Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

Edward Cunningham-Oakes; Jack Pilgrim; Alistair C. Darby; Charlotte Appleton; Chris Jewell; Barry Rowlingson; Carmen Tamayo; Richard Newton; Fernando Sánchez‐Vizcaíno; Ivo Salgueiro Fins; Bethaney Brant; Shirley L. Smith; Rebekah Penrice-Randal; Simon Russell Clegg; Ashley P. E. Roberts; Stefan H. Millson; Gina L. Pinchbeck; PJ Noble; Alan David Radford

doi:10.1101/2022.10.03.510536

GenomicsbioRxivOct 3, 2022

Preprint

Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

Edward Cunningham-Oakes iD, Jack Pilgrim iD, Alistair C. Darby iD, Charlotte Appleton iD, Chris Jewell iD, Barry Rowlingson iD, Carmen Tamayo iD, Richard Newton, Fernando Sánchez‐Vizcaíno iD, Ivo Salgueiro Fins iD, Bethaney Brant iD, Shirley L. Smith iD, Rebekah Penrice-Randal iD, Simon Russell Clegg iD, Ashley P. E. Roberts iD, Stefan H. Millson iD, Gina L. Pinchbeck iD, PJ Noble, Alan David Radford iD

Abstract

Canine enteric coronavirus (CECoV) variants have an emerging role in severe outbreaks of canine gastroenteritis. Here we used syndromic health data from a sentinel network of UK veterinary practices to identify an outbreak of severe canine gastroenteritis. Affected dogs frequently presented with vomiting, diarrhoea and inappetence. Data from sentinel diagnostic laboratories showed similar seasonal increases in CECoV diagnosis. Membrane glycoprotein (M) gene sequence analysis implied wide geographical circulation of a new CECoV variant. Whole genome sequencing suggested the main circulating 2022 variant was most closely related to one previously identified in 2020 with additional spike gene recombination; all variants were unrelated to CECoV-like viruses recently associated with human respiratory disease. Identifying factors that drive population-level evolution, and its implications for host protection and virulence, will be important to understand the emerging role of CECoV variants in canine and human health, and may act as a model for coronavirus population adaptation more widely.

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