a complete forecasting ecosystem that can continually improve as new observations become available. That has been the goal from the very beginning.

Looking Ahead

I’ve now presented MAPS twice to the World Health Network, and I expect to give at least two additional presentations as development continues.

When those talks are scheduled, I’ll post links so anyone interested can join.

If there’s enough interest, I’d also be happy to host a live Substack discussion where I’ll walk through the system in plain English, explain how it works, and answer questions you might.

If that sounds interesting, leave a comment below.

I’d love to hear what you think.

Here is a sample of the most recent forecast. Please be aware that the model is still learning and will take time to optimize. It appears we are heading towards a resurgence that will peak in the first week of September.

You can see last weeks forecast, and some sample animation in the Part II talk I gave.

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

The talk.

Sunday, March 15th, is a very special day for so many involved in the Long Covid Community, it is Long Covid Awareness Day (LCAD). I will include a brief history here, go over the meanings of the colors (teal, grey, black), and provide links to activities, organizations, and information about LCAD and Long Covid in general.

Last year, I had the pleasure of co-hosting a 12-hour online space with Becky Robertson. Unfortunately, I had norovirus and was not if much help. She handled it brilliantly and became an overnight success heralded by many.

History and Background of Long COVID Awareness Day

International Long COVID Awareness Day is observed annually on March 15. It began in 2023 as a grassroots, patient-led initiative to raise awareness of the millions of people worldwide living with Long COVID (also called post-acute sequelae of SARS-CoV-2 infection, or PASC).

The day was created by members of the Long COVID community who felt that the long-term impacts of COVID-19—chronic illness, disability, and economic hardship—were not receiving enough recognition or research attention. The awareness day aims to:

1. Increase public understanding of Long COVID

2. Remember those we have lost

3. Support patients and caregivers

4. Encourage governments and health systems to invest in research and treatments

5. Advocate for prevention and public health measures

6. Promote overall solidarity

March was also designated Long COVID Awareness Month, with activities including social media campaigns, demonstrations, educational events, monuments lit up in the colors, and policy advocacy worldwide.

The movement is largely organized online so people living with severe illness or disability can participate even when they cannot attend in-person events.

Angela Laffin, a first-wave Long COVID patient and advocate, played a central role in creating the awareness day.

• In January 2023, while largely confined to her home because of illness, Laffin began organizing the global patient community online.

• She created social media polls asking people with Long COVID what date, month, and awareness colors they wanted to represent the condition.

• Through this collaborative process, the community chose March 15 as the official awareness day.

Laffin also helped establish International Long COVID Awareness (ILCA), a grassroots advocacy network that coordinates global awareness efforts and amplifies patient voices.

The campaign grew quickly, with organizations and patient groups across countries—including the U.S., Canada, the U.K., and several European nations—joining efforts to recognize the day and advocate for Long COVID research and care.

The Long COVID Awareness Ribbon

Like many health movements, Long COVID advocates adopted an awareness ribbon to create a simple visual symbol of solidarity and recognition.

Awareness ribbons have long been used to draw attention to health and social issues—such as the pink ribbon for breast cancer and the red ribbon for HIV/AIDS—allowing people to show support for a cause through clothing, pins, social media, and public displays.

• The ribbon was designed by Tracey Thompson, an early Long COVID patient.

• The color scheme was chosen through community polling among patients and advocates to reflect the shared experience of living with the condition.

The Long COVID awareness ribbon uses three colors: teal, gray, and black.

Teal

• Represents hope, support, and the possibility of recovery or treatment.

• Symbolizes solidarity among patients, caregivers, and advocates.

Gray

• Represents loss and grief experienced by patients and families.

• Reflects the loss of health, livelihoods, and lives due to Long COVID.

Black

• Represents loneliness and isolation.

• Many Long COVID patients experience prolonged illness, disability, and social isolation.

Together, the three colors symbolize the past, present, and future of Long COVID, acknowledging suffering while emphasizing hope and community support.

LINKS

First, the marathon space hosted by Becky Robertson.

List of actions

International Long COVID Awareness Day 2026 Highlights Ongoing Impact of Long COVID

Other useful graphics

and the kind folks with an LC sense of humor.

More to come over the next few days …

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.

Remember H5N1?

The reports keep mounting for our avian friends and the deaths caused by bird flu (HPAI). I would blame them if they went Alfred Hitchcock on us. Are the kiddos running from the birds or Covid?

Since 1970, North America has lost 3 billion breeding pairs out of approximately 9 billion. Planet-wide, between 48 and 61% of bird species are in decline. Now we have new clades of bird flu that are absolutely devastating the wild and domestic bird populations. They are so pissed that they got together and decided to spill it over to mammals, with a specific species that has led to their demise in mind: humans. OK, I made that up, but I would not blame them if they did. Climate change, increased pollution, and human encroachment on their nesting grounds and migration routes. Our fragile ecosystems are heading towards collapse if we don’t get our shit together.

So, after years of neglect, is the USDA about to get serious? On the surface, it appears they might be. I think the government report on the milk supply testing (36% of the milk tested + for H5N1). When they said that around 1% of the herds had been infected, it at least made them lift their heads out of the sand.

Here is an article on the change in strategy. The headline is : ”USDA Triggers ‘Secure Our Herds’ Alert As Mandatory 2026 H5N1 Dairy Testing Threatens Midwest Milk Margins”. Of course, we have to have some economics in the headline. They state first:

The USDA just dropped a regulatory bomb on the American dairy industry. Starting immediately in 2026, the new “Secure Our Herds” initiative completely rewrites the rules of farm biosecurity. Consequently, voluntary pathogen screening is officially a thing of the past. Federal inspectors are now monitoring your bulk tank with unprecedented scrutiny. If you are milking cows today, you must prepare for sudden, devastating herd quarantines.

So are the quarantines “devastating”? Here is where the skeptic in me creeps in, and I worry about the motives of this. Are you thinking what I am thinking? There is a significant blow to small farm operations, while Big Ag operations can absorb any costs. So who would snatch up the small operators? I don’t think I need to answer that.

Oh, but I should have read further.

This new federal testing strategy specifically targets the highly pathogenic H5N1 avian influenza. Previously, the government only restricted the interstate movement of lactating dairy cattle. However, the 2026 USDA Secure Our Herds Alert authorizes routine, randomized testing of raw milk at the processor level. Therefore, your local creamery is now the frontline of federal disease surveillance.

If a positive viral load is detected in your shipment, the financial blow is immediate. Your farm will be slapped with an ironclad 30-day quarantine by the state veterinarian. As a result, you cannot sell cull cows or transport bull calves off the property. Furthermore, the sheer cost of dumping infected milk can bankrupt a heavily leveraged family farm in weeks.

Currently, feeding a lactating Holstein costs roughly $8.50 per head per day. You simply cannot afford to feed an entire freestall barn that produces zero sellable milk. Meanwhile, operating loans are carrying punishing 8.5% interest rates. You must actively defend your milk check from this invisible, margin-crushing threat

There you have it spelled out as plain as day. 8.5% interest and $8.50 per head per day. As I said, we know who can afford this and does not need the damn loan. On one hand, it is about time they implemented some policies with some substance to them, while on the other hand, they certainly are not looking out for the little guy. The soybean farmers have it better than this stinker.

So overall, I will plug my nose and say it’s about time, but please think of those who will be swept away in the wash. As I have said, we are at the doorstep of H5N1 being transmitted from human to human. Give a case-fatality rate of 48% for all known human cases, going back decades (about 1000 total). Of course, this number is inflated by missed cases, so the overall mortality rate is significantly lower. Then again, we have not had much luck with the new genotypes of 2.3.4.4b. We have seen both D1.1 and B3.13 in the dairy cattle. The chicken farms have shown a variety of B/D lineages. All are reassortments.

And then we have the increasing prevalence of PB2 E627K. This is one of the first steps toward going human-to-human, as outlined by Dr. Peacock. For completeness, here are the steps. The first 3 will facilitate human-to-human, but not efficiently. The latter steps will increase the resistance to ph. changes and replication rates. If those happen, we are in deep doo doo.

1) 𝘍𝘪𝘳𝘴𝘵 𝘴𝘵𝘦𝘱 : 𝘔𝘶𝘵𝘢𝘵𝘪𝘰𝘯 𝘗𝘉2/𝘌627𝘒

2A) 𝘚𝘦𝘤𝘰𝘯𝘥 𝘴𝘵𝘦𝘱 : 𝘊𝘩𝘢𝘯𝘨𝘦 𝘪𝘯 𝘏𝘦𝘮𝘢𝘨𝘨𝘭𝘶𝘵𝘪𝘯𝘪𝘯

2B) 𝘚𝘦𝘤𝘰𝘯𝘥 𝘴𝘵𝘦𝘱 (2) : 𝘈𝘮𝘪𝘯𝘰 𝘢𝘤𝘪𝘥 𝘤𝘩𝘢𝘯𝘨𝘦𝘴 𝘘226𝘓 𝘢𝘯𝘥 𝘎228𝘚

3) 𝘛𝘩𝘪𝘳𝘥 𝘴𝘵𝘦𝘱 : 𝘔𝘶𝘵𝘢𝘵𝘪𝘰𝘯𝘴 / 𝘈𝘤𝘪𝘥𝘪𝘤 𝘵𝘩𝘳𝘦𝘴𝘩𝘰𝘭𝘥

4) 𝘍𝘰𝘶𝘳𝘵𝘩 𝘴𝘵𝘦𝘱 : 𝘛𝘩𝘦 𝘱𝘳𝘰𝘵𝘦𝘪𝘯 𝘔𝘹𝘈

5) 𝘈 𝘧𝘪𝘧𝘵𝘩 𝘴𝘵𝘦𝘱 ? 𝘛𝘩𝘦 𝘱𝘳𝘰𝘵𝘦𝘪𝘯 𝘉𝘛𝘕3𝘈3

Here is the status of #1. The mutation E627K improves viral replication efficiency in mammalian cells by enhancing interaction with mammalian host proteins such as ANP32A. In experimental models (mice, ferrets, guinea pigs), it can increase virulence and replication efficiency in mammals. An example of environmental/cattle sequencing found ~1.7% of PB2 reads carrying E627K, up from <1%, in 2024. In 2025, it was found in several herds.

We have a ways to go, but remember the Leonardi effect. Immune dysregulation leads to more influenza cases, which in turn increase the chances of reassortment due to coinfections with H5N1. I will send out the total bird flu detections report in the next Substack.

I think it is time for some relatively good news. This is from an acquaintance on X and aligns with what I have been saying for over 3 years now. Stop your infatuation with the spike protein, start targeting sites that undergo very little change over time, and possibly activate other types of immune cells. Guess what? It appears to work, albeit the evidence is weak due to a small N. Zdenek summarizes the article, titled, “Effectiveness and safety of Autologous Virus-Specific T Cell Therapy for Persistent COVID-19 in People with Immunocompromise: A Clinical Trial Study”. FYI: Autologous - generated from their own blood. Taken it away, Zdenek:

The interesting proof-of-concept study shows that in some severely immunocompromised people with long-lasting COVID-19, it is possible to use autologous VSTs🧵

It is possible to -
Produce SARS-CoV-2–specific T cells from their own blood (autologous VSTs),
Infuse them back into the patient,
In the 3 treated patients this was temporally associated with clinical improvement, PCR turning negative, and better CT findings - without serious side effects.

How strong is the evidence of effectiveness?
Rather weak to moderate for efficacy, but fairly solid for feasibility and short-term safety. This is an early signal, no control group.

In those 3 treated patients
clinical scores improved,
PCR became negative within 2–8 weeks,
CT lung severity decreased,
SARS-CoV-2-specific immune responses increased.

What is especially interesting mechanistically?
Focus on membrane (M) and nucleocapsid (N) proteins.
The strongest T-cell responses were directed against M and N proteins, which are more conserved across variants than spike, are not the primary targets of most vaccines.

This suggests that in immunocompromised patients broad T-cell immunity against multiple viral proteins may be crucial.

Tests like
ELISPOT (IFN-γ responses),
Pentamer assays (specific CD8 T cells),
showed expansion of virus-specific T cells after infusion that correlated with viral decline.
This provides good biological support for the mechanism.

Among the 3 treated patients
No serious adverse events,
No infusion reactions,
One mild temporary leukocytosis unrelated to therapy.
Do the therapy appears low risk, but rare side effects cannot be assessed with such a small sample.

The biggest practical limitation (and paradox) - autologous T-cell production takes about 21 days.

During that time
some patients improve spontaneously,
some worsen too much to receive therapy,
some cell cultures fail.
This is a key real-world barrier.

Originally, 12 patients with persistent COVID-19 and hematologic malignancies were enrolled in the study.
10 out of 12 - virus-specific T cells were successfully manufactured
3 patients - actually received the T-cell infusion

The authors suggest future solutions -
shorten production time, pre-emptive cell banking, off-the-shelf allogeneic VST products.

Sum:
Autologous SARS-CoV-2–specific T cells can be produced in most such patients.
The therapy appeared safe in this small pilot.
It may help clear persistent infection in selected cases. M/N proteins are important T-cell targets.

The study supports the idea that in patients with
B cell depletion,
hypogammaglobulinemia,
persistent viral shedding,
lack of T-cell immunity may be a key reason for chronic infection, and restoring it may help.

However, the real future likely lies in faster, scalable T-cell therapies, not slow individualized production.

Thanks IDGuy @infektolog.

Insides.
This is not genetic modification (unlike CAR-T therapy).
The cells are not engineered - they are selected and expanded only. The therapy uses the patient’s own T cells.
The principle is amplifying an existing but insufficient immune response.

In the lab, the cells are exposed to synthetic peptide pools derived from the spike, M, N - to activate T cells that recognize SARS-CoV-2 - to effectively selects virus-specific T cells.
The activated T cells are then cultured in a medium containing interleukin-2. The goal is to expand enough virus-specific T cells, reach a therapeutic dose.

That was so exciting. How about I describe a new, exciting vaccine that follows a similar path and is now entering human trials? I had written a long document about this and just pulled the bare bones out of it. I am quite excited about this, if you could not tell already. Here you go.

Engineering Immunity: How Designed Protein Nanoparticles Could Enable Universal Coronavirus Vaccines

Joseph L. Eastman PhD, WHN Science and Policy Group Advisor

eastmanjosephlee@gmail.com

Background

The COVID-19 pandemic showed how quickly modern vaccine science can respond to a global threat. Within a year, multiple vaccines were deployed, dramatically reducing severe disease and mortality.

But it also revealed a limitation.

SARS-CoV-2 continues to evolve, and related viruses circulate widely in animal reservoirs. Each new variant or spillover event raises the same question: are we destined to keep chasing viruses with updated vaccines?

A growing area of immunology research aims to move beyond that reactive model. Instead of designing vaccines against a single strain, scientists are exploring platforms that can intentionally broaden immune responses across entire viral families.

One promising approach involves designed protein nanoparticle vaccines.

The Nanoparticle Vaccine Concept

Unlike mRNA vaccines or viral vectors, these vaccines rely on engineered protein structures.

These vaccines are composed of fully recombinant, computationally designed protein nanoparticles that self-assemble into icosahedral structures displaying tens of copies of a viral antigen, thereby decoupling antigen geometry from innate immune activation, which is provided separately by formulation with a conventional adjuvant.

In simpler terms:

• scientists design proteins that self-assemble into virus-sized particles

• each particle displays many copies of a viral antigen

• the immune system encounters something that looks structurally like a virus, but without infection

This structural mimicry turns out to be extremely important for the immune system’s response.

Why Geometry Matters to the Immune System

One of the key drivers of antibody responses is how antigens are arranged in space.

When many identical antigens appear in a repeating pattern — like on a viral surface — they can cross-link B-cell receptors efficiently. This lowers activation thresholds and triggers stronger immune responses.

Nanoparticle vaccines intentionally exploit this principle.

Multivalent antigen display can:

• recruit a broader set of B-cell clones
• sustain germinal-center reactions longer
• promote affinity maturation
• generate more durable antibody responses

The result is often stronger and more diverse neutralizing antibodies compared with traditional soluble protein antigens.

Evidence From Preclinical Studies

In animal models, nanoparticle vaccines displaying coronavirus receptor-binding domains (RBDs) have shown striking effects.

Compared with soluble antigens, nanoparticle-displayed versions frequently produce:

• significantly higher neutralizing antibody titers

• broader epitope targeting

• improved durability of immune responses

Importantly, these responses often target multiple regions of the viral protein, reducing the risk that a single mutation could allow immune escape.

This observation is central to the idea of engineering breadth into vaccine responses.

From Concept to Clinic: The GBP510 Vaccine

A major milestone for the field came with the development of GBP510, a recombinant protein nanoparticle vaccine.

GBP510 uses self-assembling nanoparticles that display SARS-CoV-2 receptor-binding domains and is formulated with the AS03 adjuvant.

Clinical trials demonstrated:

• strong neutralizing antibody responses

• favorable safety profile

• feasibility of large-scale manufacturing

Although GBP510 was designed as a strain-specific COVID-19 vaccine, it provided something just as important: validation of the nanoparticle platform itself in humans.

Once a platform is proven safe and manufacturable, the next step becomes immunogen design.

The Next Frontier: Engineering Breadth

The real promise of nanoparticle vaccines lies in their flexibility.

Because antigens can be precisely arranged on the particle surface, researchers can experiment with strategies such as:

Mosaic antigen display
Particles present multiple related viral antigens simultaneously, encouraging the immune system to recognize shared features.

Conserved epitope targeting
Designs emphasize parts of the virus that change very little across related strains.

Immunodominance reshaping
Altering antigen presentation can shift the hierarchy of immune responses away from highly variable sites.

These approaches aim to create vaccines that protect against multiple sarbecoviruses, not just SARS-CoV-2.

Measuring Whether Breadth Works

Testing a “universal” vaccine requires more than measuring antibody levels.

Researchers increasingly rely on tools such as:

Cross-neutralization panels
Testing antibodies against many related viruses.

Antigenic cartography
Mapping immune responses across viral evolutionary space.

Epitope mapping
Identifying which parts of the virus antibodies actually recognize.

Together, these methods reveal whether a vaccine truly expands immune recognition — or simply produces high titers against one strain.

Challenges Still Ahead

Universal coronavirus vaccines remain an open scientific challenge.

Several issues remain unresolved:

Breadth vs potency trade-offs
Responses that span many epitopes may reduce the peak neutralization of any single virus.

Immune imprinting
Previous exposure to coronaviruses could bias responses toward familiar epitopes.

Future viral threats
Predicting which sarbecoviruses will emerge remains uncertain.

Despite these challenges, the framework for testing these ideas now exists.

Why This Matters for Pandemic Preparedness

The next pandemic virus will almost certainly not be identical to SARS-CoV-2.

Preparedness therefore requires vaccine technologies capable of anticipating viral evolution, not simply reacting to it.

Designed protein nanoparticle vaccines offer a way to intentionally shape immune responses using structural biology, computational design, and immunology together.

Whether candidates such as GBP511 ultimately achieve broad protection across sarbecoviruses remains to be seen.

But the underlying concept — engineering immunity through antigen architecture — may represent one of the most important advances in modern vaccinology.

I hope you enjoyed that, and maybe it gave you some hope.

Sometimes you come across a thread summarizing an article that is just plain pure intriguing science. It is not even directly related to what I like to write about. Thanks, Dr. David Joffe for pointing this out and a special thanks to Dr. Jared Rosenblum

As promised, here’s the deep dive on our recent article! Did you know the brain’s “sewer drains” (dural sinuses) aren’t passive pipes—they’re dynamic, ruffling structures that actively guard immunity & regulate pressure?
As both a co-author and President & Founder of @neurosimplicity, I am excited to spotlight this groundbreaking discovery from the McGavern lab @NIH_NINDS in

Our Imaging Suite helped map the amazing cranial & neurovascular connections in unprecedented 3D detail! 🧠🔬

Link: rdcu.be/e4A8i# Neuroimmunology #BrainImmunity

or use this link for an enhanced PDF with incredible graphics!!

The meninges enclose the brain and recent studies have shown that the dura contains extensive immune networks. Dural sinuses, traditionally viewed as passive venous conduits, function as dynamic interfaces for neuroimmune regulation.

Figure 1 details the dorsal dural sinus anatomy in mice: a continuous VE-cadherin+ endothelial layer with αSMA+ smooth muscle bands and vimentin support along the transverse sinuses, sagittal sinuses, and rostral-rhinal hub.

Multi-modal imaging (confocal whole mounts, light-sheet of cleared heads, micro-CT segmentation) reveals key cranial and neurovascular connections, including diploic veins linking skull bone marrow to sinuses and anastomoses between upper and lower sagittal sinuses.

Proud that the @neurosimplicity Imaging Suite supported the micro-CT 3D reconstructions, enabling precise mapping of these structures with reproducibility and multi-modal integration.

Using intravital microscopy + multi-modal imaging, the team captured real-time sinus behavior: constant constriction/dilation to manage blood flow & intracranial pressure, plus “ruffling” of walls to let immune cells patrol & antigens sample.
Truly incredible!

Sinus endothelial cells (SECs) are fenestrated & permeable—allowing CSF-blood mixing without BBB breach. RAMP2 tunes this barrier; RAMP1 drives smooth muscle-mediated dynamics.

This setup turns sinuses into active neuroimmune checkpoints.

Building on the permeable sinus endothelial barrier, this setup enables efficient exchange between the sinus lumen and the leukocyte-rich perisinus space.
Leukocytes patrol this compartment, capturing antigens and facilitating immune surveillance under steady-state conditions. During systemic viral infection, sinus dynamics tighten the barrier while recruiting additional immune effectors, bolstering local antiviral responses and limiting pathogen access to the meninges and CNS.

These findings position dural sinuses as active regulators of meningeal immunity.

Validation in human dural samples confirms similar structural features, including fenestrated endothelium and associated immune elements, in the dorsal sinus system.

These observations suggest potential relevance to conditions involving meningeal inflammation, impaired CSF drainage, or dysregulated intracranial pressure and immunity—such as multiple sclerosis, Alzheimer’s disease, migraine, and hydrocephalus.

Further investigation into sinus dynamics and RAMP signaling in these contexts may open avenues for targeted therapeutic strategies.

Huge congrats to lead author Kelly Monaghan, Dorian McGavern, & the entire team—including our own collaborations. Proud to contribute tools that accelerate these discoveries.

Thoughts? Let’s discuss! #ScienceTwitter #Meninges

If you’re in neuro research, check out @neurosimplicity Imaging Suite for reproducible, multi-modal 3D mapping of complex brain anatomy. DM for demo!
Thanks for reading—stay tuned for more.
Visualize. Together.
http://neurosimplicity.com

And now for something completely different …

See what I mean? Terminator.

Northwestern University engineers have developed the first modular robots with athletic intelligence. They can be combined and recombined in the wild, recover from injury and keep moving no matter what's thrown at them.

Called "legged metamachines," the creations are made from autonomous, Lego-like modules that snap together into an endless number of configurations. Each module by itself is a complete robot with its own motor, battery and computer. Alone, a module can roll, turn and jump. But the real agility and indestructibility emerges when the modules combine.

To design the most effective combinations, the engineers used artificial intelligence (AI) to evolve novel body configurations. Instead of sticking with standard dog- or human-like designs, the AI churned out strange new “species” of machines that no human engineer would have conceived. When connected to other modules, the metamachines undulate like seals, bound like lizards or spring like kangaroos.

Ok, I have freaked myself out with this baby. Yikes!

Indestructible Summary

Indestructible Study

Keep up your kindness and hopefully help someone with Long Covid or prevent it by encouraging masking, boosting, and clean air!

Take care,

Joe

I should be wearing a mask for my emoji on X, but I was in the middle of a lake when I took this.