Avian Flu's Unusually Active September in the United States

 

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Until fairly recently, HPAI H5 infections in wild birds - and spillovers into poultry - were pretty much a fall and winter phenomenon. Carried, and distributed primarily by migratory waterfowl, their regular `ride' retreats to their high latitude roosting areas by late spring.

Even after our first HPAI H5 epizootic in 2014-15, the virus disappeared abruptly in mid-June, and did not reappear in North America again until 2021 (see PNAS: The Enigma Of Disappearing HPAI H5 In North American Migratory Waterfowl).

Local wild birds, it seemed - either died when infected - or survived and gained (or had) immunity.  Either way, they were unable to provide a summer `home' for the virus.  Warmer temperatures were also thought to dampen down transmission. 

By the time the HPAI H5 virus returned to North America in late 2021, it had undergone many changes.

It was H5N1 not H5N8.  It had reassorted numerous times, and had not only expanded its avian host range in Europe, it was beginning to persist (at low levels) throughout the summer. 

During its first full year in North America, we saw continued outbreaks over the summer of 2022, with a major return of the virus in September (68 outbreaks affecting > 6 million birds). 

This persistence and early arrival were likely due to new reassortments with North American LPAI viruses (see Rapid Evolution of A(H5N1) Influenza Viruses After Intercontinental Spread to North America), and biosecurity lapses on backyard and commercial poultry operations.

In 2023 and 2024, we saw far less avian flu activity over the summer months (see chart below), with outbreaks often not starting up again until October. Notice how `dead' June-September were during 2023-2024, and the circled uptick for Sept 2025.

A little over 2 weeks ago I reported on the unusually early uptick in poultry farm infections with HPAI during the first half of September (see Canada & U.S. Report Early Fall Uptick In H5N1 Outbreaks In Poultry). 

Since then, the number of U.S. poultry involved has climbed 10-fold; from 348K to 3.83 million.  

As Hogvet51 aptly pointed out in his blog yesterday (see 20 H5 Commercial Flock Infections in September, but Nobody Can Share a Genotype...), we've no idea what genotypes have returned this fall.  Whatever the NVSL lab knows, they haven't been quick to share.

As we've seen, the fall migration can often bring abrupt changes.

• Two years ago (fall/winter 2023) we saw a new H5N1 B3.13 genotype emerge that could efficiently infect dairy cattle, while mildly infecting dozens of humans. Although not as well adapted to poultry, some spillovers were reported.

• Last fall (2024), we saw 3 new genotypes emerge (D1.1, D1.2, D1.3), with D1.1 producing more severe illness in humans, while last October Canada experienced a multi-farm outbreak  that was highly resistant to NAI antivirals.

With the U.S. government in shutdown, it remains to be seen how much data we'll be getting from the USDA in the days and weeks ahead. But even under `normal' circumstances, the release of detailed HPAI information has often come at a glacial pace.

Last March, in Nature: Lengthy Delays in H5N1 Genome Submissions to GISAID, we learned that the average delay for countries to submit non-human sequences was 7 months.

This lack of data extends to reports of mammalian infections as well, as only a handful of states (6) have found, tested, and reported incidents over the past few months (8 detections over June-Sept).

Looking back over the past 4 years, we can see a decided drop in reporting to the USDA by states since March of 2025. 

While none of this guarantees we are in for a wild HPAI ride this fall and winter - with this level of testing and reporting - a viral storm could easily be brewing, and you and I probably wouldn't see it coming.  

Brace yourself accordingly.