Clade 2.3.4.4b of the highly pathogenic avian influenza (HPAI) virus causing outbreaks in wild and domestic birds around the world, continues to spread in dairy cows, poultry and other animals across the United States. Since April, the U.S. CDC confirmed 66 human cases through genome sequence analysis. In three of these cases, the amino acid substitution NA-S247N was identified that may slightly reduce susceptibility to the neuraminidase inhibitor oseltamivir in laboratory tests. The CDC also identified a different change in the polymerase acidic (PA) protein of a virus collected from a recently confirmed human case of H5N1 bird flu in California.

The current outbreak validates the unpredictability of HPAI viruses, as the route of exposure in dairy cows and mode of virus transmission remains unknown. The virus RNA was found at high concentrations in raw milk. Several animal species at dairy and poultry farms, as well as a growing number of farm workers are affected. Data from the USDA’s Animal and Plant Health Inspection Service show that the viruses in infected cows, other animals and the farm workers are closely related. A mammalian adaptation marker (E627K) was noted in only one farm worker so far, with nearly all farm workers developing mild eye symptoms, alongside respiratory symptoms. Although over a thousand genomes from this outbreak have been made available on EpiFlu, the lack of timely sharing of actionable data collected from farming animals remains a cause for concern.

On 28. December, the USDA released specimen data of the H5N1 virus (genotype B3.13) collected from raw and frozen feline pet food that according to the Oregon Department of Agriculture genetically matches the virus found in a house cat that died after eating the feline pet food.

On 30. December, the CDC released initial specimen data (HA and NA segments) from the first human cases of H5N1 in Iowa and Wisconsin, collected from farm workers that had been exposed to infected commercial poultry. Previously, the CDC released specimen data from the first U.S. case of severe illness of the HPAI virus collected in Louisiana on 11-Dec, which is of the same D1.1 genotype detected in poultry and wild birds, as well as recent human cases in Washington state and notably a severe human case in British Columbia. The latest trees, based on representative subsamples, are dated to 30. December 2024.