A novel kirkovirus may be associated with equine gastrointestinal disease.

Abstract

BACKGROUND: Many cases of equine enterocolitis are suspected to be infectious in nature, but no pathogen is identified in many cases. OBJECTIVES: Perform next-generation sequencing on faeces collected from cases of equine enterocolitis for the presence of novel viruses and determine if an identified novel virus is associated with cases of equine enterocolitis. STUDY DESIGN: Retrospective cohort study. METHODS: Next generation sequencing was performed targeting viral genomes from n = 13 pooled faecal samples (n = 5 horses/pool) with enterocolitis. Subsequent qPCR was performed targeting the highly conserved replication-associated segment of the identified kirkovirus genome on n = 218 samples (collected between 2020 and 2025), divided into 3 groups [colitis (n = 87), colic (n = 56) and clinically normal (n = 75)]. Additional qPCR was performed on a subset of cases targeting the less well-conserved open reading frame 3 (ORF3) segment of the kirkovirus genome. In situ hybridisation and electron microscopy on kirkovirus-positive samples were also performed. RESULTS: Next generation sequencing identified a novel kirkovirus in 5/13 pooled samples from enterocolitis cases, including the full genome. There was an association between the novel kirkovirus and enterocolitis, specifically in two farm outbreaks. A retrospective case review of kirkovirus-positive cases suggested a seasonal pattern, with all cases presented in the autumn, winter, and spring. Additionally, there was an association with small colon impactions, with 25% of positive cases having a small colon impaction. MAIN LIMITATIONS: Whether equine kirkovirus is a cause of equine infectious enterocolitis remains unknown. There are limited available tissue samples from positive horses and efforts to definitively identify equine kirkovirus in the gastrointestinal tract tissues have been unsuccessful. CONCLUSIONS: We identified a novel equine kirkovirus that is associated with outbreaks of enterocolitis and small colon impactions. It is rarely identified in clinically normal populations. Further study must be performed to determine if the virus infects equine tissues and/or causes disease.