H5Nx: Reassort & Repeat

#18,841

In the Northern hemisphere millions of migratory birds spend their summers in their high latitude breeding areas in Alaska, Canada, Siberia, and even the Arctic. More than 200 bird species roost in the Alaskan Arctic Refuge, after which they migrate south each fall via four North American Flyways.

While there, they hatch a new generation of (flu naive) fledglings, while at the same time they mingle with other species - potentially sharing viruses picked up during their  northbound flight the previous spring. 

A 2016 study (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1), posits that these viruses may often evolve (or reassort) over the summer, and then are redistributed by migratory birds on their southbound journey the following fall.

And indeed, particularly since 2014, the fall and early winter has seen the introduction of a number of `game-changing' HPAI H5 variants, often the product of reassortment. 

In January 2014, a reassorted HPAI H5N8 virus appeared in South Korea, decimated their poultry industry, and then began a world tour, arriving in North America in less than a year and sparking the first HPAI H5 epizootic in the US and Canada.

While better adapted to long-distance carriage by migratory birds than H5N1, this North American incursion lacked the `legs' to survive the summer, and faded after 8 months (see PNAS: The Enigma Of Disappearing HPAI H5 In North American Migratory Waterfowl).

During the summer of 2016 H5N8 reassorted into a far more robust threat (probably in China or Siberia) - arriving in Europe in October - and sparking their biggest 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 new subtypes, including H5N5, H5N3, and H5N9. 

Over the winter of 2016-17, this H5N8 virus spread from Europe, into the Middle East, and then Northern Africa. By late spring, 2017, it had crossed the equator 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 late 2021 this `new and improved' H5N1 virus had crossed both the Atlantic and Pacific oceans, spreading first to North America, followed by South America, and even the Antarctic.   

The virus has since diversified into more than 100 distinct genotypes in North America alone, and this evolution continues, albeit often outside of our view.  

• In 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. 

• Last October Canada experienced a multi-farm outbreak of emerging N1 genotype of H5N1 that was  highly resistant to NAI antivirals (carrying the H275Y mutation)

• We continue to see scattered reports of HPAI H5N5 in birds and mammals in Europe & Canada, and occasionally in birds in the United States.

• In Cambodia we've seen a reassorted clade 2.3.2.1e virus infect > 30 people since 2023, while a new triple-reassortant H5N1 clade 2.3.2.1a virus in India has reportedly infected both humans and cats.

These variants likely only represent a small tip of the rapidly expanding H5Nx iceberg. 

As the FAO graphic below illustrates, much of the world simply doesn't report on what is going on with HPAI - either due to limited surveillance capabilities - or due to political or economic concerns. 

Very little of what is actually going on in those remote high latitude roosting areas - or in those parts of the world that aren't closely monitoring (or choose to report) on the panoply of H5Nx viruses - is known, and so we need to be prepared for surprises. 

Past performance obviously doesn't guarantee future results, but HPAI H5Nx appears to be gaining in both diversity and momentum. 

While it is still only mid-August, this year's fall migration has already begun in North America, although it won't peak for several months. 

One of the publicly available tools that we can use to track bird migration comes from the Birdcast.info website, which uses weather radar, and advanced forecasting methods to track birds. 

Dokter, A. M. Year/s of live migration map image. BirdCast, 

live migration map; date and time (most easily accessible from 

image file name/s). Cornell Lab of Ornithology.

https://birdcast.info/migration-tools/migration-forecast-maps.

Screenshot 8/17/25

Over the past 3 weeks we've seen an unexpected summer surge in H5N1 outbreaks at UK poultry farms, which led Defra to increase their risk assessment for some farms this week. 

Making this a good time for poultry producers - and other stakeholders - to seriously consider now how they will deal with the arrival of the next anticipated round of avian flu this fall. 

And any surprises that might bring.