Second Strain of Bird Flu Found in US Dairy Cows: What It Means for Infection Prevention and Control

Avian flu

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On January 31, 2025, the Animal and Plant Health Inspection Service (APHIS) of the US Department of Agriculture (USDA) confirmed the first identification of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b, genotype D1.1 in dairy cattle through whole genome sequencing. This confirmation followed extensive tracing and investigation at the state (Nevada) level, after an initial detection during silo testing that formed part of the USDA’s National Milk Testing Strategy (NMTS).

A concerning development in the ongoing avian influenza outbreak has emerged: a second strain of the H5N1 bird flu virus has been confirmed in dairy cows in Nevada. This unexpected discovery raises new questions about the virus’s spread, transmission, and risks—not just for animal health but also for farmworkers and potentially the broader public.

“This is the first detection of this virus genotype in dairy cattle (all previous detections in dairy cattle have been HPAI H5N1 clade 2.3.4.4b, genotype B3.13), the announcement stated. “Genotype D1.1 represents the predominant genotype in the North American flyways this past fall and winter and has been identified in wild birds, mammals, and spillovers into domestic poultry.”

This finding underscores the growing threat of zoonotic diseases and the urgent need for enhanced surveillance, biosecurity measures, and cross-sector collaboration between human and animal health experts. The presence of multiple strains of H5N1 in dairy cows may indicate greater susceptibility in cattle than previously thought, making infection control efforts more critical than ever.

How Did This Happen? A Shift in Transmission Assumptions

Until now, federal officials believed the initial bird flu outbreak in cows originated from a single spillover event—the virus jumped from infected birds to cows in the Texas Panhandle. However, detecting a second distinct strain challenges this theory, suggesting that dairy cows may be more vulnerable to bird flu transmission than previously understood.

Influenza expert Richard J. Webby, PhD, a member of the St. Jude’s Research Hospital Faculty and the director of the World Health Organization (WHO) Collaborating Centre for Studies on the Ecology of Influenza in Animals and Birds, called this discovery a wake-up call:

“I thought the bird-to-dairy-cow transmission was an exceedingly rare event. This suggests that’s not the case, and we might fully expect it to occur more regularly.”

This revelation complicates containment efforts because officials still do not know precisely how the virus spreads between cows. Unlike poultry, which often contract H5N1 through direct contact with infected wild birds, the transmission mechanism in cows remains unclear. Could it be contaminated feed, milking equipment, or human activity on farms? Without clear answers, infection control strategies become more challenging to implement effectively.

Increased Risks to Farmworkers and Public Health

While the general public’s risk remains low, the emergence of a second strain increases concerns for dairy farmworkers and others who come into close contact with infected animals. Virologist Seema Lakdawala of Emory University warns that exposure could increase disease severity in infected workers.

The most severe human cases of H5N1 in North America have been linked to this strain, including:

• A Louisiana man died in January after exposure to infected backyard poultry
• A Canadian teenager who was hospitalized for more than two months and nearly died

The potential for increased virulence in humans raises alarms for infection preventionists in healthcare settings, especially for frontline workers who may care for infected patients. Healthcare facilities must be prepared for early detection and containment during human-to-human transmission.

Implications for Food Safety and Milk Supply

The Animal and Plant Health Inspection Service (APHIS) confirmed that the second strain was found in raw milk samples collected from silos as part of a national surveillance program. While pasteurization is highly effective at killing viruses like H5N1, the presence of the virus in raw milk raises food safety concerns.

Federal agencies should:
✔️ Expand milk testing programs to other dairy-producing states
✔️ Strengthen biosecurity measures on farms to prevent contamination
✔️ Ensure that farmworkers use personal protective equipment (PPE) to limit exposure

The USDA’s expanded milk surveillance is a step in the right direction, but more data is needed to determine the extent of this new strain’s spread in cattle.

What Infection Preventionists Can Do Now

This latest development is a reminder of the interconnectedness of human, animal, and environmental health. Infection prevention professionals should:

1️. Stay informed: Monitor CDC, USDA, and WHO updates about H5N1 developments.
2️. Educate farmworkers and healthcare staff: Ensure early symptom recognition and reporting among at-risk patients.
3️. Advocate for expanded surveillance: Push for enhanced biosecurity and monitoring efforts in the agricultural sector.
4️. Prepare for healthcare response: Review infection control protocols for potential human cases of avian influenza.

Speaking with Infection Control Today, Stacey L. Schultz-Cherry, PhD, a member of the St. Jude Faculty; and the deputy director of the World Health Organization Collaborating Centre for Studies on the Ecology of Influenza in Animals and Birds, said, “We really need to build this sense of community and that we're all in this together, and building those chains of communication, if you're a human practitioner, knowing what's happening sort of around you in the community, having those contacts in the veterinary in the agricultural world, precautions. It's the same thing with infection control. Infection control is great."

Final Thoughts: The Need for Urgent Action

Detecting a second H5N1 strain in dairy cows significantly shifts the outbreak’s trajectory. It challenges early assumptions about how the virus spreads, raises concerns about human exposure, and underscores the need for stronger infection prevention strategies in agriculture and healthcare settings.

As the situation evolves, infection preventionists must remain engaged, advocating for proactive measures to mitigate risks and rapidly respond to new developments. The longer we wait, the harder containment will become.