A Summer Snapshot Of U.S. Wild & Captive Mammals With Confirmed HPAI H5

 

#19,286

The USDA maintains a public database of wild and captive mammals (excludes livestock) infected with HPAI H5 across the country since its arrival in 2022; one which is highly dependent upon investigations and submissions by individual states and/or veterinarians. 

Last December, in Declining Mammalian Spillover Submissions To USDA Over Past 8 Months, we looked at a 90% drop in reported infections of HPAI H5 to mammalian wildlife during the 2nd half of 2025, despite increased detections in wild birds.

What the above chart did not reflect was the existing backlog, and gaps (between collection and confirmation dates) and/or delays in reporting cases (see chart below). Delays of 2 to 3 months are common (see graph below), and delays of 6 to 8 months are not unheard of. 

Graph created by Gemini using USDA data

Since April of this year, only 3 cases (2 skunks and 1 domestic cat from Utah) have been confirmed by the USDA.  While there may be as-yet unpublished data in the pipeline, the decline in case reports appears to be ongoing. 

Graph created by Gemini using USDA data

Reporting varies considerably by state (see chart below), with New Mexico reporting the highest total.

Graph created by Gemini using USDA data

But after 4 years, there are still 8 states which have yet to report a single detection.

• Alabama
• Arkansas
• Hawaii
• Maryland
• Mississippi
• New Hampshire
• South Carolina
• West Virginia

These disparities may come down to differences in climate and terrain (swamps vs. forests vs. deserts), varying activity by migratory flyways, and the fact that infected wildlife quite often die in remote, difficult to access places where their carcasses are quickly scavenged by other animals, making them unlikely to be discovered or tested.

But it is also possible that some states are simply more proactive in investigating, and reporting suspected cases, than others.

As far as host range is concerned, there are 54 different species listed in the USDA database, with the top 3; Domestic cat (155), Red fox (126), and House mouse (111) make up nearly half (48.0%) of all reported mammal submissions.

• There are, altogether, 16 different feline species (wild/captive/domestic) - which combined account for 238 submissions or (29.2%) of confirmed cases.

• Marine mammals make up another large chunk of the data accounting for 13.7% of all submissions (n=112), led by Northern Elephant Seal (57), Harbor seal (27), and Bottlenose dolphins (11)

(Excludes 22 one-off single detections)

Graph created by Gemini using USDA data

All of these numbers are presumed to represent a small fraction of the actual number of infections, as limited seroprevalence studies have found antibodies in a large array of wildlife species (see Virology: Susceptibilities & Viral Shedding of Peridomestic Wildlife Infected with Clade 2.3.4.4b HPAI Virus (H5N1).

Meanwhile, the public remains largely oblivious to the threat of HPAI (see Two Surveys (UK & U.S.) Illustrating The Public's Lack of Concern Over Avian Flu), while some state and local governments appear not to have prioritized surveillance, testing, and reporting. 

Although the decline in reported wildlife infections to the USDA may turn out to be a good sign, a lack of evidence is not evidence of lack.

New Zealand: DOC to vaccinate ‘at risk’ birds against bird flu

 
Credit Wikipedia


#19,230

Although Australia's confirmed H5N1 count remains at 5 birds - with the furthest east very near Adelaide, in South Australia - New Zealand is watching these developments with understandable concern. 

While lying some 1,600 miles east of Australia, avian flu has been carried across much larger expanses of open water. Two years ago H5N1 arrived in Hawaii, one of the most isolated (by distance) population centers in the world. 

Today New Zealand's Department of Conservation announced an ambitious plan to begin vaccinating a limited number of rare, `at risk' bird populations against H5N1. This plan was telegraphed last summer by that agency in `DOC’s bird flu vaccine trial a success', which reported:

`An internationally significant research trial carried out by DOC shows vaccination can safely be used to protect some of our most threatened birds from virulent bird flu, should it arrive here.'

First the DOC statement, after which I'll have a bit more.

DOC to vaccinate ‘at risk’ birds against bird flu

DOC is set to begin vaccinating some of New Zealand’s most threatened bird species to protect them against the highly virulent strain of H5N1 bird flu, in case it arrives here.

Date: 02 July 2026

H5N1 has been spreading around the world and has caused large die-offs in wild birds, seals and sea lions, as well as farmed poultry.

This bird flu strain is not in New Zealand but has recently been detected in migratory seabirds in Australia, which is a trigger to start vaccinating some of our most critically endangered birds as a safeguard.

DOC is working with the Ministry for Primary Industries (MPI), the Ministry of Health and Health New Zealand | Te Whatu Ora as part of a One Health approach to prepare for the possible arrival of H5N1 in New Zealand.

Last year DOC completed a world-first research trial on five native bird species that showed vaccination is safe and effective in these birds and will help protect them from bird flu.

Vaccination will begin with these five birds – kākāpō, takahē, tchūriwat’/tūturuatu/shore plover, kakī/black stilt and kākāriki karaka/orange-fronted parakeet.

About 300 core breeding birds from the five species will be vaccinated. These birds are in captivity or, in the case of kākāpō and takahē, on offshore islands.

DOC Senior Science Advisor and wildlife vet, Dr Kate McInnes, says these species were chosen because they have small populations that could be at risk and are reliant on intensive conservation efforts for their ongoing survival.

“We’re in a unique position to be able to vaccinate some of our most vulnerable birds as a precaution before H5N1 bird flu potentially arrives here.

“We’ve seen the devastating impacts of this virus on wildlife in other parts of the world, and we want to reduce the risk to our precious native birds where we can.

“It won’t be possible to vaccinate all endangered birds if bird flu arrives, but we can focus on those species where the full two doses of the vaccine can be safely given to achieve protection.”

Kate McInnes says over the past four years DOC has been researching and drawing on overseas evidence and experience to develop a vaccination plan for the New Zealand situation.

A team of DOC vets and specially trained staff will administer the vaccine, supported by species rangers and facilities staff. The work will start this month to avoid the breeding season and give birds time to develop full immunity before spring.

MPI has approved the vaccination plan for the five species and the release of the avian influenza vaccine for the programme to begin. The vaccine contains dead virus and cannot cause bird flu infection.

The vaccination programme is part of DOC’s broader plans to mitigate risks to threatened wildlife and public conservation land should H5N1 bird flu arrive in New Zealand. DOC has worked closely with iwi, species recovery groups, wildlife facilities and conservation groups to get their input into its bird flu response plans.

Early detection of H5N1, if it arrives here, will be crucial. We are asking everyone to be alert when outdoors.

People who spend time outdoors – including tramping, duck hunting and bird watching – can form good habits now that will help protect wildlife if bird flu arrives here. Keep your distance from sick or dead wildlife, keep your gear clean, and know when to report.

Please report groups of three or more sick or dead birds, marine mammals or other wildlife to the MPI exotic pest and disease hotline: 0800 80 99 66.

Do not touch, handle or collect dead or dying birds to avoid spread of the virus and protect yourself.

 

Regular readers will recall that three years ago the U.S. Fish & Wildlife Service issued a statement announcing that HPAI Was Confirmed As Cause Of Death For 3 California Condors found in Northern Arizona.

Ten days later that number had risen to 20. 

With fewer than 500 birds in existence, the USFWS & USDA began studying the feasibility of vaccinating captive (and released) condors against H5N1. 

Details on this program can be found at EID Journal: Safety and Immunogenicity of Poultry Vaccine for Protecting Critically Endangered Avian Species against HPAI Virus, United States.

In recent years, we've also seen a number of zoos around the world use H5 vaccines to protect rare, captive birds (see Research project: vaccination of zoo birds against highly pathogenic avian influenza).

Eighteen months ago, in Nature Reviews: The Threat of Avian Influenza H5N1 Looms Over Global Biodiversity, we looked at the massive, and often underappreciated, impact of HPAI H5 on both avian and mammalian wildlife around the globe.

While numbers are impossible to quantify, hundreds of millions of wild and captive birds have died, and hundreds of thousands - perhaps millions - of wild mammals have succumbed to the virus.

Despite heavy losses, most of these species will survive their encounter with HPAI H5, but for some rare, endangered populations, H5N1 could be an extinction level event. 

Hopefully, programs like these will limit those risks.  

MMWR: Knowledge, Attitudes, and Practices Regarding Avian Influenza Among Owners of Backyard Flocks

 

#19,169

Although numbers vary between published sources, since 2020 there has been a significant increase in the number of people who have decided to raise backyard poultry - especially hens for eggs - across the United States (see Chicken Coops Market Outlook 2025 to 2035).

The APPA estimates `Eleven (11) million U.S. households own backyard chickens (a 28% increase from 2023)'

 

Since late 2021, HPAI H5 avian influenza has become endemic in wild North American birds, and has affected both commercial and backyard poultry flocks in all 50 states (see graphic below).

 While the CDC has released biosafety guidelines (see Backyard Flock Owners: Protect Yourself from Bird Flu) - it is unknown how many backyard poultry owners have actually read it, or would be willing to follow their recommendations. 

And while H5Nx is our biggest concern, there are other avian subtypes which have been reported in North America with zoonotic potential, including several subtypes of H7. 

Over the past 18 months we've seen at least 3 U.S. backyard flock owners infected with HPAI H5, resulting in 2 deaths. This is an all-too familiar pattern, which we've seen repeated dozens of times in many other countries. 

Last year, after Hawaii's first detection of H5N1, their DOH conducted a survey of local residents aged 18 years or older who either kept birds at home, performed animal rescue, or engaged in other bird-related activities.  The results indicated more education was needed:

All of which brings us to a new survey, published last week in the CDC's MMWR, which looks at similar knowledge and practices among backyard poultry owners in the United States.  It is subject to some significant limitations, including:

• This survey used an online convenience sample of highly educated (47% held held graduate or professional degrees) respondents, which is far higher than the general population (and likely target group of backyard poultry owners). 

• And people often over-state their intentions in these types of surveys, much as we saw a dozen years ago (see BMJ: The `Hawthorne Effect’ On Hospital Hand Hygiene Compliance); where HCWs who knew they are being observed washed their hands far more often than when believed unobserved.

But, it's a starting point.  And even with these advantages, the survey turned up some important gaps in knowledge about avian flu. I've posted the summary, abstract, and some excerpts from the MMWR report below. 

Follow the link to read it in its entirety. I'll have a bit more after the break.

Knowledge, Attitudes, and Practices Regarding Avian Influenza Among Owners of Backyard Flocks — United States, July–December 2025

Weekly / May 14, 2026 / 75(18);234–239
Print

Melissa A. Rolfes, PhD1; Leah Bauck, MPH2; Beth A. Lipton, DVM3; Sara F. Margrey, DVM4; Rebecca A. Campagna, DVM5; Elizabeth Harker, MPH1; Colin A. Basler, DVM6; Courtney M. Dewart, PhD4,7; Sascha R. Ellington, PhD1; Stacy M. Holzbauer, DVM2,7; Malia J. Ireland, DVM2; Jeremy W. Kuo, MPH8; Christine M. Szablewski, DVM1; Lizette O. Durand, PhD, VMD1; Carrie Reed, DSc1 (VIEW AUTHOR AFFILIATIONS)View suggested citation

Summary

What is already known about this topic?

Since 2024, three human influenza A(H5) cases have been reported among people in the U.S. who own backyard birds. Although previous surveys suggest that backyard flock owners are aware of avian influenza, information on knowledge, attitudes, and practices is needed to guide development of education and prevention materials.

What is added by this report?

A survey of 638 U.S. backyard flock owners revealed incomplete knowledge about signs and symptoms of avian influenza in humans and birds. Respondents who knew more about avian influenza were more likely to report an intention to use personal protective equipment if they were to interact with potentially infected birds.

What are the implications for public health practice?

Education of backyard flock owners by health partners regarding signs and symptoms of avian influenza can help flock owners keep their flocks, themselves, and their families healthy.

Article PDF

Full Issue PDF

Abstract

Many U.S. households keep backyard bird flocks for their personal food supply or as garden partners. Backyard flocks in the United States have occasionally been infected with avian influenza A viruses, putting flock owners at risk for exposure. During July–December 2025, CDC, in collaboration with state health and agricultural partners, conducted an online survey to learn more about backyard flock owners and their knowledge, attitudes, and practices related to avian influenza.

Among 638 respondents who completed the survey, 92% were White (and not Hispanic or Latino), and approximately one half had a graduate or professional degree; a majority kept small, predominantly chicken flocks; and many reported that wild birds could access their flock or the flock’s food or water, which increases the flock’s risk for avian influenza exposure.

Although a majority of respondents had heard of avian influenza, approximately one third were unaware of the signs and symptoms of infection in their birds or humans. If they needed to interact with ill or dead birds, a majority of owners knew the recommended precautions to take and indicated willingness to use most, though not all, recommended personal protective equipment. These findings highlight important topics for risk messaging and educational resources so that backyard flock owners are better informed and better able to protect their flocks, themselves, and their families from avian influenza.

Introduction

Avian influenza A(H5) viruses, commonly referred to as bird flu, circulate among wild waterfowl and seabirds and are causing outbreaks in domestic poultry, dairy cows, and other mammals in the United States; 71 human cases of influenza A(H5) have been reported in the United States since March 2024. Three of these cases, including two deaths (1–4), occurred among persons who were owners of backyard flocks.

Surveys of U.S. backyard flock owners conducted in 2013 (5) and 2018 (6), found that a majority of respondents kept small flocks (fewer than 10 birds, primarily chickens) for <5 years. Most respondents were aware of avian influenza, and few reported using personal protective equipment (PPE) during regular interactions with their birds (6). To update and build on previous surveys, CDC and state partners conducted a survey among backyard flock owners aimed to assess knowledge of specific signs and symptoms of avian influenza and planned practices if their flock were to become infected with avian influenza viruses. These data might help guide and refine public health messaging to U.S. backyard flock owners.

 (SNIP)

Discussion

A majority of surveyed U.S. backyard flock owners had heard about avian influenza, were aware that U.S. backyard flocks have been infected, and knew that human cases of avian influenza have occurred in the United States. However, important gaps in knowledge and prevention practices remain among flock owners, suggesting opportunities for focused public health, animal health, and agricultural outreach.

(SNIP)

Backyard flock owners should know how to protect themselves from avian influenza. Although most survey respondents reported willingness to use some types of PPE, fewer indicated they would use eye protection or coveralls. Messages to flock owners could highlight reasons to use each piece of recommended PPE, when to use it, and how to use it correctly.

Recent incidences of influenza A(H5) human cases among backyard flock owners in the United States underscore the importance of flock owners knowing the signs and symptoms of possible human A(H5) virus infection. The survey identified limited awareness of nonrespiratory symptoms of avian influenza in humans (such as conjunctivitis, diarrhea, and vomiting) and low perceived personal risk, which could result in delays in seeking health care. Flock owners should be encouraged to seek prompt medical evaluation for any potential symptoms of avian influenza virus infection and report recent bird exposure to health care providers to support timely diagnosis and further infection prevention and control measures. 

(Continue . . . )

The need to improve both knowledge and biosecurity practices among backyard flock owners isn't just an American problem.  

Last March, in EFSA: Risk communication on Avian Flu Biosecurity, we looked at a proposed, phased 3-year program to increase biosecurity awareness in small holdings across the EU. 

As we discussed in 2024's Mixed Messaging On HPAI Food Safety, there is some degree of risk in the slaughtering of live birds and preparation of raw poultry; especially from birds raised at home or purchased from live markets.

PAHO (the Pan-American Health Organization) mentions this on their Avian Influenza landing page:  Plucking, handling infected poultry carcasses, and preparing poultry for consumption, especially in domestic settings, may also be risk factors.

Also in 2024 the WHO published  Interim Guidance to Reduce the Risk of Infection in People Exposed to Avian Influenza Viruses, which lists a number of `risk factors', including:

• keep live poultry in their backyards or homes, or who purchase live birds at markets;

• slaughter, de-feather and/or butcher poultry or other animals at home;

• handle and prepare raw poultry for further cooking and consumption;

Over the past few years the threat from H5N1 has grown markedly in the Western Hemisphere. Things we used to do without much thought - like raising a few chickens the backyard - carry more risks today. 

The $64 question is whether we can adjust to those changing risks fast enough to prevent even bigger bio-shocks in the future. 

Several States Warn On Contact With Wild Birds/Mammals

#19,052

Two months ago, in Declining Mammalian Spillover Submissions To USDA Over Past 8 Months, we looked at the recent drop in reported spillovers of HPAI H5 to mammalian wildlife, despite increased detections in wild birds.

The above graph is based on collection dates, not confirmation dates (which may come months later). During the 1st 3 months of 2025, the USDA averaged 43 positive submission per month.

Over the past 11 months, the USDA has averaged 10 positive submissions per month (range 1-17), a decline of over 75%.

Reporting by states remains uneven, with 9 states (Alabama, Arkansas, Hawaii, Maryland, Mississippi, New Hampshire, South Carolina, Tennessee, and West Virginia) yet to submit a case, while New Mexico (n=73) and Colorado (n=77) top the list.

These disparities may come down to differences in climate and terrain (swamps vs. forests vs. deserts), varying activity by migratory flyways, and the fact that infected wildlife quite often die in remote, difficult to access places where their carcasses are quickly scavenged by other animals, making them unlikely to be discovered or tested. 

But it also possible that some states are simply more proactive in investigating, and reporting suspected cases, than others.

While the USDA now lists 51 unique mammalian species of wildlife (excluding livestock) confirmed with HPAI H5N1 in the United States, the bulk of reports come from 10 species:

Although domestic cats lead the list, the number of reports has declined sharply over the past 12 months (see chart below).  This may be due, in part, to  changes ordered by the FDA in the manufacturing of pet food.

All of these numbers are presumed to represent a small fraction of the actual number of spillovers, as limited seroprevalence studies have found antibodies in a number of wildlife species (see Viruses: The Seroprevalence of Influenza A Virus Infections in Polish Cats During a Feline H5N1 Influenza Outbreak in 2023).

Despite these declining numbers a number of states have issued fresh warnings to the public over the past week on avoiding contact with wild birds and/or potentially infected mammalian wildlife. 

While it has yet to be posted on a state website, yesterday media outlets in Colorado were reporting that a Skunk tests positive for Avian Influenza in Pueblo County, and warning of the risks of avian flu to both humans and pets. 

Yesterday, the state of Arkansas released the following:

State Agencies Urge Public to Avoid Contact With Wild Birds Due to Avian Influenza
Posted on February 12, 2026

LITTLE ROCK, AR –Arkansas agriculture and health agencies are urging the public to avoid contact with wild birds, especially birds that appear sick or are found dead, due to detections of highly pathogenic avian influenza (HPAI) in Arkansas.

Testing has confirmed HPAI in wild birds and in backyard and commercial flocks statewide. Wild birds, particularly migrating waterfowl, are the primary source of virus spread to domestic poultry and other birds.

Agencies warn that handling sick or dead wild birds, or bringing them into homes, barns, or vehicles, can spread the virus and pose risks to people, pets, and domestic flocks.

Key Guidance for the Public

• Do not touch, move, or attempt to rescue wild birds that appear sick or are found dead.
• Do not bring wild birds into your home, vehicle, barn, or coop for any reason.
• Keep your distance from wild birds, especially waterfowl, that appear lethargic or disoriented.
• Keep pets away from wild birds and carcasses.
• Avoid areas where large numbers of wild birds are congregating when possible.
• Hunters and bird watchers should take precautions, including wearing gloves when handling birds or equipment, washing hands thoroughly after contact, and avoiding consumption of birds that appear sick or were found dead.

Who to Call

Wild bird activity: Report concentrations of sick or dead wild birds, or other unusual activity, to the Arkansas Game and Fish Commission at agfc.com/education/avian-influenza/.
Backyard or commercial poultry: Report suspected or confirmed poultry illness or deaths to the Arkansas Department of Agriculture’s sick bird hotline at (501) 823-1746.

Biosecurity for Bird Owners

Poultrygrowers should follow basic biosecurity practices to reduce the risk of HPAI. These include washing hands and footwear before and after contact with birds, restricting visitors to poultry areas, limiting exposure to wild birds, and quarantining new birds for at least two weeks before introducing them to existing flocks.

Human Health Precautions

Although human cases of HPAI are rare, people exposed to infected birds or contaminated environments should wash hands thoroughly with soap and water and wear appropriate protective equipment if handling birds is necessary. Anyone who develops flu-like symptoms after exposure to birds or other animals potentially infected with HPAI should contact the Arkansas Department of Health (ADH) Zoonotic Disease Section at (501) 280-4136 or adh.zoonotic@arkansas.gov. ADH can coordinate appropriate testing and, if indicated, post-exposure antiviral treatment. To help prevent unnecessary exposure to others and ensure proper evaluation, individuals are encouraged to contact ADH before seeking in-person medical care.

And this week, from Texas a warning from the Amarillo health authorities (see 12 birds test 'non-negative' for bird flu after hundreds of dead birds found in Amarillo), and this reminder from the Houston Health Department.

The public remains largely apathetic to the threat of HPAI (see Two Surveys (UK & U.S.) Illustrating The Public's Lack of Concern Over Avian Flu), and many governments appear more than happy to downplay the threat for political or economic reasons.

While the decline in reported spillovers to the USDA may turn out to be a good sign, a lack of evidence is not evidence of lack. 

Given that many other signs suggest we are at or near the peak of the fall/winter avian flu season, a modicum of caution around wild birds, poultry, and other wildlife seems more than prudent. 

EID Journal Dispatch: Novel Highly Pathogenic Avian Influenza A(H5N1) Virus, Argentina, 2025

 

#18,988

Last August, in H5Nx: Reassort & Repeat, we looked at HPAI's promiscuous ways, and its propensity to reinvent itself - via reassortment - after it meets up with compatible LPAI viruses.  

Twenty years ago, H5N1's range was primarily limited to Southeast Asia, and so its reassortment opportunities were limited to LPAI viruses common to the region. 

But a chance reassortment near Qinghai Lake, Tibet in 2005 produced a more biological `fit', and far more easily carried (by migratory birds) clade 2.2 of the virus (see H5N1 Influenza Continues To Circulate and Change 2006 by Webster et. al.), which led to the first major diaspora of the virus (eventually spreading to Europe, the Middle East, and Africa). 

Over the years, as the virus spread around the globe, it encountered - and reassorted with - scores of  different LPAI viruses, producing hundreds of new clades, subclades, genotypes, and even new subtypes (H5N5, H5N6, H5N9, etc.).

While many were biological failures, some proved competitive enough to advance the spread, evolution, and diversity of the virus. We saw huge changes to HPAI in 2014 (changeover to H5N8), in 2016 (the first major European Epizootic), and in 2017 the virus crossed the Equator on its way to South Africa.

As H5's range increased, so did its genetic diversity, giving it even more reassortment opportunities. While it was growing stronger,  HPAI's first attempt to invade the Western Hemisphere (in 2014-2015) fizzled after 6 about months (see map below).

In 2020 the virus reassorted back to H5N1 - and having become even more `biologically fit' - in 2021 it make a far more successful 2nd invasion of the western hemisphere. 

Remarkably, within months of arriving in North America, it had already generated more than 100 new genotypes, and for the first time became capable of infecting mammalian livestock (goats, cattle, alpaca, etc.)

The pattern has been pretty consistent; as HPAI spreads, it encounters new opportunities to increase its genetic diversity. It is one of the reasons why its recent spread to Hawaii, and its feared spread into Oceania, are of great concern. 

Today we've a report from South America, published in the CDC EID Journal, which describes a unique 4:3:1 triple-reassortment of HPAI H5N1 detected in a mixed backyard flock (chickens, ducks, and turkeys) in Chaco Province, northern Argentina.

This outbreak was notable because the infected flock presented with severe, and atypical (dominated by diarrhea) symptoms. The authors wrote: 

The predominance of gastrointestinal signs suggests possible shifts in tissue tropism or virulence. Also, the detection of a North American NP segment not previously identified in LPAI viruses from Argentina or elsewhere in South America highlights the need to strengthen regional AIV surveillance, even in the absence of active HPAI circulation.

 I've posted the link, and some excerpts, from the dispatch below. Follow the link to read it in its entirety.  I'll have a brief postscript when you return.

Volume 31, Number 12—December 2025
Dispatch
Novel Highly Pathogenic Avian Influenza A(H5N1) Virus, Argentina, 2025

Ralph E.T. Vanstreels, Martha I. Nelson, María C. Artuso, Vanina D. Marchione, Luana E. Piccini, Estefania Benedetti, Alvin Crespo-Bellido, Agostina Pierdomenico, Thorsten Wolff, Marcela M. Uhart, and Agustina Rimondi

Abstract

Genomic sequencing of reemerging highly pathogenic avian influenza A(H5N1) virus detected in Argentina in February 2025 revealed novel triple-reassortant viruses containing gene segments from Eurasian H5N1 and low pathogenicity viruses from South and North American lineages. Our findings highlight continued evolution and diversification of clade 2.3.4.4b H5N1 in the Americas.

Highly pathogenic avian influenza (HPAI) viruses were introduced to South America in 2022 by migratory birds from North America. The viruses belonged to the 2.3.4.4b clade of HPAI A(H5N1) virus that became widespread in Europe in 2020 and spread to North America in 2021. The trajectory of H5N1 in South America has differed from H5N1 in North America in several critical ways. First, nearly all South America outbreaks stem from a single introduction of H5N1 viruses from North America (1,2), whereas the North America epizootic was reseeded by multiple independent introductions from Europe and Asia (A1–A6) (3,4). Second, South America H5N1 outbreaks were driven by a single genotype (B3.2) that was introduced from North America and remained genetically stable during its spread across South America. In contrast, H5N1 viruses in North America underwent frequent reassortment with low pathogenicity avian influenza (LPAI) viruses, prompting new genotype nomenclature (using B, C, D) (3). Third, South America’s H5N1 epizootic is unique in establishing mammal-to-mammal transmission in marine mammals, enabled by the H5N1 (B3.2) virus acquiring mammalian-adaptive polymerase basic (PB) 2 mutations (Q591K and D701N) (1,2). That pattern has not occurred in North America, where H5N1 spillover into terrestrial and marine mammals was transient, except in United States dairy cattle (3).

Beyond the ecologic devastation among coastal wildlife, in 2023, H5N1 (B3.2) virus spread widely in birds across mainland South America, leading to poultry and wild bird outbreaks (5–8). Although in 2024 HPAI outbreaks occurred in Brazil and Peru (World Organisation for Animal Health, https://wahis.woah.orgExternal Link), there were no detections in Argentina during March 2024–January 2025.

The Study

On February 11, 2025, Servicio Nacional de Sanidad y Calidad Agroalimentaria (SENASA; Buenos Aires, Argentina), Argentina’s national organization for agricultural health and safety, was notified of an outbreak in a mixed backyard flock (chickens, ducks, and turkeys) in Chaco Province, northern Argentina. The flock experienced high mortality (33/81 chickens, 37/99 ducks) in just 1 week. When we inspected the living flock, two thirds of the remaining 48 chickens had diarrhea and 1 of the remaining 62 ducks was lethargic; 2 turkeys were asymptomatic.

The household was located within a remnant fragment of the Dry Chaco biome, a hot and semi-arid tropical dry forest, surrounded by agriculture cropland. The affected flock had free access to a small pond frequently visited by wild waterfowl (Appendix 1). We depopulated and disinfected the area. We inspected backyard poultry within the 3 km perifocal zone (1 household) and the 3–10 km surveillance zone (7 households) and detected no illness or death. We did not find any affected wildlife on site.

       (SNIP) 

Conclusions

We have documented a reassortment event between HPAI H5N1 and endemic South America LPAI viruses. South American PB2 and PA segments are divergent from global AIV diversity (9) (Figure 1), indicating reassortment has expanded H5N1 polymerase diversity. Although the H5N1-Arg_Feb2025 viruses have exchanged 5 gene segments, they retained the original Eurasian MP segment (Figure 2), which remains conserved in most reassortant H5N1 viruses in North America. That segment conservation suggests the Eurasian MP segment might confer a selective advantage in HPAI H5 viruses. To date, we found no evidence of those novel 4:3:1 triple reassortant viruses in other South America countries; however, if future detections confirm wider spread, designation of a new H5N1 genotype would be warranted. Of consequence, genotyping tools such as the US Department of Agriculture’s GenoFlu should be expanded to include South American lineage genes for systematic classification of new virus genotypes.

(SNIP)

Further research on the diversity of LPAI viruses circulating in Neotropical wildlife will be essential to understand potential interactions between H5N1 and South American lineage strains and to assess the long-term consequences of the introduction of HPAI viruses into the region. Our findings underscore the critical importance of sustained influenza surveillance coupled with whole-genome sequencing to track the evolution of HPAI H5N1 and support efforts to control and mitigate its effect on domestic animals, wildlife, and human health.

Dr. Vanstreels is a veterinarian and an associate researcher with the Karen C. Drayer Wildlife Health Center at the University of California, Davis. His research interests include South American and Antarctic wildlife health, with a special interest in the ecology and effects of highly pathogenic avian influenza H5N1 on wild bird and marine mammal populations.

As the following FAO map illustrates, there are large swaths of the globe where the HPAI virus is presumably circulating, but which provide little (or no) surveillance and/or reporting.  

Blind spots include all of Russia, Central Asia, much of Africa, Northern Canada, and the interior of South America (note: Australia/NZ are testing, but the virus has not shown up yet).

While many of these  regions are impossibly remote, or lack the resources to do in-depth surveillance, there are many countries that simply choose not to report outbreaks for political or economic reasons.

Once again (see here, here, here, here, and here) the authors of today's report call for improved influenza surveillance and the timely reporting of data. 

And rightly so - because with rapidly evolving HPAI viruses - what we don't know can hurt us.  

Hawaii: State Agencies Respond to 3rd Possible Case of HPAI H5 (Kauaʻi)

Hawaii lies beneath the West Pacific Flyway

#18,986

Separated as it is by vast ocean distances - 2,400 miles to the U.S., 4,000 miles to Japan - Hawaii is considered the world's most isolated populated place on earth. 

And not surprisingly - until just over a year ago  - the state of Hawaii had never reported H5N1 in wild or domesticated birds. 

All that changed in November of 2024 after the virus was first detected in wastewater samples on Oahu, and at least two outbreaks in captive and/or wild birds the following week. 

A month later, another treatment plant on the island of Hilo reported the virus.

This year, the first reported case came in mid-October (see Hawaii: DOH, DAB, DLNR Investigate Possible Avian Flu Case in Waterfowl), followed a month later by Hawaii: State Agencies Respond to 2nd Confirmed Case of HPAI H5 (Maui).

Yesterday the State of Hawaii announced their 3rd presumptive positive HPAI H5 case of this fall (see below) - this time affecting a 4th Hawaiian  island (Kauaʻi).  

What was once unheard of has now become increasingly common now that the HPAI H5 virus has better adapted to seabirds (see 2022's Unprecedented `Order Shift' In Wild Bird H5N1 Positives), with many species; including gannets, gulls, guillemots and great skua now hosting the virus.

The behavioral shift has not gone unnoticed by Oceania (Australia/NZ) which have been on HPAI watch for several years (see Australia: Confirmation of H5 Bird Flu on Sub-Antarctic Heard Island).

First the announcement from the Hawaiian Department of Land and Natural Resources, after which I'll return with a bit more.

12/11/25 – STATE AGENCIES RESPOND TO THIRD POSSIBLE CASE OF HIGHLY PATHOGENIC AVIAN INFLUENZA IN HAWAIʻI

Posted on Dec 11, 2025 in Forestry & Wildlife, Main, News Releases, slider

HONOLULU – Three state agencies remain on alert after a third presumptive case of avian influenza was found in a wild bird — this time in an endangered native duck on Kauaʻi. Preliminary testing performed by the Hawaiʻi State Laboratory showed the bird was infected with an influenza A virus, though confirmation and subtype identification (e.g., H5N1) are pending further analysis by the National Veterinary Services Laboratories (NVSL).

A Koloa Maoli (Hawaiian duck) was found sick on November 26 at the U.S. Fish and Wildlife Service’s Hanalei National Wildlife Refuge in Hanalei, Kauaʻi. The bird died within 24 hours.

H5N1 is a highly infectious and often deadly subtype of influenza A that mainly affects birds. Human infections are rare but can occur with close contact. Hawaiʻi’s first detection of H5N1 occurred in November 2024 in a backyard flock on Oʻahu, followed by a hybrid duck found on Oʻahu’s North Shore. This year, two additional cases have been confirmed in migratory Koloa Māpu ducks—one on Oʻahu and one on Maui. This Kauaʻi detection is the first potential case in a native bird, likely introduced through infected migratory waterfowl.

The Hawaiʻi Department of Health (DOH), Department of Agriculture & Biosecurity (DAB), and Department of Land and Natural Resources (DLNR) continue coordinated monitoring of public health reports, poultry operations and wild bird populations for any signs of virus spread.

With migratory bird season underway, more birds traveling through the islands may carry avian diseases and it is recommended that the public avoid touching or handling wild birds, especially waterfowl or shorebirds.

If you encounter sick or dead birds, such as waterfowl:

• Avoid touching or handling wild birds, especially waterfowl or shorebirds.
• If capturing a dead or sick bird is necessary, wear gloves, minimize contact and follow biosafety protocols.
• To report multiple or unusual illnesses in poultry, livestock or other wild birds or animals, contact DAB’s Animal Industry Division at 808-483-7100, Monday through Friday from 7:45 a.m. to 4:30 p.m., or 808-837-8092 during non-business hours and holidays. Send email to DABIC@hawaii.gov

About H5N1/Avian Influenza:

• H5N1 is an avian influenza virus that mainly affects birds; human infections are uncommon but can happen following close contact with infected birds.
• The public risk in Hawaiʻi is currently low, so the DOH does not recommend restricting outdoor activities.
• Routine influenza vaccines in humans do not protect against H5N1; the best prevention is avoiding contact with sick or dead birds.

For more information, visit:

DOH: https://health.hawaii.gov/docd/disease_listing/avian-influenza/

DAB: https://dab.hawaii.gov/ai/ldc/avian-influenza-information/

This fall we've seen unprecedented numbers of avian flu reports across North America and much of Europe -  particularly in wild birds - but also affecting commercial and backyard flocks.

Credit ECDC/EFSA Avian influenza overview Sep–Nov 2025

After two less impactful years (see chart above), avian flu has reinvented itself and is back with a vengeance.  While it could fizzle again, right now there appears to be an immense amount of the virus circulating in wild birds, increasings the risks of spillovers into poultry, mammalian wildlife, and even humans.

Last July we looked at the results of a survey of stakeholders (backyard poultry owners, animal rescue, etc.) on their knowledge of HPAI (see Hawaii: Findings From DOH Bird Flu Survey For Backyard Flock Bird Owners And Bird Rescuers), which found sizeable knowledge gaps.

 

Two months ago, in UF/IFAS Extension: What Backyard Flock Owners Need to Know about Bird Flu (Influenza H5N1) we looked at some common-sense steps people who raise birds can take to reduce the risk of infection.

Admittedly, trying to predict what HPAI does next is a mug's game, but if there was ever a time to be extra diligent in avoiding exposure to wild birds, and for flock owners to increase their biosecurity, it is probably now. 

For some official advice from the ECDC/EFSA, you may wish to revisit:

Avian influenza in Europe: enhanced surveillance and strict biosecurity needed as detections surge

Hawaii: State Agencies Respond to 2nd Confirmed Case of HPAI H5 (Maui)

Hawaii lies beneath the West Pacific Flyway 

#18,949

In most places (outside of Oceania) outbreaks of HPAI H5 in wild birds and/or poultry have become commonplace to the point they are barely newsworthy, but it is still an unusual occurrence in Hawaii. 

It was just a year ago that the virus was first detected in wastewater samples on Oahu, and at least two outbreaks in captive and/or wild birds the following week.

Last month, we saw a lone duck presumptively test positive for the virus at the University of Hawaiʻi at Mānoa (Oahu). On Friday the state announced a second detection this time on the island of Maui, more than 100 miles to the south and east.

There are no details provided as to this year's genotype, but last year's arrival was characterised as  (A3).

First the announcement, after which I'll have a bit more. 

11/14/25 – STATE AGENCIES RESPOND TO SECOND CONFIRMED CASE OF HIGHLY PATHOGENIC AVIAN INFLUENZA IN HAWAIʻI

Posted on Nov 14, 2025
JOSH GREEN, M.D.
GOVERNOR
DAWN CHANG
CHAIRPERSON


STATE AGENCIES RESPOND TO SECOND CONFIRMED CASE OF HIGHLY PATHOGENIC AVIAN INFLUENZA IN HAWAIʻI



HONOLULU – Three state agencies are on alert after a second case of highly pathogenic avian influenza (HPAI) was confirmed in a migratory duck – this time on the island of Maui. This is the first confirmed detection of H5N1 on Maui.

The Northern pintail (koloa māpu) was found along the Wailea shoreline and submitted to the U.S. Geological Survey’s National Wildlife Health Center – Honolulu Field Station. Samples were sent to the National Wildlife Health Center in Madison, Wisconsin, where it tested positive for influenza H5. The National Veterinary Services Laboratories in Iowa later confirmed the bird was infected with the H5N1 virus.

H5N1 is a highly infectious and often lethal subtype of influenza A that primarily affects birds but can sometimes be transmitted to humans. H5N1 was first detected in Hawaiʻi in November 2024 in a backyard flock in Central Oʻahu and subsequently in a hybrid duck from the north shore of Oʻahu. This Maui case follows the October 2025 confirmation of H5N1 in another koloa māpu found on Oʻahu at the University of Hawaiʻi Mānoa campus.

This year to date, the USGS has tested 77 birds for influenza all of which have been negative except for the Maui koloa māpu. Given these data, the risk of infection to humans and poultry remains low.

The Hawaiʻi Department of Health (DOH), Department of Agriculture & Biosecurity (DAB) and Department of Land and Natural Resources (DLNR) continue coordinated monitoring of public health reports, poultry operations and wild bird populations for any signs of virus spread.

During the Hawaiʻi migratory bird season, migratory birds may carry diseases to the islands, so the public should remain vigilant.

If you encounter sick or dead birds such as waterfowl:

• Avoid touching or handling wild birds, especially waterfowl or shorebirds.
• If capture of a dead or sick bird is necessary for investigation or handling is necessary by wildlife professionals, use gloves, minimize contact and follow biosafety protocols.
• To report multiple or unusual illnesses in poultry, livestock, or other wild birds or animals, contact the Hawaiʻi Department of Agriculture and Biosecurity (DAB) Animal Industry Division at 808-483-7100, Monday to Friday from 7:45 a.m. to 4:30 p.m., or 808-837-8092 during non-business hours and holidays. You may also e-mail HDOAIC@hawaii.gov.

Continued Public Support Needed for Seabird Fallout Response

State agencies also remind the public that we continue to rely on community participation in responding to seabird fallout events, especially during peak fledgling seasons. If you find a grounded seabird – such as a wedge-tailed shearwater – please report it and consider assisting the bird by bringing it into a rescue facility. If you find a downed seabird and decide to rescue it, you can follow recommendations and information provided by the State Department of Health and guidance from the Centers of Disease Control. Practice proper hygiene and sanitize hands, clothes, towels and other items after handling any animal. Community assistance remains critical to ensuring these birds receive timely care and can be returned safely to the wild. For more information visit:

https://dlnr.hawaii.gov/wildlife/seabird-fallout-season/

About H5N1 / Avian Influenza:

•  H5N1 is an avian influenza virus that primarily affects birds; human infections are rare but can occur from close contact with infected birds.
• The public risk in Hawaiʻi is low at this time and DOH does not recommend limiting outdoor activity.
• Routine influenza vaccines in humans do not protect against H5N1; the best prevention is avoiding contact with sick or dead birds.

For more information, visit:

https://health.hawaii.gov/docd/disease_listing/avian-influenza/

Over the summer we looked at the results of a survey of stakeholders (backyard poultry owners, animal rescue, etc.) on their knowledge of HPAI (see Hawaii: Findings From DOH Bird Flu Survey For Backyard Flock Bird Owners And Bird Rescuers), which found sizeable knowledge gaps.

Since then avian flu has returned with a vengeance this fall in both North America and much of Europe, affecting both commercial and backyard flocks.

 

A little over a month ago, in UF/IFAS Extension: What Backyard Flock Owners Need to Know about Bird Flu (Influenza H5N1) we looked at some common-sense steps people who raise birds can take to reduce the risk of infection.

Hopefully people are taking this, and the USDA's advice, seriously, as we could be looking at a protracted, and heavy, avian flu season ahead.