The 2.3.4.4b clade of the highly pathogenic avian influenza (HPAI) virus causing outbreaks in wild and domestic birds around the world, continues to spread in dairy farms across the United States since March 2024, with 45 human cases reported thus far. These HPAI viruses cause morbidity and mortality in over 60 mammalian species, mostly carnivores, after consuming infected carcasses. Although cows had not been considered to be at risk of infection, the current outbreak in the U.S. demonstrates influenza remains unpredictable.

The route of exposure of 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.

Over a thousand full virus genome sequences from this outbreak, collected from mammalian and avian specimens in at least 18 States are shared via GISAID EpiFlu. This includes specimen data collected from farm workers in California and poultry farm workers in Washington State made available by the U.S. CDC. For the latter, it appears that the NA segment may have been reassorted from avian H1N1 strains circulating in the U.S. in 2023.

Since the last update on 1 November, data from 99 specimens collected in the U.S. have been made available by the USDA. Although these submissions only provide the collection year and United States as a location, the phylogenetic trees place several of them close to the human specimens collected in California. The latest trees, based on representative subsamples, are dated to 8 November 2024.