The clade of highly pathogenic avian influenza (HPAI) viruses causing outbreaks in wild and domestic birds around the world, is appearing in dairy farms across several U.S. states since at least April 2024. 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 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 were 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 only one farm worker so far, and all farm workers suffered from conjunctivitis. In recent human cases, workers have 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.

Over a thousand full virus genome sequences from this outbreak, collected from mammalian and avian specimens in at least 18 States, have thus far been made available in GISAID EpiFlu. Since the previous update on 12 August 2024, sequences from 30 new specimens collected in nine U.S. States (Colorado, Georgia, Idaho, Kansas, Kentucky, Minnesota, Oklahoma, South Dakota and Texas), between 2024-04 and 2024-07-24, have been submitted by the USDA. These specimens cover different types of milk, ice cream and cheese from retail dairy products. While viral RNA was found in 17% of specimens, all specimens tested negative for live virus as described in this preprint publication by Suarez et al titled "Testing of retail cheese, butter, ice cream and other dairy products for highly pathogenic avian influenza in the US." This latest submission includes first dairy cow specimens collected in Georgia, Kentucky and Oklahoma. All trees, based on representative subsamples, are dated to 15 August 2024.

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 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.