HPAI H5N1 Bird Flu Outbreak in the United States and bordering countries

The clade 2.3.4.4b of the highly pathogenic avian influenza (HPAI) virus continues to spread globally among wild and domestic birds. In the United States, it is actively transmitting through dairy cows, poultry, other animal species, and exposed farm workers.

Recent situation:
Authorities in Washington State reported three human cases of H5N1 infections (EPI_SET_261109up) including the first U.S. fatality of 2026. Sequences from two of those cases carry a new mutation (A676T) in PB2 segment and cluster with recent samples from Idaho, Utah. The sequences can be visualized on the phylogenetic trees below.

Background:
Since April 2024, the U.S. CDC has confirmed 74 human cases through genomic sequencing. USDA data reveals a close genetic relationship between the viruses found in infected dairy cows, other farm animals, and humans. Notably, high concentrations of the virus have been found in raw milk as the number of affected farm workers grows.

On 06 January 2025, the CDC announced the first U.S. human fatality involving a patient from Louisiana that had been exposed to non-commercial backyard poultry and wild birds. Concurrently, the USDA shared data linking deceased animals at a Washington wildlife sanctuary and raw feline pet food samples to B3.13 genotype.

On 11 February 2025, the USDA released specimen data confirming the first detection of D1.1 genotype in dairy cows. This same genotype was subsequently identified in samples from farm workers in Iowa, Wisconsin, Washington, and British Columbia, Canada.

Meanwhile, the B3.13 (ggFlu genotype E.2) lineage has expanded beyond dairy cows. It has been detected in captive American mink as well as in recent cases from Idaho and Utah that present mutations associated with antigenic drift/escape and mild drug resistance. 

Continued genomic surveillance and sequence sharing are critical to monitor the outbreaks closely and to mitigate identified human and animal health risks.

The latest trees, based on representative subsamples, are dated to 9. November 2026