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.

Since the last update update on 1. May 2024, genetic sequences of 302 (HPAI) H5N1 viruses collected from animals were added to GISAID EpiFlu, with 214 from 6 mammalian hosts (dairy cattle, goat, domestic cat, skunk, mountain lion and raccoon) collected in 13 U.S. States (Idaho, Kansas, Michigan, Minnesota, Montana, New Mexico, North Carolina, Ohio, Oklahoma, South Dakota, Texas, Utah, Washington) between 10. January 2024 and 4. May 2024. The new sequences suggest a shared common ancestor between Texas and New Mexico cattle sequences with earliest detection in March, before appearing in other states. Also, new raccoon and domestic cat samples clustering with the ongoing cattle outbreak sequences.