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 16 human cases reported thus far. These HPAI viruses recently caused 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 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.

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 last update on 27 September, two new specimens collected from farm workers in California on 30-Sep and 1-Oct, have been made available by the U.S. CDC. The latest trees, based on representative subsamples, are dated to 7 October 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.