Avian Flu Diary: EM&I: Genetic evolution, phylodynamics, geographic spread of H9N2 avian influenza viruses in China from 2014 to 2025: an increasing potential zoonotic risk

Geographic distribution of of 1,583 H9N2 AIVs in China in 2014‒2025.

#19,278

Although pandemics are often known for their abrupt appearance and rapid spread, our understanding of how long each pandemic virus simmered - either ignored or largely unobserved - remains limited.

Precursors to the 2009 H1N1 pandemic virus, which emerged from North American pigs, appear to have been circulating for at least a decade before it began its world tour.
It has been estimated that ancestral strains of COVID-19 may have been circulating for 4 to 7 decades in bats before spilling over into humans.

We've been watching HPAI H5Nx for 3 decades, and while it continues to improve its game, it has yet to adapt well enough to human physiology to spread efficiently.

The same could be said for many other novel viruses, including both swine and avian flu, henipaviruses like Nipah, scores of other coronaviruses, and of course `Disease X'; the placeholder for those threats yet to be discovered.

One of the `usual suspects' we keep coming back to is LPAI H9N2, which is ubiquitous in Asian poultry, has spread to both Africa and the Middle East, and just recently turned up in Europe.

While roughly 200 human (mostly mild) cases have been reported over the past 30 years - mostly from China - recently we've seen an uptick in cases, with 9 reported in China/Hong Kong over the past 2 months (see WHO WPRO Reporting 4 More H9N2 Cases on Chinese Mainland).

Several recent studies have found signs that LPAI H9N2 is becoming better adapted to mammals, warning of its pandemic potential; including:

Two months ago, in Viruses: Epidemiological and Virological Characteristics of H9N2 Avian Influenza Virus in Jiangsu Province, China, 2024, researchers warned that that Jiangsu’s circulating H9N2 viruses have acquired human receptor preference and mammalian adaptation, posing silent infection and pandemic risks

Last October, in China CDC Weekly: Epidemiological and Genetic Characterization of Three H9N2 Viruses Causing Human Infections, investigators reported a number of indicators of increased mammalian adaptation within the virus, including an enhanced ability to infect upper respiratory (α2,6-sialic acid) tract receptors, and a number of HA protein mutations, including; H191N, A198V, Q226L, and Q234L.

The Asian Y280/G57 lineages have shown increasing signs of mammalian adaptation (see EM&I: Enhanced Replication of a Contemporary Avian Influenza A H9N2 Virus in Human Respiratory Organoids)), while the African and Middle Eastern Lineages (mostly European G1-like) are older and less evolved.

Last summer, in Nature: Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission, researchers reported rising prevalence of key mutations associated with increased infectivity and pathogenicity in mammals.

Despite being clearly zoonotic - LPAI H9N2 is considered a `non-reportable' disease in poultry or wild birds by WOAH (see Terrestrial Animal Code). As a result, there are huge gaps in surveillance and reporting around the world.

Complicating matters, China's attempts to control LPAI H9N2 through vaccines have been less than successful.

In 2025's NPJ Vaccines: Impact of Inactivated Vaccine on Transmission and Evolution of H9N2 Avian Influenza Virus in Chickens, we saw evidence that inactivated vaccines failed to prevent - or even reduce - H9N2 in China's poultry, and may have driven viral evolution (including mammalian adaptations).

All of which brings us to yet another Chinese study which - once again - finds that China's LPAI H9N2 continues to diversify and accrue worrisome mammalian adaptations, which they suggest increase its zoonotic risk.

Due to its length and technical nature, I've only posted some excerpts from the abstract and narrative. Those looking for a deeper dive will want to follow the link to read it in its entirety.

I'll have a brief postscript after the break.

Genetic evolution, phylodynamics, geographic spread of H9N2 avian influenza viruses in China from 2014 to 2025: an increasing potential zoonotic risk
Zifeng Pang ,Peiting Zhong ,Cuishan Mai ,Junkun Fan ,Yejia Wu ,Yao Zhang , show all
Article: 2713320 | Accepted author version posted online: 03 Aug 2026
Cite this article https://doi.org/10.1080/22221751.2026.2713320
Abstract
Subtype H9N2 of the avian influenza virus (AIV) poses a growing threat to the poultry industry and public health. However, since 2014, there has been no systematic study of its genetic evolution, genotype, spatial dynamics, and pathogenicity in China. Therefore, we performed a large-scale sequence analysis of the genome of Chinese H9N2 viruses from 2014 to 2025 using public databases and laboratory isolates. We identified 52 different genotypes in 1,591 H9N2 viruses, including 4 previously recognized genotypes (G6, G57, G58, and G68) and 48 newly defined genotypes (G118–G163) in this study. G57 and G118 were the main epidemic genotypes in China from 2014 to 2025.
Bayesian phylogeographic analysis showed that there were 12 obvious migration paths for the spread of H9N2 AIVs in China from 2017 to 2022. In particular, the South China region was the main transmission centre. H9N2 AIV continues to circulate in chickens and ducks in China and spreads to other hosts.
The H9N2 AIVs with the G57 and G118 genotypes could effectively replicate in MDCK, CEF, A549, and HBE cells with titres of 0.97–8.5 lgTCID50/mL. The G57 and G118 genotypes H9N2 viruses preferentially bound to α–2,6–linked sialic acid glycopolymers (human receptors), and effectively replicate in multiple organs of mice and chickens and cause pathological changes in the lungs. Thus, it is necessary to strengthen the monitoring and prevention of H9N2 AIVs in China.

(SNIP)

These mutations can increase the replication of H9N2 virus in mammalian cells and enhance the pathogenicity of the virus to mammals. In vitro replication experiments showed that the current H9N2 virus could replicate efficiently in MDCK, A549 and HBE cells, and the titer of CK225/22 was higher than that of the other strains.

In vivo experiments showed that the current G57 and G118 genotype H9N2 viruses replicated effectively in the turbinate and lungs of mice and caused body weight loss.

In summary, our results showed that the current H9N2 virus has obtained some mutations adapted to mammals, increasing the potential threat to public health.

(Continue . . . )

Trying to predict the source of the next pandemic is a mug's game, but H9N2 constantly ranks in the top 10 zoonotic influenza A viruses the CDC has pegged as having some pandemic potential.

And many will be surprised to see that, in terms of risk of emergence, the H9N2 Y280 lineage is ranked higher than H5N1, while the G1 lineage is ranked only slightly lower.