Every foaling season, a familiar concern can surface on breeding farms: a young foal that was alert at breakfast is suddenly lethargic, refusing to nurse and passing watery diarrhea. One of the most common causes is equine rotavirus A (ERVA), a highly contagious virus that primarily affects foals younger than six months and can become serious quickly without treatment. This is where the University of Kentucky Martin-Gatton College of Agriculture, Food and Environment steps in.
Feng Li, Ph.D., a virologist at the University of Kentucky Maxwell H. Gluck Equine Research Center, says the long-running challenge is that ERVA is not a fixed target.
"It's an old virus, but it keeps changing," Li said. "Those changes can add up in ways that matter on farms. Vaccines and mare antibodies can lower risk, yet infections still break through in some settings, especially as foals age and protection fades."
Looking inside the 'genetic toolbox'
Li is taking a step that has long been missing in equine rotavirus research: building a genetic toolbox that allows scientists to study ERVA in a controlled, repeatable way and connect what they see in the lab to what happens in barns.
Rotaviruses carry their genetic instructions in 11 separate segments, a structure that allows them to change in ways that are difficult to track. Over time, ERVA can accumulate genetic variation and produce multiple variants in the field.
That matters because immune protection is not simply "on" or "off." Vaccinated mares pass antibodies to her foal through colostrum. This can reduce severe disease in very young foals - a strategy many farms still rely on. Even so, ERVA-associated diarrhea continues to appear, including in older foals.
Li compares the problem to lessons learned during COVID-19. Vaccines can provide strong protection, but shifting viruses can still pose challenges.
"You can have a vaccine and still see breakthrough infection," Li said. "The question is why, and which viral changes are linked to that slip."
The project centers on three connected efforts.
First, Li's team plans to collect ERVA from diarrheic foals and map their full genomes to show which versions are circulating.
Next, the lab aims to build a research system that produces standard reference forms of ERVA for study. This will allow them to work with defined virus versions rather than a constantly changing mix. With that foundation, the team can compare strains side-by-side and ask focused questions about which natural changes matter.
The final step links genetics with functional antibody testing - cell culture studies measuring how well antibodies neutralize different ERVA strains. This step is key, Li said, because it links "what changed" to "does it change protection."
The goal is to identify the genetic changes that help ERVA evade immunity and identify antibody levels most associated with protection - information that can guide future countermeasures.
Why rotavirus A gets the focus
ERVA is widespread globally and remains the virus most horse operations plan around each year. A system addressing the problem at the genetic level, rather than relying solely on vaccines, would benefit the entire industry.
"Right now, we don't have good lab tools to study how rotavirus A mutates and how those mutations affect immunity. That's what we're building here at the University of Kentucky," Li said. "This toolbox will let us isolate different rotavirus A strains, read their full genome sequences and see how each mutation affects virus behavior. We're creating a system where we can introduce changes we see from naturally occurring field isolates into the virus one at a time and ask: Does this make it escape antibodies or vaccine-mediated protection?"
ERVA outbreaks pose major challenges for Kentucky's $6.5 billion equine industry. Infections can strain staff time, increase medical costs and force farms into intensive isolation and sanitation protocols.
At the same time, the basic biology of rotavirus makes control difficult. Li notes that vast numbers of virus particles can be shed in diarrhea and that only a small dose may be needed for fecal oral transmission. ERVA can also spread through contaminated hands, boots and equipment if biosecurity slips.
Li emphasized that research takes time, and farms still need practical steps now. Veterinary groups commonly recommend vaccinating pregnant mares against ERVA and prioritizing colostrum management and hygiene in foaling barns. The American Association of Equine Practitioners recommends a three-dose vaccination series for pregnant mares at eight, nine and 10 months of gestation, paired with strong biosecurity and prompt veterinary care for sick foals.
"This toolbox we are working on will let us isolate different rotavirus A strains, read their full genome sequences, and see how each mutation affects antibody protection," Li said.
This work is supported by the National Institute of Food and Agriculture (NIFA), project award no. 2025-67016-44998 from the U.S. Department of Agriculture's National Institute of Food and Agriculture. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and should not be construed to represent any official USDA or U.S. Government determination or policy.
