H5N1 Bird Flu Circulating in Dairy Cows in the United States

The clade of highly pathogenic avian influenza (HPAI) viruses causing outbreaks in wild and domestic birds around the world, is now appearing in dairy farms across several U.S. states. These viruses recently caused morbidity and mortality in over 60 mammalian species, mostly carnivores, after consuming infected carcasses. Although cows were until recently not considered to be at risk of infection, the current outbreak demonstrates influenza remains unpredictable. 

The route of exposure of these dairy cows and the mode of virus transmission are still unknown. The virus RNA was found at high concentrations in raw milk. Several animal species at dairy farms and one farm worker were also affected. Initial data released by the USDA's Animal and Plant Health Inspection Service on GISAID show that the viruses in these cows, other animals and a farm worker are closely related. A mammalian adaptation marker (E627K) was noted in the farm worker who suffered from conjunctivitis. GISAID teams continue to facilitate the work of their U.S. based colleagues and assist with the timely sharing of the latest genomic data that will help to monitor the outbreak and stop it. 

Samples of hundreds of sequences from the outbreak are available from multiple mammalian and avian hosts in over 13 U.S. States. Latest trees are dated to 22. May 2024 featuring 18 new entries collected in three U.S. States (New Mexico, South Dakota and Texas) between 2024-03-20 and 2024-04-05. All of the 18 entries were submitted by USDA.

H5N1 HA subsampled tree US 2024-05-22
H5N1 NA subsampled tree US 2024-05-22
H5N1 PB2 subsampled tree US 2024-05-22

Subsampled phylogenetic trees with focus on recent U.S. H5N1 samples shown for HA, NA or PB2, respectively
(as of 22 May 2024)