USDA genome study sheds light on H5N1 bird flu spreading to cows, but data gaps remain

The H5N1 virus infecting dairy cattle in several states was likely circulating in the animals for 4 months before scientists confirmed it in late March, and missing data and gaps in surveillance raise the possibility of unrelated chains of transmission. detected, a research team led by the U.S. Department of Agriculture (USDA), the National Veterinary Services Laboratory (NVSL), reported in a new preprint study.

In the first published report to weave together genetic sequencing findings with what is known from epidemiological research, the group said the movement of asymptomatic cattle to other states is likely driving transmission and that they are already seeing some variants with mutations that could lead to interspecies transmission. The group posted their findings yesterday on the preprint server. bioRxiv.

In other H5N1-related developments, the USDA announced last night that its tests on retail ground beef from affected states were negative, and two affected states, Michigan and Colorado, announced new emergency measures.

Data gaps and timeline questions

Phylogenetic analysis by genome sequencing suggests that there was a recombination event in late 2023 between the current highly pathogenic clade in wild birds and a low pathogenic wild bird strain, which produced the B3.13 genotype now circulating in dairy cows.

The NP gene acquired during recombination may have played a role in the emergence in cattle, they wrote, noting that the NP gene appears to allow influenza viruses to spread more easily in pigs.

Their analysis suggests there were up to five introductions of B3.13 from cattle to poultry, one to a raccoon, two to domestic cats, and three to wild birds. Although the findings are consistent with epidemiological findings of spread through the movement of herds to other states, they emphasized that gaps still exist. “We cannot exclude the possibility that this genotype is circulating in unsampled locations and hosts, as existing analysis suggests that data are missing and that surveillance may obscure transmission inferred using phylogenetic methods,” they wrote.

For example, they said the human infection B3.13 virus does not nest within cattle sequences, which could suggest that viruses from unsampled cows were the source of the infection or that evolution within the host was sufficient to give as a result a different phylogenetics. grouping. “More likely, however, asymptomatic transmission and lack of surveillance in epidemiologically important populations drove this pattern.”

They conclude that the potential for B3.13 to become endemic in livestock will influence the zoonotic risk of the virus and warned that if the low level of mammalian adaptations they are observing become dominant, the risk of interspecies transmission will be greater.

Scientists welcome new data

After the group released its report, Angela Rasmussen, PhD, a virologist at the Vaccine and Infectious Diseases Organization at the University of Saskatchewan, in X (formerly known as Twitter), praised the group for sharing critical data.

However, he said more information is needed, such as the tissue or type of sample each genome comes from, which is essential to understanding how cows transmit the virus and planning experiments to test transmission hypotheses. “This is an all-in situation and transparency and access to data is required for an effective response,” Rasmussen wrote.

Michael Osterholm, PhD, MPH, director of the Center for Infectious Diseases Research and Policy (CIDRAP) at the University of Minnesota, editor of CIDRAP News, also credited the USDA group for sharing its findings and said the scientific community has been eagerly awaiting critical information.

“This will help people better understand how the overflow developed,” he said.

Ground beef tests negative for traces of H5N1

In its update, the USDA said it tested 30 samples of retail ground beef from states where dairy herds tested positive for H5N1. The samples underwent polymerase chain reaction (PCR) testing, which can identify traces of the virus but not live virus, at the NVSL. They were all negative.

“These results reaffirm that the meat supply is safe,” the agency said.

The USDA added that PCR testing is being performed on muscle samples from cull dairy cows at select USDA Food Safety and Inspection Service (FSIS) slaughterhouse facilities and that its Agricultural Research Service is conducting a cooking study using a virus substitute in ground beef to examine the impact of different cooking temperatures on virus levels.

Michigan and Colorado announce emergency measures

Two states affected by H5N1 outbreaks in dairy herds yesterday announced emergency measures aimed at controlling the spread of the virus.

In Michigan, where recent outbreaks in dairy cows and massive outbreaks in poultry have been reported in seven counties, the Department of Agriculture and Rural Development (MDARD) Announced an extraordinary emergency measure requiring commercial dairy and poultry farms to implement biosecurity measures such as designating a biosecurity manager, establishing cleaning procedures, and maintaining a log book of vehicles and people who have crossed access points to the farms.

The order also prohibits all lactating cattle from being exhibited until the state has gone 60 days without new detections on dairy farms. Authorities also announced a similar restriction for poultry, but for 30 days with no new detections.

Separately, Colorado’s agriculture commission approved, and the state’s agriculture commissioner yesterday adopted, an emergency rule designed to limit the spread of H5N1. Colorado is the state most recently affected by the outbreak involving dairy cattle, and so far it is unclear how the cows were exposed to the virus.

In its advertisementThe Colorado Department of Agriculture said the emergency rule requires mandatory testing of lactating cattle moving interstate, which they said allows for implementation of the recent federal order, which went into effect April 29.