Wednesday, October 14, 2026

Saying Goodbye to An Infectious Disease Reporting Legend

 

#19,373

I've lost count how many times I've featured a Helen Branswell story in this blog, but it must run into the hundreds. She was, quite simply, one of the most prolific and capable infectious disease reporters in the world. 

Her loss, and legacy, are detailed in the STAT obituary, published yesterday. 

While I never got to meet Helen, we corresponded a number of times. Sometimes to share information, other times less formally.  She was exceptionally kind to this humble blogger, and I am saddened  - and Flublogia is diminished - by her passing.


BMC Public Health: 2018–2025 Serological study on avian influenza among occupationally exposed populations in the Poyang Lake area

 

#19,372

In 2025 a Chinese research study reported on testing environmental samples collected from southern and northern Chinese live poultry markets during 2019–2023 for evidence of avian influenza viruses. 

They examined > 64,000 samples, and found the incidence of H5, H7, and H9 influenza A detections substantially higher in southern provinces. Jiangxi, Yunnan, and Guangxi showed the highest level of environmental contamination, with positive rates of  82.3%, 49.41%, and 45.47%. 

Today we have a research study into the seroprevalence of  influenza A viruses among occupationally exposed individuals in the Poyang Lake area - located in Jiangxi province - which reported the highest environmental readings in the above report. 

Poyang Lake is the largest freshwater lake in China, and lies beneath the East Asian-Australasian Flyway. Poyang Lake also provides a habitat for more than a million migratory birds, including endangered Siberian cranes. 

Researchers tested blood from 2,437 poultry-exposed people around Poyang Lake, China, from 2018 to 2025 using hemagglutination inhibition assays. Predefined HI positivity thresholds were ≥ 1:20 for H3N8, H5N8, H5N1, H7N9, and H10N3 and ≥ 1:40 for H5N6 and H9N2.

Participants were mostly backyard poultry keepers and their households (90.3%) and live-market workers (9.7%). The median age was 62.  

While HI reactivity can't conclusively prove that an individual was previously infected by a specific virus (there's always a possibility of cross-reactivity with other viruses), it does suggest that a subject might have had a mild, or subclinical, infection with that virus sometime in the past. 

Admittedly, it would have been nice to see confirmatory Microneutralization (MN) testing of these samples, but they are considerably more resource intensive and technically demanding. HI titers also tend to fall faster than MN titers, and may drop below the positive cutoff within the span of a couple of years, which means that HI assays may miss older infections.  

With those limitations in mind, the authors found samples meeting the study's HI thresholds were 4.43% for H5N6 and 4.39% for H9N2, with lower rates for H7N9 (2.74%), H3N8 (1.44%), H5N8 (1.27%) and H10N3 (0.26%). 

First the link and abstract from the open-access study, after which I'll return with a postscript:

2018–2025 Serological study on avian influenza among occupationally exposed populations in the Poyang Lake area — the region with the highest environmental surveillance positive rate in China
Research Open access
Published: 14 October 2026 Cite this article
 
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Chuang Nie, Yawei Li,Wenjing Xie, Ke Qian, Ting Xu, Fenglan He, Zhiqiang Deng, Wanting Wei, Yujie Hou, Xiang Tu, Tianxin Xiang & Wentao Song


We’re sharing this article early to provide faster access to peer-reviewed, accepted research. It is citable and carries a permanent DOI. This version is subject to further edits and will be replaced automatically by the final Version of Record. All legal disclaimers apply.

Abstract

Background

An avian influenza virus positivity rate as high as 82.3% has been reported in Jiangxi Province, China, underscoring this region as a potential hotspot for avian influenza virus circulation. As a crucial hub for migratory birds and a region where wild birds, domestic poultry, and humans frequently overlap, Poyang Lake provides favorable ecological conditions for cross-species transmission of avian influenza viruses. This study aimed to describe the seroprevalence of antibodies against selected avian influenza virus subtypes among occupationally exposed populations at surveillance sites around Poyang Lake from 2018 to 2025, and to provide data to inform ongoing surveillance and risk assessment.

Methods

A cross-sectional serological surveillance was conducted annually during winter and spring from 2018 to 2025 in Nanchang County (Nanchang) and Duchang and Wuning Counties (Jiujiang), Jiangxi Province. Serum samples were collected from occupationally exposed individuals, including backyard poultry keepers and their household members and live poultry market workers with direct poultry contact.
Hemagglutination inhibition assays were performed by the National Influenza Center to assess antibody reactivity against the test antigens representing H5N6, H9N2, H7N9, H3N8, H10N3, H5N8, and H5N1. Predefined HI positivity thresholds were ≥ 1:20 for H3N8, H5N8, H5N1, H7N9, and H10N3 and ≥ 1:40 for H5N6 and H9N2.

Results

A total of 2,437 valid serum samples were analyzed (1,599 from Jiujiang and 838 from Nanchang). Overall, 108 samples (4.43%) met the predefined HI positivity threshold for H5N6, and 107 (4.39%) met the threshold for H9N2. During 2018–2020, 25 of 914 samples (2.74%) met the threshold for H7N9.
During 2021–2025, 22 of 1,523 samples (1.44%) met the threshold for H3N8, including 9 of 100 samples (9.00%) collected in Nanchang in the 2024 surveillance year. Four of 1,523 samples (0.26%) met the threshold for H10N3; all four were from Jiujiang in the 2024 surveillance year. Four of 314 samples (1.27%) met the threshold for H5N8 in 2020. None of the 600 samples tested for H5N1 in the 2024 and 2025 surveillance years met the predefined threshold.

Conclusions

HI antibody reactivity varied across subtypes, surveillance locations, and years among occupationally exposed participants around Poyang Lake. The H3N8 finding in Nanchang and the H10N3 finding in Jiujiang in the 2024 surveillance year warrant further investigation. H5N6 peaks in Jiujiang in 2021 and in Nanchang in 2022; H9N2 peaks in 2021 in Jiujiang and 2023 in Nanchang. HI reactivity alone does not establish subtype-specific human infection or local virus circulation. Continued serological surveillance, interpreted alongside poultry and environmental virological data, may inform risk assessment.

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We've previously looked at a number of human seroprevalence studies which have also suggested more human spillovers occur than have been reported, including:

The good news is, this strongly suggests the 50% CFR (Case fatality rate) of H5N1 is badly overstated, since many mild infections are never counted.  

Conversely, it also suggests that novel flu infections may occur far more often than previously thought, which increases the risks of viral adaptation to a human host, and provides additional opportunities for novel/seasonal coinfection, which could lead to a reassortment. 

Either way, this is a reminder that a lot more goes on with the evolution and spread of novel flu viruses than our limited surveillance might suggest.

Tuesday, October 13, 2026

BMJ Public Health (Review): Public health risks and control measures associated with live animal and animal product trade in traditional food markets in low- and middle-income countries


#19,371


In the summer of 2025 we looked at a review article (see J. Virology: Zoonotic Disease Risk at Traditional Food Markets) by Frida E. Sparaciari, Cadhla Firth, Erik A. Karlsson, and Paul F. Horwood which concluded that traditional food markets (TFMs) provide essential community services (both economic and social), but they can also be hotspots for zoonotic disease transmission.
 
Live bird markets (LBMs) have long been linked to human exposure to (and infection by) avian influenza viruses, so much so that in 2014, in CDC: Risk Factors Involved With H7N9 Infection, we looked at a case-control study that pretty much nailed visiting LBMs as the prime risk factor for infection.

Four years ago, in Zoonoses & Public Health: Aerosol Exposure of Live Bird Market Workers to Viable Influenza A/H5N1 and A/H9N2 Viruses, Cambodia, we looked at a study that documented high levels of H5 & H9 viruses in the air at a Cambodian LBM during the `high season' for avian flu, and more importantly, that a large percentage remained viable (and infectious).

In low and middle-income countries (LMICs) - where home refrigeration is less common - the ability to buy freshly killed poultry is often viewed as a necessity. 

Larger, more modern cities like Hong Kong have gone to great lengths to regulate and restrict live bird markets, while early in 2025, Shanghai suspended Live Poultry Sales altogether.

During past avian flu outbreaks - when authorities ordered LBMs closed - clandestine and unregulated markets sometimes sprang up, which only exacerbated the problem.

The authors of the above mentioned J.Virology review are back today (with several other contributors) with a follow-up scoping review based on 87 studies published between 2017 and the end of 2025 that reported on public health outcomes, risk factors or control measures associated with TFMs in LMICs.

Most of these studies centered on TFMs in China and Bangladesh, and while avian flu was the primary focus, other public health risks (primarily bacterial zoonoses, e.g. Campylobacter spp, Salmonella spp, and multi-drug resistant E. coli) were also considered.

While the authors offer up a number of suggestions that may help reduce the risks, this is a complex and varied problem, and solutions will likely have to be tailored to each TFM.   

Follow the link to read the review in its entirety. 


Public health risks and control measures associated with live animal and animal product trade in traditional food markets in low- and middle-income countries: a scoping review

Author affiliations• Frida E Sparaciari1 2,  Alfonso I Vargas Huaco3 4,  Charifa Zemouri5,  Anna Signe Fomsgaard1 2, Wei Ning Chen3 4, Cadhla Firth2 6, Paul F Horwood2 7, Erik Karlsson1 8

        BMJ Public Health 2026;4:e006159. doi:10.1136/bmjph-2026-006159 

Abstract
Introduction 

Traditional food markets (TFMs) support food security and livelihoods in low- and middle-income countries (LMICs), but the trade of live animals and products of animal origin may facilitate zoonotic and foodborne disease transmission. Evidence on associated risks and control measures remains fragmented across pathogens, market types and interventions. This scoping review maps the literature on zoonotic and foodborne public health risks, risk factors and control measures related to the trade of live animals and animal products in TFMs in LMICs.

Methods 

Web of Science, PubMed and Scopus were searched on 24 April 2026 for primary, English-language studies published from 1 January 2017 to 31 December 2025. Eligible studies reported public health outcomes, risk factors or control measures associated with TFMs in LMICs. Reviewers screened titles/abstracts and full texts against predefined criteria, resolving disagreements by consensus. Data were charted and checked using a standardised pro forma; no methodological quality appraisal was conducted.

Results 

87 studies were included; 61 (70.1%) reported public health risks and 35 (40.2%) examined control measures, with 9 (10.3%) addressing both domains. Most studies were observational and focused on poultry markets and avian influenza viruses (AIVs), particularly at the human–market interface. Reported risks included occupational exposure among market workers, exposure among community members and contamination of animal products and market environments.
Common risk factors included poor hygiene, weak biosecurity, on-site slaughter, species mixing, inadequate waste management, prolonged animal holding and unsafe handling. Control measures included market closure, rest days, species separation, cleaning and disinfection, infrastructure improvements and policy-based interventions such as China’s ‘1110’ policy.
Across distinct studies, several measures were associated with lower pathogen detection or modelled infection estimates, whereas other findings were non-significant or inconsistent. Implementation was constrained by economic losses, limited infrastructure, weak enforcement, low awareness and poor adherence to protective practices.

Conclusions 

TFMs are important human–animal–environment interfaces where zoonotic and foodborne risks arise from interacting biological, structural and behavioural factors. The findings from this scoping review provide a rationale for context-specific, multilevel One Health approaches combining infrastructure improvements, biosecurity, surveillance, regulation, compensation and vendor engagement. However, because most evidence was observational and concentrated on AIV-focused poultry markets, the effectiveness and generalisability of these approaches require further evaluation across diverse TFM settings. 
What is already known on this topic

Traditional food markets are essential to food access and livelihoods in many low- and middle-income countries, but the trade of live animals and products of animal origin can create human–animal–environment interfaces where zoonotic and foodborne pathogens circulate. Existing evidence remains fragmented and is largely concentrated on avian influenza in poultry markets.

What this study adds

This scoping review maps 87 studies and uses a One Health framework to integrate evidence on public health risks, exposure pathways, human health outcomes and control-measure implementation in traditional food markets. It shows that risk is produced by interacting market infrastructure, hygiene, biosecurity, animal management and human practices, rather than by live animals or animal-origin products alone.

How this study might affect research, practice or policy

The findings suggest potential value in adaptive, context-specific One Health approaches rather than isolated technical controls. Policy and research should evaluate combinations of infrastructure, water, sanitation and hygiene, biosecurity, surveillance, vendor engagement, market regulation and livelihood-sensitive incentives, while expanding evaluation beyond avian influenza virus-focused poultry systems.  

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Monday, October 12, 2026

Preprint: Human Infection with Avian Influenza A(H7N7) Virus, Taiwan, 2026

 

#19,370

Last April 2nd, in Taiwan CDC: Human Infection with a Novel H7 Avian Virus, we looked at a lengthy report on Taiwan's first detection of a locally acquired human H7 LPAI infection in a poultry farmer.

The patient (a man reportedly in his 70s) was hospitalized with fever on March 22nd and subsequently developed pneumonia. He remained hospitalized and in isolation in early April, although his condition was said to be improving. 

The CDC also reported:
Currently, 33 close contacts are under health monitoring and management, and 3 have been given preventative medication based on risk assessment. Tests were conducted on 6 family members, all of whom tested negative.

The following day, we saw another Taiwan CDC Update: Novel H7 Infection Identified as H7N7.  We also saw a letter to physicians posted on April 8th.  At that time only the HA (H7) has been identified, with additional tests still pending.

We looked at a follow-up statement in early May (see Taiwan CDC: Statement/Update On Locally Acquired H7N7 Infection) after additional testing revealed the virus's PB2 gene carried the E627K mutation (PB2 E627K).

PB2-627K - which can often develop after a human/mammal is infected - is associated with enhanced replication and pathogenicity in mammals (see A rapid review of the avian influenza PB2 E627K mutation in human infection studies).

Yesterday an unusually terse (the abstract run just 50 words) preprint was posted on the medRxiv server which fills in some of the gaps on this event. 

We learn that virus (A/Taiwan/1/2026) was a low-pathogenic H7N7 bird flu virus from the wild-bird gene pool of Eurasia. The authors wrote:

Although the HA and M genes clustered with an A/environment/Kagoshima/KU-24-D10/2024(H7N7)-like virus isolated in Japan, the other gene segments were most closely related to different source viruses. Across the genome, 138A/Taiwan/1/2026 is distantly related to previously detected viruses from Taiwan and to reported human H7 viruses from China, Europe, and North America. 

The authors stated this suggests a recent spillover from a wild bird gene pool, as the virus is distinct from earlier H7N7 poultry viruses which have spilled over into humans. 

While it carried the PB2 E627K mammalian-adaptation marker, the authors cannot say whether that mutation was present in the bird host or arose post-infection in the patient (although the latter is suspected). 

Although no avian influenza virus was reported to have been detected in the duck farms visited by the patient, the authors suggest:

Based on the patient's occupation background, domestic ducks at the workplace may have served as an intermediate source of infection after introduction of the virus into Taiwan by migratory birds. However, direct exposure to migratory birds or their feces could not be excluded. 

None of the contacts tested showed serological evidence of infection. 

Follow the link to read the preprint in its entirety.  I'll return after the break with a postscript.

Human Infection with Avian Influenza A(H7N7) Virus, Taiwan, 2026

Yao-Tsun Li, Yun-Tong Lin, Bao-Shan Chen, Chuan-Yi Kuo, Hsiang-Yi Huang, Hui-Ying Ko, Pei-Yu Huang, Gavin JD Smith, Yi-Ling Lin, Ming-Tsan Liu
doi: https://doi.org/10.64898/2026.10.09.26365013
This article is a preprint and has not been certified by peer review [what does this mean?].  
 
Preview PDF

Abstract

Low pathogenic avian influenza A(H7N7) virus detected in a poultry worker in Taiwan, 2026 was related to viruses circulating in Asian wild birds and possessed PB2 E627K, a mammalian adaptation marker. Enhanced surveillance for H7 viruses in poultry and rapid characterization of human cases are essential to assess pandemic potential.

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While H5Nx gets most of our attention these days, H7 viruses have a fairly impressive track record of their own.
NYC's 2016 dramatic H7N2 outbreak in hundreds of cats, and spillover into animal shelter workers (see J Infect Dis: Serological Evidence Of H7N2 Infection Among Animal Shelter Workers, NYC 2016) - and a 2018 report of a severe H7N4 infection out of China - further illustrate the risks.

Of the 27 novel influenza viruses ranked by the CDC using their IRAT tool, H7 viruses make up 2 of the top 5 (in terms of emergence), and rank higher (in terms of impact) than any of the H5Nx viruses listed. 


Which is why we continue to follow these cases with considerable interest. 

Sunday, October 11, 2026

Reminder: The Great Shakeout is set for This Week (Oct 15th)

 

#19,369

Not quite 3 years ago the USGS unveiled a new seismic risk map (see below), increasing the percentage of Americans at risk of experiencing a damaging earthquake to nearly 75% (roughly 240 million people).

Globally, large swaths of southern and central Europe and Asia - and significant portions of South America, Africa, Oceania and Canada - are at risk as well.

GEM_Global-Seismic-Hazard   DOI 10.5281/zenodo.20208536 (CC BY-NC-SA 4.0)

Publication:

Pagani M, Garcia-Pelaez J, Gee R, et al. (2020) The 2018 version of the Global Earthquake Model: Hazard component, Earthquake Spectra, vol. 36, no. 1_suppl, 2020, pp. 226–251. https://journals.sagepub.com/doi/abs/10.1177/8755293020931866

Data:

Johnson, K., Bayliss, K., Villani, M., Brooks, C., Styron, R., Simionato, M., Chen, Y., Rood, A., & Pagani, M. (2026). Global Earthquake Model (GEM) Seismic Hazard Map (v2026.1). [Data set] Zenodo. https://doi.org/10.5281/ zenodo.8409646

While yearly totals fluctuate, on average the USGS expects approximately 16 earthquakes of magnitude 7.0 -7.9 per year - and one of magnitude 8.0 or greater.

Over the past 4 months we've seen 7 Magnitude 7.0+ quakes, but that came after a nearly 2 month lull. Despite the internet clickbait hype machine, we are still well within expected norms.

But the fact remains, billions of people around the world live in active seismic zones, and knowing what to do during - and after - an earthquake can be lifesaving information. 

Eighteen years ago (Nov 2008) Shakeout.org held the first their first event - dubbed The Great Southern California ShakeOut - which involved over five million participants across the region. 

Since then, that event has grown - first nationally - and then internationally, and now it encompasses numerous states, territories, and a number of other countries.


This year's International ShakeOut Day is October 15, when millions of people worldwide will participate in earthquake drills at work, school, or home!

At 10:15 a.m. (local time) on 10/15, you can join millions of people across the world practicing earthquake safety.

While we encourage participation with everyone, you can register your ShakeOut drill for any day of the year, and drill at a time of your choice. You can also include people in multiple locations through video conferencing.
While I don't have to worry much about earthquakes where I live (I make up for it with hurricanes. sinkholes, and alligators), I put high value in being prepared for all natural disasters, and I strongly urge others to do so as well.

If you live in, work in, or ever plan to visit a seismically active area, I strongly would urge you, your family, and your employees take part in these yearly drills.

Once the shaking stops, you'll have to find ways to cope with the aftermath.

While the government will send help, you could find yourself pretty much on your own for several days and living in less than comfortable conditions for weeks (see #NatlPrep: 75% of Americans At Risk Of Experiencing A Damaging Earthquake).

For starters - and as a bare minimum - every household should have a disaster plan, a good first aid kit (and the knowledge to use it), an emergency battery operated NWS weather radio, and emergency supplies to last at least 72 hours during a disaster.


While 72 hours is an admirable start, I wouldn't feel comfortable stopping there. Here in the United States many agencies and organizations recommend that households work towards having a 10-to-14 day supply of food, water, and emergency supplies on hand.

In addition to earthquakes, there are nearly a dozen `very high risk' volcanoes in the continental US (4 in Washington, 4 in Oregon & 3 in California), along dozens of `lesser' threats. While earthquake damage is generally localized, volcanic eruptions can affect property and populations thousands of miles away.


Over the years we've looked at a number of scientific or review articles on earthquake risks, including: 

Saturday, October 10, 2026

WHO DON : Pneumonia of undetermined etiology - Russian Federation

 

#19,368

For the past week we've been following unverified media reports (see here, here, and here) of a Russian lab leak - supposedly of plague - (vigorously denied by Rospotrebnadzor) after the death of a lab worker from severe pneumonia in early October. 

Despite the Russian denials and reassurances, we really don't know exactly what happened - or may still be happening - at that Siberian lab.  

Today the WHO published a lengthy DON (Disease Outbreak News) report on the incident. While it provides several new details from the Russians, this report continues to stress that there are still a number of unknowns.

The WHO now offers a limited-confidence risk assessment, but it is tempered  by the lack of a confirmed diagnosis in the deceased laboratory worker, and ongoing uncertainty over the `source and mode of exposure'.

Due to its length, I've only posted the link, and a few excerpts.  Follow the link to read the DON in its entirety. 

Pneumonia of undetermined etiology - Russian Federation
10 October 2026

Situation at a glance

On 2 October 2026, WHO became aware through media reports of the death of an employee of the Irkutsk Antiplague Research Institute (APRI) of Siberia and the Far East, the Russian Federation. According to these reports, the individual died on 2 October following hospitalization for severe pneumonia on 29 September, and pneumonic plague was suspected as the cause of death, following occupational exposure in laboratory settings. 

Following requests for verification from WHO, the National Focal Point for the International Health Regulations (2005) (NFP) of the Russian Federation confirmed the death and informed WHO that no case of plague had been registered recently in Irkutsk Oblast, that preventive and control measures had been implemented in accordance with national sanitary legislation, and that the laboratory testing of contacts detected no high-threat pathogens. 

The authorities also reported that no biosecurity incidents had occurred in the laboratory, contrary to reports in the media, and that there were no further case of severe pneumonia linked to this case. The NFP informed WHO that the case and all contacts had been tested for a range of microorganisms, including high-threat pathogens. Test results were negative for the tested high-threat pathogens. All contacts had been medically followed up in healthcare facilities or at home, and all remained asymptomatic throughout. Quarantine measures were instituted in the hospital where the patient was being treated. 

Based on the information provided by NFP, WHO has not identified evidence of ongoing transmission associated with this event. A key uncertainty remains the absence of a confirmed diagnosis in the deceased laboratory worker. WHO will continue to monitor the situation and assess any potential public health implications as further information becomes available.

        (SNIP)

WHO risk assessment

WHO’s rapid risk assessment is a systematic and continuous process that characterizes the risk posed by a public health event and informs measures to reduce its impact and prevent international spread.

A key uncertainty for this event is the absence of a confirmed diagnosis in the deceased laboratory worker. According to information provided by the national authorities, testing did not identify plague or other tested high-threat pathogens, and the death has been classified as pneumonia of undetermined etiology. However, WHO has not received information identifying the causative agent responsible for the fatal illness. Given the absence of a confirmed diagnosis, WHO is not in a position to independently assess whether the duration of the reported monitoring period for contacts was sufficient to exclude all plausible causes of the fatal illness.

The occupational setting of the case remains an important consideration. The deceased individual worked at an institution that handles high-consequence pathogens, and precautionary public health measures were reportedly implemented because of the individual's professional activities. While the information provided by the authorities does not indicate infection with tested high-threat pathogens or identify additional linked cases, the source of the fatal illness remains undetermined. A laboratory-associated exposure therefore cannot be fully excluded at this stage.

Based on the information provided by NFP, WHO has not identified evidence of ongoing transmission associated with this event.

However, confidence in the assessment remains limited by the absence of a confirmed etiological diagnosis, and the remaining uncertainty regarding the source and mode of exposure. Additional clinical, epidemiological and laboratory information, including confirmation of the diagnosis in the deceased laboratory worker, is required to improve confidence in the assessment. WHO will continue monitoring the situation and assess any potential public health implications as further information becomes available. 

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