New Jersey's Wild Bird Die-Off

 

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The Northern Hemisphere is at - or near - peak avian flu for this winter season, with literally scores of outbreaks being reported on a daily basis.  So much so, that reporting on individual outbreaks has become nearly futile. 

While we get reasonably accurate numbers of poultry lost to HPAI H5, its impact on wild birds and mammals can only be guesstimated. 

A year ago, in Nature Reviews: The Threat of Avian Influenza H5N1 Looms Over Global Biodiversity, we looked at some of those estimates:

An estimated half a billion domestic fowl have died of H5N1 (ref. 4), and this number is rising; mortality in wildlife is more difficult to quantify than in poultry, but the effects are substantial. By mid-2024, H5N1 infections were documented in at least 406 bird and 51 mammal wild species (according to reports on the World Animal Health Information System (WAHIS)), and available reports suggest that multiple millions of wild animal individuals may have died (Fig. 1a).

The most noteworthy mass-mortality events include more than 200,000 wild birds in coastal areas of Peru6; 24,000 sea lions in South America7; 20,500 wild birds in Scotland8; 6,500 Cape cormorants in Namibia9; and 17,400 elephant seals, including >95% of the pups in Argentina10. These figures, however, largely underestimate actual mortalities, owing to a pervasive lack of monitoring, testing and reporting — particularly in inaccessible areas and in disadvantaged countries4,7.

These numbers are now 18 months old, and H5's carnage has only increased since then (see ISIRV: Update on H5N1 Panzootic: Infected Mammal Species Increase by Almost 50% in Just Over a Year). While H5N1 has yet to crack the human code, it is already a devastating pandemic (panzootic) in animals. 

The long-term impact of this loss of biodiversity remains uncertain. By the time we know, however, it will be a fait accompli. 

Last week, in Several States Warn On Contact With Wild Birds/Mammals, we looked at a sampling of recent non-poultry outbreaks across the country. This week, the hot-spot (at least based on media reporting) for avian flu appears to be New Jersey. 

As the following FluTracker's Thread illustrates, over the past few days the NJ Department of Environment has been flooded with reports of hundreds of dead birds (mostly in Snow geese and Canadian geese) littered across the state. 

Credit NJ Fish & Wildlife

What Agencies are Responding to the Outbreak?

The U.S. Centers for Disease Control and Prevention  states that the ongoing nationwide H5N1 outbreak is primarily an animal health issue that poses low risk to the health of the public. The three principal state agencies involved in monitoring and responding to avian influenza are NJDEP Fish & Wildlife, the New Jersey Department of Health, and the New Jersey Department of Agriculture, which provide the following updates:

• Between August 2025 and February 17th,2026, we have confirmed detections in 8 counties (Bergen, Burlington, Middlesex, Monmouth, Salem, Somerset, Sussex and Warren) and a preliminary detection in 5 counties (Atlantic, Cape May, Cumberland, Essex, and Hunterdon).
• The New Jersey Department of Health  continues to closely monitor H5N1 and collaborate with state and federal partners on preparedness and response to H5N1. There are no reports of H5N1 in humans in NJ, but the virus has been detected in multiple domestic cats: H5 Highly Pathogenic Avian Influenza Confirmed in New Jersey Cat 
• The New Jersey Department of Agriculture  reports that there have been confirmed detections in domestic poultry in Hudson, Mercer, Union and Essex Counties.

While tests on these most recent bird deaths are pending, yesterday the Burlington County Department of Health Posted:

The Burlington County Health Department is reminding residents to be aware of the potential spread of Highly Pathogenic Avian Influenza, also known as bird flu, following the discovery of large numbers of dead geese in Hainesport and other South Jersey locations this week.

The Health Department has not been notified of any positive tests confirming the birds died from bird flu, however, officials are treating it as a likely bird flu case.

Residents are encouraged to review avian flu information and guidance on the County Health Department website and follow all recommended precautions. The webpage is at https://www.co.burlington.nj.us/2115/H5N1-Bird-Flu . Information is also posted in County parks.

Among the recommended precautions:

• Avoid contact with wild birds;

• Avoid unprotected contact with wild or domestic birds;

• Report cases of dead or sick wild birds to the NJ Dept. of Environmental Protection at 877-927-6337;

• Report cases of dead or sick domestic birds or livestock to the NJ Dept. of Agriculture at 609-671-6400 or state.veterinarian@ag.nj.gov .

• Pet owners should keep dogs and cats away from areas of high concentrations of geese or geese waste;

• Pet owners who notice signs of illness in their pet bird, cat, dog or any other domesticated animal should immediately contact their family veterinarian to safely examine your pet and test for bird flu if needed.

Additional guidance is available on the New Jersey H5N1 page at https://www.nj.gov/.../divi.../ah/livestockhealth/h5n1.shtml .

On Tuesday, the Borough of Pitman announced the closure of two parks on their Facebook page due to excessive bird deaths.

 This was followed up by a more detailed announcement:

It was just about a year ago, we were following the outbreak of H5N1 among colony of domestic cats on a property in western New Jersey (see Hunterdon County DOH Reports 4 More Cats Test Positive for HPAI H5N1 (Ttl=6)).

While we await test results, for now the NJ Fish and Wildlife Department is offering the following :

What Do You Do if You See a Group of Sick or Dead Wild Birds?

Please fill out the Wild Bird Disease Reporting Form .

How Do I Report Sick or Dead Domestic Birds?

If you are reporting sick or dead domestic poultry, please call the New Jersey Department of Agriculture Division of Animal Health at (609) 671-6400.

What if I Have Questions About Human or Domestic Pet Health Due to H5N1?

If you have questions about human or domestic pet health due to H5N1, please direct your questions to your local health department .

What are Disposal Options for Property Owners?

While NJ DEP Fish & Wildlife does not advise that the public handle sick or dead wildlife, if you have a dead bird on your property and are electing to dispose of the carcass, precautions should be taken:

• PPE should be worn, including gloves, a mask, and eye protection.
• Avoid direct contact between you and the animal by using a shovel to move the carcass.
• Double-bag each bird, close the bag using a zip-tie, and place in an outdoor trash bin inaccessible to pets and other wildlife.
• Following disposal, immediately wash your hands with soap and water and disinfect any non-disposable items using a diluted household bleach solution. Allow the disinfectant to sit on the item for 10 minutes before rinsing with warm water.

Residents can also contact their local municipality or county to inquire about animal control services or private wildlife control services able to dispose of dead wildlife.

Sage advice, assuming anyone is listening.   

When You're in the Market For Bird Flu

 
Based on USDA Data - Graph created with Gemini

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Since the arrival of H5N1 in late 2021, the USDA has reported 64 outbreaks in live bird markets (LBMs) across 6 states (NY, NJ, PA, FL, VA, CA), with 10 outbreaks reported over the past 60 days.

While outbreaks in live bird markets continue to be reported to the USDA, they appear to be getting far less press coverage than they were a year ago. 

The link between live bird markets and the spread (and potential reassortment of) avian flu strains has been long established. LBMs typically bring together birds of varying species (chickens, ducks, geese, quail, and others) - often imported from different farms - which are housed in cramped quarters. 

A dozen years ago, in CDC: Risk Factors Involved With H7N9 Infection we looked at a case-control study conducted by an international group of scientists, including researchers from both the Chinese and the US CDC that concluded.

Exposures to poultry in markets were associated with A(H7N9) virus infection, even without poultry contact. China should consider permanently closing live poultry markets or aggressively pursuing control measures to prevent spread of this emerging pathogen. 

In 2016's Interventions in live poultry markets for the control of avian influenza: A systematic review Vittoria Offeddu , Benjamin J. Cowling, and J.S. Malik Peiris laid out the risks of avian influenza from live bird markets, reviewed some of the possible interventions, and concluded: 

Highlights

• Avian influenza viruses (AIVs) can infect humans. Bird-to-human transmission is particularly intense in live poultry markets.
• Periodic rest days, overnight depopulation or sale bans of certain species significantly reduce AIV-circulation in the markets.
• Market closure would lastingly reduce the risk of animal and human infection.

Admittedly, practices and hygienic standards vary greatly between countries, but last summer in J. Virology: Zoonotic Disease Risk at Traditional Food Markets (Minireview), we looked a review that cautioned that `. . . their sustainability and safety depend on integrating evidence-based strategies to mitigate zoonotic disease risks.'

While less common here than in Asia and the Middle East, the United States has hundreds of live bird markets, clustered primarily in the mid-Atlantic region (see Live Bird Markets of the Northeastern United States by Jarra F Jagne, DVM et al.)

Live bird markets serve mainly ethnic immigrant populations in large urban centers of Northeastern states. The markets are important in the epidemiology of avian influenza viruses (AIV) especially H5 and H7 strains that have zoonotic potential and an effect on trade with United States trading partners.

Until four years ago, HPAI H5 was not endemic in North America, which greatly reduced (but didn't completely eliminate) the risks of avian flu transmission in U.S.  live bird markets (see 2016's H5 Avian Flu Reported In NE U.S. LBMs (Live Bird Markets) - UPDATED).

Over the past few years the threat from H5N1 has grown markedly in the Western Hemisphere. So far, the strains of HPAI H5 in the United States have been generally milder in humans than those seen in Asia and the Middle East, but serious illnesses and deaths have occurred, and further increases in virulence are possible. 

 

Practices (like fur farming, drinking raw milk, letting your cat run free outdoors, or working at or visiting an LBM) - that were once presumably less dangerous  - are arguably more dangerous now. 

But we resist adapting to - or preparing for - new threats like avian flu because of the `Normalcy bias', the belief that tomorrow will be more-or-less like yesterday. We cling to the notion that all future changes will be small, incremental, and manageable. 

While that may bring comfort, and a sense of stability, it also brings risk. 

Whether HPAI H5 has the `right stuff' to spark a pandemic is unknown. But somewhere out there, the next pandemic virus is honing its skills.  And our laissez faire attitude towards pandemic prevention and preparedness will eventually prove costly. 

EID Journal: Vaccine-Like African Swine Fever Virus Strain in Domestic Pigs, Thailand, 2024

 

How ASF Spreads

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We've a bit of a medical mystery today courtesy of an early release research article published this week in the EID Journal; one that touches on several topics we've discussed previously. 

In a nutshell, researchers in Thailand recently tested two unvaccinated swine herds - hundreds of miles apart - which were showing signs of chronic infection. 

The pigs tested positive for ASF, and sequencing of field samples from each herd revealed a unique genomic signature; one that indicates they originated from a live attenuated vaccine-derived virus.

The problem being, there are no globally approved and licensed ASF vaccines on the market (and these pigs were never vaccinated). 

Vietnam is the only country permitting commercial use of an ASF vaccine (NAVETCO), and while based on a similar backbone ASF virus, it uses a different technique to attenuate the virus and contains an easily recognizable DIVA (Differentiating Infected from Vaccinated Animals) marker.

In 2024, however,  we learned that a genetically modified live-attenuated African swine fever virus (ASFV-GUS-Vietnam) had been found circulating in Vietnamese swine. 

While the Vietnam strain's origin remains unknown, it was thought likely the result of unauthorized experimental use, a black-market vaccine, or a lab accident. And it is a much closer match to the strains recently detected in Thailand. 

How it - or a close relative to it - ended up in Thailand is unknown, although possibilities include the use of illicit or illegal vaccines, cross border trade of pigs or pork products, and/or the horizontal transmission of the virus. 

First some excerpts from the EID letter, after which I'll have a postscript.

Volume 32, Number 2—February 2026
Research Letter
Vaccine-Like African Swine Fever Virus Strain in Domestic Pigs, Thailand, 2024

Trong Tung Nguyen, Dhithya Venkateswaran, Anwesha Prakash, Quynh Anh Nguyen, Roypim Suntisukwattana, Anan Jongkaewwattana, Theeradej Thaweerattanasinp, Janya Saenboonrueng, Van Phan Le, and Dachrit Nilubol

Abstract

African swine fever virus genotype II is endemic in Thailand, typically causing acute disease. We investigated a vaccine-like strain, characterized by 6 multigene family gene deletions, from nonvaccinated herds. We found this strain was associated with chronic disease in pigs.


African swine fever (ASF) is a fatal hemorrhagic disease of pigs, caused by African swine fever virus (ASFV), a complex DNA virus in the Asfarviridae family (1). Researchers first identified ASF in Kenya in 1921, and subsequent reports identified 24 genotypes in Africa on the basis of nucleotide variations within the partial B646L gen (2,3). Reports in the medical literature confirm incidence of only ASFV genotype I and genotype II outside Africa.

In 2018, researchers identified ASFV genotype II in China (4), and it rapidly spread across Asia within a few months. Since then, the situation in Asia has shifted from an epidemic to an endemic stage, with the highly virulent genotype II strain causing peracute, acute, and subacute disease. Recent research suggests the emergence of more genetically diverse ASFV variants, including chronic disease–associated genotype I, highly virulent recombinants of genotypes I and II, and naturally and artificially attenuated strains in domestic pigs in China and Vietnam (5–7).

Thailand health authorities officially reported ASFV in Thailand in 2022 (8), and the strain was genetically identical to the strain first reported in China and Vietnam. Currently, ASF cases in Thailand involve patients with chronic symptoms and low mortality rates, suggesting the emergence of low-virulent strains. We conducted a survey of ASFV from recent outbreaks in Thailand, employing whole-genome sequencing to investigate the underlying causes.

Veterinary clinicians reported suspected disease in pigs from 2 herds located in the western region of Thailand, ≈500 miles apart, all displaying clinical signs related to chronic forms of ASF: chronic respiratory disease, joint swelling, slow weight gain, and sporadic deaths. Both herds housed only finishing pigs, operating on an all-in/all-out basis, and pigs were not vaccinated with any types of ASF vaccines.

(SNIP)

We detected ASFV in 18 of 25 samples; cycle threshold (Ct) values ranged from 19.82 to 33.83. We performed whole-genome sequencing on samples with the lowest Ct from each herd,(Ct 19.82 for sample TH1_24/RB and Ct 21.25 for sample TH2_24/RB).

        (SNIP)

Both genomes revealed the deletion of 6 genes in the multigene family (MGF) region (MGF 505-1R, MGF 360-12L, MGF 360-13L, MGF 360-14L, MGF 505-2R, and MGF 505-3R) and 2,348 bp of an Escherichia coli GusA gene (GUS) inserted at the deletion site (Figure 1).

This deletion pattern was like a live-attenuated vaccine strain (ASFV-G-ΔMGF) and a field-attenuated isolate (ASFV-GUS-Vietnam) described in previous studies (6,10). Phylogenetic analysis based on full-length genome indicated that the 2 isolates belonged to genotype II; however, the isolates were genetically distinct from the genotype II variant responsible for the first outbreak in Thailand (Figure 2). The 2 variants contained a total of 15 mutations throughout the genome, mostly silent and in noncoding regions, when compared with the Georgia 2007/1 strain. In addition, a 3-nucleotide insertion resulted in 1 additional amino acid in the MGF 110-10-L-MGF110-14L fusion protein.

In conclusion, we characterized a vaccine-like genotype II strain, similar to ASFV-G-ΔMGF, detected in finishing pigs unvaccinated against ASFV in Thailand. The spread of such vaccine-like strains with MGF deletions in this region is of concern, and the origin of the strains remains unknown. Further genomic surveillance and epidemiologic tracing would assist in clarifying the route of introduction. Possible explanations include the unauthorized use of live attenuated vaccines or cross-border movement of pigs and pork products.

Mr. Nguyen is a veterinarian and a graduate student at the Department of Veterinary Microbiology, Chulalongkorn University, Thailand. His research interests focus on molecular characterization and virology.

It was just two weeks ago, in Taiwan: Another Avian Flu `Incident', that we looked at Taiwan's latest seizure of shipments of illegal `bird flu' vaccines being smuggled in from China.  

In the past, we've seen reports of vaccines being manufactured in squalid and primitive conditions (see YouTube video) with absolutely no testing for purity, contents, or strength.

The trade in illegal and often counterfeit vaccines, drugs, and medical devices fuel a global multi-billion-dollar industry, and we've seen repeated warnings (see The Lancet: WHO Estimates That 50% Of Drugs For Sale Online Are Fake) of the harm they can cause.

While exact numbers are impossible to come by, there are estimates that hundreds of thousands of people are killed each year from fake or adulterated drugs, and they can also help generate antibiotic and antiviral resistance. 

While ASF doesn't pose a direct human health threat, we've seen the enormous economic and societal damage that it can spark (see Report: China To Release 40,000 Tons Of Frozen Pork Reserves Due To ASF Shortage), and the introduction of new variants is only likely to exacerbate the problem.  

While pandemics may be inevitable, self-inflicted wounds are often the hardest to deal with.   

Pathogens: Clinical and Laboratory Findings in Cats with Confirmed Avian Influenza A/H5N1 Virus Infection During the 2023 Outbreak in Poland

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Three summers ago, when domestic feline infection with HPAI H5N1 was still considered a fairly rare event, we followed an unusually widespread outbreak in both indoor and outdoor Polish cats (see Media Reports Of Unusual Cat Deaths In Poland).

Two weeks later a government announcement (see Poland's National Veterinary Institute Genome Sequence Analysis Of H5N1 Viruses Detected In Cats), stated early testing suggested that the feline H5N1 avian influenza viruses analyzed all originated from a single, unidentified source.

While it was quickly and vehemently denied by both the government and the nation's poultry industry, the media and some local experts raised Concerns Over The Possibility Of H5N1 In The Food Chain (i.e. poultry).

Poultry production in Poland is a multi-billion dollar industry, with 20% of their earnings coming from exports (mainly to EU nations).

While Polish authorities pushed back hard against any suggestion that the virus might be in locally produced (and sold) poultry, on July 13th, 2023 the ECDC reported:

Among the affected cats, 13 were kept indoors with only occasional access to outdoor areas (i.e. balconies or terraces), whereas four were free-ranging and reportedly had contact with wildfowl. Raw poultry meat and offal were fed to 13 of the affected cats, but the exact time of feeding is unknown and no causal relationship has been established

The following advice was offered:

It is recommended to avoid exposure of domestic cats and dogs, and in general carnivore pets, to dead or diseased animals (mammals and birds), and to avoid feeding domestic cats and dogs offal and raw meat from wild or kept birds in areas where mortality in gulls or other potentially HPAI virus-infected animals are reported. Possible measures are keeping dogs on a leash, and confining cats indoors in areas where extensive circulation of HPAI viruses in wild birds has been confirmed. 

In August of 2023, Eurosurveillance published Two Papers On HPAI H5N1 clade 2.3.4.4b virus in cats, Poland, June to July 2023, which described several mutations (PB2-E627K and PB2-K526R) considered to be mammalian adaptation markers, and warned `Although the most likely source appears to be poultry meat, no such meat has been identified to date.'

Officially, commercial poultry was never linked to this outbreak. 

Last summer  we looked at a study (see Viruses: The Seroprevalence of Influenza A Virus Infections in Polish Cats During a Feline H5N1 Influenza Outbreak in 2023) that reviewed 835 cat serum samples submitted for routine bloodwork during June of 2023 from cats not exhibiting influenza symptoms.

Out of those 835 cat serum samples - 68 cats (8.1%) tested positive for influenza A virus antibodies in the primary screening (with 3 more suspected). Of those 68 IAV positive samples, 23 were positive for H5-specific antibodies.

This suggests that some cats can be infected with H5 and survive, and that cats are also susceptible to a much wider range of influenza A viruses. 

Since then we've seen pet-food related outbreaks in South Korea and in the United States, and today domestic cats are the most commonly reported (non-livestock) American mammal with H5N1. 

 Today we've got a highly technical report (of greatest interest to veterinarians) on the laboratory and clinical findings on 22 cats from the Polish outbreak of 2023.  Some of the highlight, however, include:

• These 22 cats came from different regions of Poland, and included both males and females, across a wide range of ages. 

• Many had outdoor access, but six were strictly indoor cats.​

• At least 13 of the 22 cats were known to eat raw meat, usually raw chicken or other poultry 

• The outbreak in cats happened currently with H5N1 reports in both poultry and wild birds in Poland, suggesting a link between infections in birds and spillover to cats.

The authors describe the infection as a `rapidly fatal respiratory and neurological disease', as most cats died or were euthanized within 2–3 days of the first signs, making the fatality rate 100%.

I've posted the abstract and a brief excerpt below. Those wanting a deeper dive can follow the link to read it in its entirety.  I'll have a brief postscript after the break.

Clinical and Laboratory Findings in Cats with Confirmed Avian Influenza A/H5N1 Virus Infection During the 2023 Outbreak in Poland: A Retrospective Case Series of 22 Cats
Dawid Jańczak1,*, Anna Golke2, Karol Szymański3, Ewelina Hallmann3, Katarzyna Pancer3, Aleksander Masny3, Tomasz Dzieciątkowski4 and Olga Szaluś-Jordanow5,*

Pathogens 2026, 15(2), 200; https://doi.org/10.3390/pathogens15020200 This article belongs to the Section Viral Pathogens
Published:10 February 2026

Abstract

Highly pathogenic avian influenza (HPAI) A/H5N1 has emerged as a cause of severe disease in domestic cats, but clinical data from field outbreaks remain limited. We retrospectively reviewed medical records, laboratory results, and ancillary examinations from 22 domestic cats with RT-qPCR-confirmed A/H5N1 infection diagnosed in Poland in June 2023.

To the best of our knowledge, we report the first comprehensive retrospective case series from the 2023 Polish outbreak, combining 22 laboratory-confirmed cats with detailed clinical timelines and laboratory findings. For each cat, the temporal progression of clinical signs, hematology, serum biochemistry, and, when available, imaging findings were evaluated. Post-mortem examination data were not systematically available in this retrospective cohort.

Notably, six of these cats were strictly indoor cats that received raw poultry meat as part of their diet. Disease onset was acute, with fever, lethargy, and anorexia rapidly progressing to severe dyspnea and neurological signs, including ataxia, seizures, and paraplegia; case fatality was 100%, with a typical interval of ≤3 days from first signs to death or euthanasia. Hematologic changes were dominated by thrombocytopenia, lymphopenia, and marked eosinopenia, consistent with a systemic inflammatory/stress leukogram. Biochemistry indicated marked tissue injury, with increased AST, LDH, and CK activities, whereas creatinine and urea remained largely within reference intervals, arguing against primary renal failure. Imaging supported the presence of interstitial to diffuse pneumonia. These data characterize the clinical and laboratory phenotypes of feline A/H5N1 infection and underscore its importance as a rapidly fatal respiratory and neurological disease with One Health implications.

(SNIP)

5. Conclusions

Our findings confirm that A/H5N1 infection in domestic cats is associated with highly fatal, rapidly progressive respiratory and neurological disease, in which pneumonia and acute respiratory failure are central features. The clinical pattern, observed acute onset, fever, and depression, followed within 1–3 days by severe dyspnea, radiographic or sonographic evidence of lung involvement, and frequent neurological signs, should alert veterinarians to the possibility of HPAI infection, especially in cats with outdoor access, exposure to raw poultry meat, or contact with wild birds or their feces. Early recognition, targeted diagnostics, and the implementation of appropriate biosafety measures are essential for potential zoonotic and epidemiological risks.

        (Continue . . . )

As we discussed last week in Several States Warn On Contact With Wild Birds/Mammals, there is a high level of H5N1 in the environment right now, which raises the risks to both humans and their pets.  

Outdoor cats, or those fed a died of raw meat, are obviously at highest risk.

But when H5N1 is circulating at high levels, any pet that suddenly falls ill with fever, rapidly develops breathing problems or shows neurological signs, should be regarded as a possible H5N1 case until proven otherwise. 

For more on pets and H5N1, you may wish to revisit:

A Brief History of Influenza A in Canines & Canadian Report On A Recent Fatal H5N1 Dog Infection

JAVMA: Companion Animals and H5N1 Highly Pathogenic Avian Influenza: Cause for Concern? 

CDC Guidance on Bird Flu in Pets and Other Animals

WHO: Mpox: Recombinant Virus With Genomic Elements of Clades Ib and IIb - Global

 
Mpox Multi-country external situation report no. 62 

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Although details were scant, on December 8th, 2025 the UKHSA Identified a New Recombinant Strain of Mpox Virus in a traveler recently returning from an (undisclosed) country in South-East Asia.

For the very first time, genomic sequencing showed this mpox genome contained elements of clade Ib and IIb mpox.  

While a new development, we've seen warnings for more than a decade on the potential for Mpox to mutate (see 2014's Genomic Variability of Monkeypox Virus among Humans, Democratic Republic of the Congo).

Two days later we looked at academic reactions to this announcement (see  The UK Recombinant Mpox Case: Reactions from the UK Science Media Centre), which included the following:

Dr Boghuma Titanji, Assistant Professor of Medicine, Emory University, said:

“The identification of a recombinant mpox strain containing elements of both Clade I and Clade II is precisely what experts in the field feared would happen if the virus continued to spread globally without a decisive response to stop it.

Orthopoxviruses are well known for their ability to exchange portions of their genome and recombine to generate new variants, this is a core mechanism of their evolution. The key concern now is whether events like this will alter the virus’s transmissibility or virulence. There are also implications for how well existing testing platforms can identify these emerging recombinant strains. 

The more mpox circulation we permit, the more opportunities the virus has to recombine and adapt, further entrenching mpox virus as a human pathogen that is not going away.”

Since then, a second (albeit, earlier) case has been identified, which was reported by India in a resident with recent travel to another (undisclosed) country on the Arabian Peninsula.  

Despite originating from two different regions of the world, Whole‑genome sequencing (WGS) showed >99.9% similarity between the two viruses.

While routine PCR tests can identify these cases as Mpox, it requires full WSG to identify correctly flag them as being a `mixed-strain' virus; tests that are generally only run in a minority of cases, and mostly by high-income nations.  

 Leaving us with an uncomfortably large knowledge gap at this point. 

I've reproduced several excerpts from the WHO DON report below. Follow the link to read it in its entirety.  I'll have a bit more after the break.

Mpox: recombinant virus with genomic elements of clades Ib and IIb - Global
14 February 2026

Situation at a glance

Recombination of monkeypox virus (MPXV) strains has been documented in recent months, with two cases of a recombinant strain comprising clade Ib and IIb MPXV reported. Recombination is a known natural process that can occur when two related viruses infecting the same individual exchange genetic material, producing a new virus.

The first case was detected in the United Kingdom of Great Britain and Northern Ireland (hereafter “United Kingdom”), with travel history to a country in South-East Asia, and the second in India, with travel history to a country in the Arabian Peninsula. 

Detailed analysis of the virus genomes shows that the two individuals fell ill several weeks apart with the same recombinant strain, suggesting that there may be further cases than are currently reported. Both cases had similar clinical presentation to that observed for other clades. Neither patient experienced severe outcomes. Contact tracing for both cases in the reporting countries has been completed; no secondary cases were detected. 

Based on available information, the overall WHO public health risk assessment for mpox remains unchanged: the risk is assessed as moderate for men who have sex with men with new and/or multiple partners and for sex workers or others with multiple casual sexual partners, and low for the general population without specific risk factors.

Description of the situation

In December 2025, the United Kingdom detected the first reported case of a clade Ib/IIb MPXV recombinant strain.​5​ After classification of this case and posting in a public database as a novel MPXV recombinant strain, a case of mpox detected in India in September 2025 was retrospectively reclassified as a closely-related recombinant strain based on sequencing data. To date, these are the only known cases of this recombinant virus.

Case detected in the United Kingdom of Great Britain and Northern Ireland

The case was identified following testing of a vesicular swab from a traveler who had returned from a country in the Asia Pacific region in October 2025. During laboratory confirmation, the virus was initially typed as clade Ib MPXV by qPCR. Subsequent whole genome sequencing revealed that the MPXV strain identified was distinct from other known clade Ib MPXV strains with phylogenetic analysis indicating that the genome had regions similar to both clade Ib and clade IIb MPXV reference sequences, suggesting that it is an inter-clade recombinant. 

To confirm this unusual finding, sequencing was repeated on the original extract from the primary sample, a fresh extract from the same primary sample, a second swab collected from the patient at the same time, and a cultured isolate derived from the initial swab. This repeat sequencing yielded identical viral genome sequences from the two clinical swabs and the cultured isolate, supporting the initial findings of a new recombinant strain, and showing that it can replicate and presents potential for onward transmission. 

This strain is a recombinant MPXV, containing genetic elements from both clade Ib and clade IIb MPXV. A small number of contacts were identified and followed up in the United Kingdom; none developed any clinical features of mpox. Health worker contacts had worn full personal protective equipment (PPE) during provision of medical care to the patient. The authorities of the United Kingdom continue to investigate the significance of this recombinant MPXV strain through phenotypic characterization studies.

Case detected in India

On 13 January 2026, the National IHR Focal Point (NFP) of India notified WHO of a mpox case with an inter‑clade recombinant MPXV which was, upon whole-genome sequencing, found to have genomic elements of clades Ib and IIb MPXV.

The recombinant virus was found in samples from a man with mpox who had presented for care in September 2025. The patient had reported recent travel from a country in the Arabian Peninsula, where he resides as an overseas worker.

He developed symptoms on 1 September 2025, while still abroad. After his return to India, real‑time PCR confirmed MPXV infection on 11 September 2025. Clade differentiation PCR performed on 15 September 2025 initially identified this virus as clade II MPXV. Initial genomic sequencing analysis suggested features consistent with clade IIb MPXV. However, following the update of the global Nextclade database on 16 December 2025, which included the recombinant clade Ib/IIb MPXV strain reported by the United Kingdom, the virus from the patient in India was reclassified as belonging to the recombinant strain. Recombination analysis demonstrated mosaic patterns containing genomic regions derived from both parent clades.

Following the initial diagnosis, the patient was hospitalized, did not experience any medical complications, and fully recovered, testing negative for MPXV on 29 September 2025. The case reported no close contacts in India, and no known secondary cases were identified following this introduction of the recombinant clade Ib/IIb MPXV in India.

Full or near‑full genome retrieval (>99%) from both the sample and a sample-derived virus isolate enabled phylogenetic analysis showing >99.9% similarity to the recombinant strain detected in the United Kingdom. A total of 34 recombinant tracts were observed in the sequence reported by India, while 28 recombinant tracts were observed in the sequence reported by the United Kingdom; 16 recombinant tracts were common to both strains. This case in India therefore represents the earliest known detection of this recombinant strain globally, having preceded the event reported in the United Kingdom.

Consistent with the case reported in the United Kingdom, clinical presentation was consistent with cases due to clade I or clade II MPXV (non-recombinant MPXV) infection.

(SNIP)

WHO risk assessment

Mpox outbreaks must be considered in their local context, with meaningful involvement of affected communities, to ensure an in-depth understanding of the epidemiology, modes of transmission, risk factors for severe disease, viral reservoir and evolution, and relevance of strategic approaches and countermeasures for prevention and control.

Multiple strains of MPXV are circulating through interconnected sexual networks across many countries and settings. Co-infection with different strains, that could lead to emergence of recombinant virus strains, while rare, can be expected. The case in India was infected with the same recombinant Ib/IIb MPXV strain detected in the United Kingdom. Symptom onset in the case reported in India occurred more than two months earlier than the case in the United Kingdom, and the great degree of similarity between their sequences suggests a common evolutionary history. This information has two important implications: i) the origin of the recombinant strain remains unknown; and ii) transmission of this recombinant virus already involves at least four countries in three WHO regions, and is therefore likely to be more widespread than currently documented.

For the cases in the United Kingdom and India, the initial clade differentiation PCR results indicated clade Ib and IIb MPXV, respectively. Thus, clade differentiation PCR assays alone may not reliably identify recombinant MPXV strains, and genomic sequencing is likely to be required for their detection.

Due to the small number of cases found to date, conclusions about transmissibility or clinical characterization of mpox due to recombinant strains would be premature, and it remains essential to maintain vigilance regarding this development.

In light of the limited information available on this recombinant MPXV strain, the overall WHO public health risk assessment for mpox remains unchanged: the risk is assessed as moderate for men who have sex with men with new and/or multiple partners and for sex workers or others with multiple casual sexual partners, and low for the general population without specific risk factors.

All countries should remain alert to the possibility of MPXV genetic recombination. The public health risk posed by any newly detected recombinant strain should be assessed on a case-by-case basis, considering available epidemiological, clinical and genomic information.

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Increasingly over the past few years we've entered the age of the `redacted' epidemiological report (see last December's ECDC Epidemiological Update: 2 Imported MERS-CoV Cases In France), where key details are sometimes omitted in order to encourage countries to report without fear of stigma or economic/political fallout.

While disappointing, it is probably safe to assume this recombinant has already spread beyond the borders of the two undisclosed countries. 

With only limited data, the WHO appears to be taking a conservative, but cautious, approach. For now, their risk assessment remains unchanged, but they urge member nations to expand WGS in order to detect hidden spread of this emerging strain. 

Sound advice, since this is unlikely to be the last evolutionary leap that Mpox makes. 

Cambodia Reports 1st H5N1 Case of 2026

 

#19,054

Just three days before the Lunar New Year, Cambodia's MOH has announced the first HPAI H5 human infection since last November. This is the 36th case reported since February of 2023, and unlike the milder H5N1 cases reported in the United States, > 40% of those have died. 

Cambodia's recent cases are due to a new reassortment of an older clade of the H5N1 virus (recently renamed 2.3.2.1e) - which appears to be spreading rapidly through both wild birds and local poultry.

While we are usually informed by Cambodian officials  as soon as a diagnosis is made, this afternoon the Cambodian MOH Facebook page  announced their latest (now fully recovered) case, that of a 30-year-old man from Kampot Province.

It isn't clear exactly when this person was infected, or how long he was hospitalized.  

I've provide a translation of the announcement below.  

(Translation)

Kingdom of Cambodia

Ministry of Health

Press Release

A case of bird flu in a 30-year-old man

The Ministry of Health of the Kingdom of Cambodia would like to inform the public: There is 1 case of bird flu in a 30-year-old man who was confirmed positive for the H5N1 avian influenza virus by the National Institute of Public Health. The patient resides in Meanrith village, Kandol commune, Teuk Chhou district, Kampot province and has symptoms of fever, cough and abdominal pain.

After receiving careful care from the medical team, the patient recovered and returned home on February 14, 2026. Investigations revealed that there was a dead chicken in the patient's house and it was cooked 3 days before the patient started feeling sick.

The emergency response team of the national and sub-national ministries of health has been collaborating with the teams of the provincial agriculture departments and local authorities at all levels to actively investigate the outbreak of bird flu and respond according to technical methods and protocols, find the source of transmission in both animals and humans, and search for suspected cases and contacts to prevent further transmission in the community, as well as distribute Tamiflu to close contacts and conduct health education campaigns among residents in the affected villages.

The Ministry of Health would like to remind all citizens to always pay attention to and be vigilant about bird flu because H5N1 bird flu continues to threaten the health of our citizens. We would also like to inform you that if you have a fever, cough, runny nose, or difficulty breathing and have a history of contact with sick or dead chickens or ducks within 14 days before the onset of symptoms, do not go to gatherings or crowded places and seek consultation and examination and treatment at the nearest health center or hospital immediately. Avoid delaying this, which puts you at high risk of eventual death.

How it is transmitted: H5N1 bird flu is a type of flu that is usually spread from sick birds to other birds, but it can sometimes be spread from birds to humans through close contact with sick or dead birds. Bird flu in humans is a serious illness that requires prompt hospital treatment. Although it is not easily transmitted from person to person, if it mutates, it can be contagious, just like seasonal flu.

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While we tend to focus on clade 2.3.4.4b H5N1 viruses, these case remind us that there are several other subclades of HPAI H5 circulating around the globe - with new ones emerging at an increasing rate - each on their own evolutionary trajectory.