Cornell virology experts are sequencing the bird flu virus that struck cows in the Texas panhandle last week, after work at Cornell and two other veterinary diagnostic laboratories found the highly pathogenic avian influenza (HPAI) virus in cattle samples, a first for this species. 

Sequencing of the virus may help scientists understand why it jumped to cows and how future outbreaks may be prevented. 

“When there is spillover of HPAI to a new species, especially to mammals, it is always concerning, as the virus may adapt and gain the ability to transmit between animals,” said Dr. Diego Diel, associate professor of virology in the Department of Population Medicine and Diagnostic Sciences and director of the Virology Laboratory at the Animal Health Diagnostic Center (AHDC). 

HPAI is well-known for its ability to infect various animal species. It is fatal among birds, where it attacks the gastrointestinal tract and the nervous system. Since 2022, the HPAI outbreak has killed millions of commercial poultry and wild birds, and the virus has been detected in many wild carnivores such as foxes that feed on carcasses of dead birds and often suffer the same fate. 

Currently there is no evidence that these mammalian species can transmit the virus to other animals, but its detection in ruminants is new. The USDA recently reported HPAI in a juvenile goat, but there were no previous reports of infection in cattle. 

When assistant professor of practice Elisha Frye, D.V.M. ’10, first got the call about a disease outbreak of unknown origin among dairy herds in Texas, she advised the caller to send samples to the AHDC for immediate testing. 

“The cows in Texas weren’t producing as much milk, and milk consistency was very different,” Frye said. The cows had mild respiratory signs, weren’t eating well and some had short-term, low-grade fevers.  

Several types of samples were sent to the AHDC, where Diel’s team conducted exploratory next generation sequencing (NGS) that detects viruses in a wide variety of species and samples, casting a wide net that gives scientists the ability to look for virtually anything. 

Frye received another call a few days later with an update: Grackles and pigeons were found dead at the same facilities, alongside some farm cats. While samples from cows were being sequenced, tests from the birds and a cat performed in the Molecular Diagnostics Laboratory at the AHDC came back positive for HPAI. Analysis of the NGS data then detected influenza sequences in the nasal swabs and milk samples from the sick cows. 

“Within five days of receiving the samples, we were able to identify HPAI in association with this outbreak in dairy cows,” Diel said. This was then confirmed by the National Veterinary Services Laboratory at the USDA.

The Cornell researchers detected the event around the same time as the Texas A&M Veterinary Medical Diagnostic Laboratory and the Iowa State Veterinary Diagnostic Laboratory.

When infected birds migrate through an area or farm, they can contaminate water or food sources with the virus. This is likely how the cows first encountered the virus. Whether all affected animals became infected through these sources or whether there was cow-to-cow transmission in herds is under investigation. Unlike birds, these cows did not die due to HPAI and recovered well. 

As the New York State Veterinary Diagnostic Laboratory, the AHDC supports the state’s animal agriculture and promotes the health of animals and humans by testing hundreds of thousands of samples a year. With its subject matter expertise, advanced testing capabilities and membership in the National Animal Health Laboratory Network, the AHDC is well suited to respond to such outbreaks.  

“We’re very familiar with the unique testing needs of the animal agriculture both in the state and through strong national connections with clients, referring veterinarians and alumni,” Frye said. 

“We will study how HPAI spilled over into dairy cows to understand why this outbreak happened,” Diel said. “There are a number of very important questions about its source and the risk of transmission to other animals and humans that need to be addressed.” 

The AHDC is encouraging veterinarians to send samples from cows and other animals for any disease outbreak for testing. Instructions on how to submit samples is available here online.

The methods used for sequencing and employed in this diagnostic investigation were supported by the USDA National Institute of Food and Agriculture and APHIS.

Melanie Greaver Cordova is director of communications and client relations at the Animal Health Diagnostic Center.