AAAP: Trends for H5 avian influenza in waterfowl
The emergence of H5N1 in poultry correlates with a shift in virus trends in waterfowl
14 January 2026
2 minute read
By: [Excerpts of poster presentations at the 2025 annual meeting of the American Association of Avian Pathologists]
Joseph Huitt and Troy Cline, California State University, noted that avian influenza viruses (AIV) circulate naturally in wild waterfowl, typically without causing disease. However, waterfowl are important vectors spreading AIV to susceptible populations where infection often causes severe disease or fatality. For example, a highly pathogenic avian influenza (HPAI) H5N1 virus emerged in North America in 2022 and has affected more than 130 million wild aquatic birds, and commercial and backyard poultry.
Early detection of AIV through surveillance is one measure to prevent or limit the extent of disease in humans or economically important poultry flocks. Surveillance efforts designed to identify or account for host species and environments that correlate with greater susceptibility to AIV infection are likely to be most effective.
AIV prevalence is monitored in hunter-killed waterfowl in the Sacramento Valley of California. Overall virus prevalence in waterfowl between 2014-2015 and 2021-2022 was 9.8%. Virus prevalence rates are highest in northern shovelers (20.9%) and lowest in wood ducks (1.3%).
HPAI H5N1 prevalence was 1.8% and 4.7% during the winters of 2022-2023 and 2023-2024, respectively. HPAI H5 was not detected in 2024 to mid-2025. In contrast to data prior to 2022, the emergence of HPAI H5N1 correlates with a shift in AIV prevalence trends. While AIV prevalence remains around 20% in northern shovelers, the American wigeon represents the species with the highest virus prevalence (19.6% in 2022-2023 and 28.5% in 2023-2024).
Philippine outbreak
H5 subtype high pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, H5 HPAI outbreaks have been reported in 2020, 2022, and 2023.
Zyne Baybay and researchers from BioAssets Corporation, the University of the Philippines Los Baños, the Department of Agriculture Regional Field Office III, the Philippine College of Poultry Practitioners, and the Department of Science and Technology, Philippines described the first publicly available whole genome sequences of an H5N1 HPAI virus from a case in Central Luzon, Philippines.
Samples were collected from a flock of layer chickens exhibiting signs of lethargy, droopy wings, and ecchymotic hemorrhages in the trachea with excessive mucus exudates. High mortality of about 95% was observed within the week. Days prior to the high mortality event, migratory birds were observed around the chicken farm. Pooled lung samples and oropharyngeal-tracheal swabs were taken from two chickens from this flock.
These samples were positive in quantitative RT-PCR assays for influenza matrix and H5 hemagglutinin (HA) genes. The same samples were subjected to whole virus genome amplification and sequencing. Phylogenetic analysis of the HA genes revealed that the H5N1 HPAI virus from Central Luzon belongs to the Goose/Guangdong lineage clade 2.3.4.4b viruses. Other segments also have high sequence identity and the same genetic lineages as other clade 2.3.4.4b viruses from Asia.
Collectively, these data indicate that wild migratory birds are a likely source of the 2021 H5N1 virus that caused outbreaks in the Philippines. Thus, biosecurity practices and surveillance for HPAI viruses in both domestic and wild birds should be increased to prevent and mitigate future HPAI outbreaks.
