New Avian Influenza Genotype Found in Dairy Cattle

A genotype of avian influenza type A H5N1 mostly found in wild birds and poultry has now been discovered in dairy cattle.

On January 31, the U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection Service’s (APHIS) National Veterinary Services Laboratories (NVSL) confirmed by whole genome sequence the first detection of H5N1 clade 2.3.4.4b, genotype D1.1 in dairy cattle.

This confirmation was a result of state tracing and investigation, following an initial detection on silo testing under the USDA’s National Milk Testing Strategy(NMTS) in Nevada. APHIS plans to publish a technical brief on the findings on its website and post the sequence data on GenBank, the National Institutes of Health’s genetic sequence database, in the coming week.

All previous detections of the virus in dairy cattle have been HPAI H5N1 clade 2.3.4.4b, genotype B3.13. Infection in dairy cows has become widespread in the U.S. since last March, affecting at least 957 herds in 16 states.

Genotype D1.1 represents the main genotype in the North American flyways this past fall and winter and has been identified in wild birds, mammals, and spillovers into domestic poultry.

Given H5N1’s circulation among wild and migratory bird populations and its knack for infecting a broad range of mammalian species, experts have expressed concern that H5N1 will eventually mutate into a strain capable of human-to-human transmission.

While the current public health risk is low, according to the Centers for Disease Control and Prevention (CDC), the agency says it is watching the situation carefully and working with states to monitor people with animal exposures.

Since April 2024, the CDC has confirmed H5N1 clade 2.3.4.4b infections in 67 people in the U.S. Twenty-three of these cases were associated with exposure to infected poultry, 40 were associated with exposure to infected dairy cows, and four sources of infection remain unknown with potential exposure to other animals such as backyard flocks, wild birds, or other mammals. While most of the human H5N1 infections have involved genotype B3.13, the D1.1 genotype was confirmed in one person in December.

APHIS says it continues to work with the Nevada Department of Agriculture by conducting additional on-farm investigation, testing, and gathering additional epidemiological information to better understand this detection and limit further disease spread.

Federal authorities say the detection does not change USDA’s HPAI eradication strategy and credit the NMTS for doing what it was designed to do, which is facilitate comprehensive H5N1 surveillance of the nation’s milk supply and dairy herds.