Pathogen's Progress (H5N1) - Canada CFIA Reports 1st Poultry Outbreak of Fall 2026

[Michael Coston]

Pathogen's Progress​

H5 Affected States & Provinces June 2015


#19,326

Prior to 2021, North America had only had one brush with the Asian-origin HPAI H5 virus; a reassorted H5N8 subtype which appeared in South Korea in January of 2014 before beginning a world tour.

It crossed the north Pacific - carried by migratory birds - the following fall, arriving in the Pacific Northwest in December 2014, sparking the first HPAI H5 epizootic in the United States and Canada (see map above).

That H5Nx virus, however, disappeared completely the following summer, apparently still ill-suited for long-term carriage by wild and migratory birds (see PNAS: The Enigma Of Disappearing HPAI H5 In North American Migratory Waterfowl).

That limitation would evaporate in the summer of 2016 when H5N8 reassorted into a far more robust threat (probably in China or Siberia) - arriving in Europe in October - and sparking their biggest (at that time) epizootic on record. EID Journal: Reassorted HPAI H5N8 Clade 2.3.4.4. - Germany 2016).

This new H5N8 was not only deadlier to some bird species, it was more easily carried by others, increasing its range and impact dramatically over the next 6 months.

We also saw this virus spin off several short-lived subtypes, including H5N5, H5N3, and H5N9.

Over the winter of 2016-17, this H5N8 virus spread from Europe, into the Middle East, and then North Africa. By late spring, 2017, it had crossed the equator for the first time, and set up shop in South Africa, making it the most successfully disseminated HPAI H5 virus we'd seen.

A European H5N6 briefly appeared in 2018, but H5N8 held on until a new, reassorted H5N1 virus appeared in Europe in 2020, and began to supplant H5N8.

Unlike previous H5Nx incarnations, this new H5N1 showed an increased affinity for infecting mammals, and a much wider avian host range (see DEFRA: The Unprecedented `Order Shift' In Wild Bird H5N1 Positives In Europe & The UK).

By 2022 this `new and improved' H5N1 virus had crossed both the Atlantic and Pacific oceans, spreading first to North America, followed by South America, the Antarctic, and most recently (2026) into Australia/New Zealand.

While avian flu activity still decreased during the hotter months, no longer did HPAI H5 disappear completely each summer. It could be maintained (at low levels) in local birds, livestock, small mammals, and likely even the environment.

All of which makes the HPAI H5 threat of today far different from what it was even a decade ago. The H5N1 virus of today has expanded not only its geographic range, but its host range as well.

And it isn't done evolving.

Since its arrival in 2021, the H5Nx virus has diversified into more than 100 distinct genotypes in North America alone, with scores of others emerging around the globe. A few notable North American examples include:

• In late 2023 a new B3.13 genotype emerged that could efficiently infect dairy cattle while mildly infecting dozens of humans
• Last fall we saw 3 new genotypes emerge (D1.1, D1.2, D1.3), with D1.1 producing more severe illness in humans.
• In October 2024 Canada experienced a multi-farm outbreak of emerging N1 genotype of H5N1 that was highly resistant to NAI antivirals (carrying the H275Y mutation)

These variants illustrate just how quickly (and dramatically) the avian `fluscape' can change, and we generally see those changes in the fall, when migratory birds - which spent their summers in their high latitude roosting areas - return.

A 2016 study (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1), suggests that waterfowl pick up new HPAI viruses in the spring (likely from poultry or terrestrial birds) on their northbound trip to their summer breeding spots - where they spread and potentially evolve - and then redistribute them on their southbound journey the following fall.

Our own Arctic Refuge, where more than 200 bird species spend their summers, serves as a central hub, and funnels migratory birds south via all four North American Flyways.


While this fall's HPAI viruses could be similar to what we saw last year - they might include new, potentially game-changing, genotypes - which could either increase or decrease their threat.

Evolution is a double-edged sword, and what it adds it can also take away. But the trajectory of H5N1 over the past 4+ years has been towards more mammalian adaptation, and increased host range.

We've also seen reports of H5N5 activity above the Arctic Circle (see Norwegian Veterinary Institute Reports Another HPAI H5N5 Infected Polar Bear on Svalbard Island), and H5N5 claimed the life of a Washington state bird keeper last fall.

The APPA estimates `Eleven (11) million U.S. households own backyard chickens (a 28% increase from 2023)', yet a recent survey (see MMWR: Knowledge, Attitudes, and Practices Regarding Avian Influenza Among Owners of Backyard Flocks) found significant gaps in their knowledge of dealing with avian flu.

While no one can predict with any confidence what HPAI will look like later this fall, the one thing we can be sure of is the 2026 fall southbound migration has already begun, and the time to prepare for its arrival grows shorter with every passing day.

And if recent history is any guide, we should be preparing for additional surprises.


https://afludiary.blogspot.com/2026/09/pathogens-progress.html

 

[Michael Coston]

Canada: CFIA Reports 1st HPAI Poultry Outbreak SInce May​

Screenshot CFIA
#19,332

While HPAI H5 no longer completely retreats each summer, the warmer months of the year usually see far less activity than the fall and winter. And each fall, as we await the arrival of the annual southbound migration of birds, we ponder what changes that might bring (see H5Nx: Reassort & Repeat).

In the 2023-2024 avian flu season, we famously saw the emergence of a `bovine' H5N1 genotype B3.13, which has since infected (at least) 1,179 cattle herds across 20 states.

Avian flu's return in the fall of 2024 brought with it a far more aggressive poultry/wild bird strain (D1.1) (which can also infects humans), along with a spate of oseltamivir resistant outbreaks in Canada.






Abrupt Shift in H5N1 Genotypes in Wild Birds in US/Canada
Nature https://www.nature.com/articles/s41591-026-04300-1
Last fall - while both D1.1 and B3.13 continued to dominate - we saw the first known human infection with HPAI H5N5 in a backyard bird keeper in Washington State.

While each fall doesn't guarantee a new wrinkle in the avian flu story, we often first notice big changes in the makeup and behavior of avian flu when migratory birds return from their high latitude roosting spots (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1).

We've already witnessed a noticeable uptick in outbreaks in commercial and backyard poultry in the United States over the past couple of weeks (see USDA dashboard below).





To this we can add Canada's first poultry outbreak since May 16th, a poultry farm in the rural municipality of De Salaberry, in Manitoba.

Canada's first poultry outbreak of the new season comes at roughly the same time as last year (Sept 9th), and considerably earlier than the first Canadian outbreak of fall 2024 (Oct 21st).

Whether this fall brings anything substantially different remains to be seen, and unfortunately, we probably won't learn about any genetic changes for several months. As we saw last year, in Nature: Lengthy Delays in H5N1 Genome Submissions to GISAID, the average delay in submitting sequences to GISAID was 7 months (228 days), with some countries taking nearly 2 years.

And genetic sequences - even when they are submitted to GISAID - are often devoid of crucial metadata (i.e. collection date, exact location, host-specific information, etc.), limiting their value to the scientific community.

For now, we'll have to content ourselves with less specific data; where, when, the size, and the type of outbreak (commercial poultry, backyard flocks, livestock, peridomestic mammals, or even humans).

In the meantime, if you raise backyard birds, or frequent live markets, now is a good time to familiarize yourselves with the risks of avian flu, and the things you can do to reduce those risks.

UF/IFAS Extension: What Backyard Flock Owners Need to Know about Bird Flu (Influenza H5N1)

https://afludiary.blogspot.com/2026/09/canada-cfia-reports-1st-hpai-poultry.html