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 two farm workers 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 the farm workers are closely related. A mammalian adaptation marker (E627K) was noted in one farm worker, both farm workers suffered from conjunctivitis. In the most recent human case, a third worker developed mild eye symptoms alongside respiratory symptoms.  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.

Full virus genome sequences are available from hundreds of samples collected from mammalian and avian hosts in at least 13 States. Since the previous update on 15 July 2024, one new sample collected from a farm worker in Colorado on 2024-07-11 (EPI_ISL_19263923) was submitted by the U.S. CDC.  Latest trees are dated to 16 July 2024 featuring a representative subsample.

This collection includes many virus sequences from dairy cows, but also closely related viruses detected in poultry and wild birds and in mice, cats and other mammals as well as the 3 recent human infections. Although metadata such as sampling date and location are unfortunately missing from recent datasets, the available data allow a close watch on mutations that may arise as a consequence of virus adaptation to new hosts.

H5N1 HA subsampled tree US 2024-07-16
H5N1 NA subsampled tree US 2024-07-16
H5N1 PB2 subsampled tree US 2024-07-16

Subsampled phylogenetic trees with focus on recent U.S. H5N1 samples shown for HA, NA or PB2, respectively
(as of 16. July 2024)