The Agriculture Department is ordering the dairy industry to test milk-producing cows for infections from highly pathogenic avian influenza, or HPAI H5N1, before they’re moved between states, federal officials announced Wednesday.

USDA’s move to ramp up testing requirements for HPAI H5N1 comes after the Food and Drug Administration disclosed Tuesday that samples of pasteurized milk that had been sold on grocery store shelves had tested positive for the virus, prompting further research to verify if the positive test was caused by lingering dead “virus particles” or live infectious virus.

It also comes after federal authorities say they have now spotted some “isolated” but worrying changes to the virus in cows, which are believed by U.S. officials to have contracted the virus from wild birds.

State veterinarians and labs that find that cattle have tested positive for the virus will be required to report their results to the USDA. Farms with cows that are sick will need to undergo investigations before moving cattle across state lines.

“The primary focus of the order, initially, will be lactating cattle. But we will certainly have the opportunity to expand beyond that as necessary,” Mike Watson, head of the USDA’s Animal and Plant Health Inspection Service, told reporters Wednesday.

Officials previously said that the unprecedented spread of the virus among dairy cattle likely traces to a single spillover event from wild birds, based on an analysis of genetic sequences collected from sick cattle.

Since then, genetic data and investigations suggest the virus has spread to infect cows across at least eight states and a human dairy worker in Texas. Egg farms from Texas and Michigan are also suspected to have been infected by virus that spread from cows, adding to millions of poultry culled because of infections from wild birds.

“Those farms have been in close proximity to affected dairy farms. And so there could be lateral flow from the dairy farms to these poultry operations, to these egg laying operations. This could be such things as transfer of the virus through fomites, such as on clothing or on vehicles,” National Milk Producers Federation chief science officer Jamie Jonker said at recent Swine Health Information Center webinar.

The virus was not initially found in the respiratory tract of most infected cows, officials said, suggesting it is not spreading through the air between cows like other kinds of influenza. Instead, H5N1 HPAI in the current outbreak has been found almost exclusively in raw milk and the cow organs that produce it. Officials think the virus may have spread between cows during the milking process on farms, through surfaces contaminated with infected raw milk. 

However, Watson said that at least one cow headed to slaughter has now been found with signs of the virus in its lung tissue. The cow was condemned by USDA inspectors and did not enter the food supply, Watson said.

Federal scientists have also found a mutation in another sick cow from Kansas that had a genetic change that adapted the flu to spread better in mammals.

“The one sequence shift and the one dairy cow with H5N1 in the lung tissue so far appear to be isolated events. However, the novel movement of H5N1 between wild birds and dairy cows requires further testing,” Watson said. 

Cows mostly have been recovering from the virus without dying, Watson said. That’s in stark contrast to the kind of mass die-offs seen in birds and some other species. However, dairy industry officials have previously said some cows have yet to recover their ability to produce milk, raising concerns of long-term issues for some cattle.

“We need time to develop an understanding to support any future courses of action. So this federal order is critical to increasing the information available for USDA,” said Watson.

H5N1 HPAI virus found in pasteurized milk

While health authorities say they think previous work pasteurizing eggs for HPAI H5N1 and milk for other germs suggests the process will be enough to eradicate the danger from any lingering traces of the virus found in milk, they say studies are also ongoing now to verify that pasteurized milk remains safe.

“A positive PCR test does not necessarily mean that the sample contains an intact infectious pathogen and that additional testing is required to determine whether intact pathogen is still present and if it remains infectious,” Don Prater, head of the FDA’s food safety center, said at the news briefing.

This involves what FDA says is the “gold standard” for checking if the virus that they found is potentially infectious, taking the H5N1 HPAI particles they found and seeing if it will grow in chicken eggs. 

Research backed by the National Institutes of Health has also found H5N1 HPAI fragments in milk. Early testing of those samples suggests the virus in the pasteurized milk was not infectious, trying to grow the virus in cells and chicken eggs.

“While this is welcome news, the effort studied a small number of samples that is not necessarily representative of all retail milk. So to really understand the scope here, we need to wait for the FDA,” said National Institute of Allergy and Infectious Diseases Director Dr. Jeanne Marrazzo.

Prater said that the samples had come from a national survey of the U.S. milk supply, but declined to share details of where they had been found and what kinds of milk have tested positive. 

“We don’t have information yet to share but it will be coming out very shortly and that’s what I can share at this point,” said Prater.

Milk from cows known to be sick with symptoms of the virus is not entering the supply chain, Prater said. But it is possible that the virus could be making it into the supply chain from other sources, Prater said, possibly from cows that are not yet symptomatic or have previously recovered.

FDA has some data that could help investigators trace where the milk with the virus made it into the food supply, Prater said.

“Right now we will be able to look at information that we are collecting as part of this. Our traceability information is good, but it’s not perfect,” said Prater.