Avian Influenza: An Overview of the H5N1 Virus in North America

After three years of avian influenza outbreaks and the culling of hundreds of millions of poultry, one question keeps coming up: What is the main cause of these epizootics? Research published this fall provides some answers.  

Backyard flocks as sentinels

By cross-referencing the analysis of more than 1,800 viral genomes with Atlantic and Pacific migration routes, an international team has shown that the North American H5N1 avian influenza epizootic was repeatedly fueled by rapid spread among wild birds, which then spread in step with migration patterns. Backyard flocks appear to act as “receptors” for persistent viral pressure in avifauna. The study also reveals that cases detected in backyard flocks appear, on average, nine days earlier than those identified in commercial poultry farms. This means, in particular, that backyard flocks must be given greater consideration, as they can serve as sentinels providing early warning signals.  

Multiple Introductions

Another study confirms the role of avifauna in the avian influenza epizootic. Phylodynamic analysis of 2,955 viral genomes shows significant diversification of A (H5N1) viruses through reassortment with low pathogenicity avian influenza viruses. The results reveal repeated replacements of ancestral strains by their direct descendants, resulting from reassortment with viruses already circulating in wildlife, indicating a cumulative increase in viral replication capacity. Spatio-temporal modeling identified critical geographic areas that facilitate transcontinental spread and demonstrated genotype-specific host dynamics. This scenario is consistent with the migration phenology of Anatidae (geese, swans, ducks, etc.) and Charadriiformes (oystercatchers, plovers, snipes, stilts, etc.). Outbreaks in poultry farms reflect “airborne” transmission rather than high-level spread from farm to farm.  

Very high viral pressure

Between March 2024 and June 2025, new genotypes of the highly pathogenic H5N1 avian influenza virus (clade 2.3.4.4b) were identified across the Atlantic. These caused unprecedented outbreaks, affecting poultry farms and dairy cattle operations, as well as resulting in human infections. The United States reported 13,225 positive wild birds, 175 million affected poultry, and 1,075 affected dairy herds across 17 states. Transmission from wild birds to poultry (genotype D1.1) and from wild birds to cattle (B3.13 and D1.1) is placing a heavy strain on the health surveillance system: the zoonotic risk is considered low for the general population, but heightened vigilance is required for exposed professionals. The data are consistent with the 2021–2025 epizootic, which was initiated by migratory birds spreading the virus to domestic livestock operations and then sustained by sporadic local transmissions.