UK Team Builds Genetic 'Toolbox' To Pinpoint Mutations Behind Equine Rotavirus A Breakthroughs

Every foaling season, breeding farms face a familiar and urgent problem: a foal that was bright at breakfast can become suddenly listless, stop nursing and develop watery diarrhea. One of the most common causes is equine rotavirus A (ERVA), a highly contagious virus that primarily affects foals under six months and can escalate rapidly without treatment.

The Martin-Gatton College of Agriculture, Food, and Environment at the University of Kentucky is tackling that challenge. Feng Li, a virologist at the university's Maxwell H. Gluck Equine Research Center, says the difficulty for farms and researchers alike is that ERVA is not static.

"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 maternally derived protection fades."

What the Project Will Do

Li's team is building a genetic "toolbox" — a set of lab tools and standardized virus references — to study ERVA in a controlled, repeatable way and connect laboratory findings to what happens on farms. The project has three connected aims:

• Field Sequencing: Collect ERVA from diarrheic foals and sequence full genomes to document which viral versions are circulating on farms.
• Reference Strain System: Produce standardized, reproducible reference strains so researchers can compare defined viral versions rather than an ever-changing field mix.
• Functional Antibody Testing: Run cell-culture neutralization assays to measure how well antibodies—whether from vaccinated mares or other sources—neutralize different strains, linking specific genetic changes to immune escape.

Why This Matters

Rotaviruses package their genome across 11 separate segments, a structure that allows the virus to accumulate variation and generate multiple co-circulating variants. That variation helps explain why vaccinations and maternally transferred antibodies reduce, but do not always eliminate, disease. By isolating specific mutations and testing them one at a time, the toolbox aims to answer the crucial question: Which changes materially reduce antibody or vaccine protection?

Li compares the challenge to lessons learned during the COVID-19 pandemic: vaccines can provide strong protection overall, but viral evolution can still produce breakthrough infections. Identifying the mutations that matter most will guide vaccine updates, diagnostics and biosecurity strategies tailored to the equine industry.

Practical Steps for Farms Today

While laboratory research proceeds, Li emphasizes that farms should continue proven prevention measures: vaccinate pregnant mares against ERVA, prioritize colostrum management, and maintain strict hygiene in foaling barns. The American Association of Equine Practitioners (AAEP) recommends a three-dose vaccination series for pregnant mares at eight, nine and ten months of gestation, combined with rigorous biosecurity and prompt veterinary care for sick foals.

Industry Impact and Funding

ERVA outbreaks impose significant burdens on Kentucky’s $6.5 billion equine industry and on horse operations worldwide—raising medical costs, consuming staff time and requiring intensive isolation and sanitation protocols. The research is supported by the U.S. Department of Agriculture’s National Institute of Food and Agriculture (NIFA), project award no. 2025-67016-44998. The investigators note that any opinions or conclusions are those of the authors and do not represent official USDA policy.

This story was originally published by Paulick Report on Dec 18, 2025, in the Horse Care section.