H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: introductions into the United States and reassortments, December 2021-April 2022

Authors: YOUK, SUNGSU - Orise Fellow; TORCHETTI, MIA - Animal And Plant Health Inspection Service (APHIS); LANTZ, KRISTINA - Animal And Plant Health Inspection Service (APHIS); LENOCH, JULIANNA - Animal And Plant Health Inspection Service (APHIS); KILLIAN, MARY - Animal And Plant Health Inspection Service (APHIS); LEYSON, CHRISTINA - Orise Fellow; BEVINS, SARAH - Animal And Plant Health Inspection Service (APHIS); DILIONE, KRISTA - Animal And Plant Health Inspection Service (APHIS); IP, HON - Us Geological Survey (USGS); STALLKNECHT, DAVID - University Of Georgia; POULSON, REBECCA - University Of Georgia; Suarez, David; Swayne, David; Pantin Jackwood, Mary

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2023
Publication Date: 8/2/2023
Citation: Youk, S., Torchetti, M.K., Lantz, K., Lenoch, J.B., Killian, M.L., Leyson, C., Bevins, S.N., Dilione, K., Ip, H.S., Stallknecht, D.E., Poulson, R.L., Suarez, D.L., Swayne, D.E., Pantin Jackwood, M.J. 2023. H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: introductions into the United States and reassortments, December 2021-April 2022. Virology. 587. Article 109860. https://doi.org/10.1016/j.virol.2023.109860.
DOI: https://doi.org/10.1016/j.virol.2023.109860

Interpretive Summary: Highly pathogenic avian influenza (HPAI) viruses of the subtype H5N1 clade 2.3.4.4b are a major threat to poultry and are spread by wild birds. These viruses were detected in North America late in 2021 and were found to be similar to viruses circulating recently in Europe and Asia. Disseminated by migratory wild birds, these viruses have spread across all the United States (US) impacting many wild bird species as well as poultry, with sporadic spillover into wild mammals. In this study full genome sequence analyses using 1,369 viruses detected in the US in wild birds, commercial poultry, and backyard flocks, from December 2021 to April 2022, was conducted. Separate introductions of H5N1 viruses were detected, and reassortments with North American low pathogenicity avian influenza viruses were common and predominated. In contrast to the prior 2014-2015 H5N2, HPAI major outbreak in the US, the current outbreak is characterized by predominantly independent wild bird introductions with only limited farm-to-farm spread. This study highlights the distinct epidemiology of the current outbreak and has implications for its control and management.

Technical Abstract: Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American wild bird avian influenza viruses. Reassortments of up to five internal genes generated a total of 21 distinct clusters; of these, six genotypes represented 92% of the HPAIVs examined. By phylodynamic analyses, most detections in domestic birds were shown to be point-source transmissions from wild birds, with limited farm-to-farm spread.