Molecular Screening and Characterization of Canine Coronavirus Types I and II Strains from Domestic Dogs in Southern Italy, 2019–2021

Canine coronavirus (CCoV) is a common agent of gastroenteritis in dogs, although some variants have been found associated with systemic and often fatal diseases. Distinct genotypes (CCoV-I and CCoV-II) and subgenotypes (CCoV-IIa and CCoV-IIb) are worldwide distributed. In Italy, CCoV infections have been occasionally evaluated, but information about the molecular epidemiology and the genomic features of currently circulating strains is limited. This study reports the detection and molecular characterization of CCoV strains from samples collected from 284 dogs in Italy between 2019 and 2021. CCoV RNA was detected in 39 (13.7%) dogs, as a single viral agent (5 animals, 12.8%) or with other viral pathogens (canine parvovirus types 2a/2b/2c; canine adenovirus type 1; norovirus GIV.2) (34 animals, 87.2%). A total of 48 CCoV strains were detected either alone (CCoV-I: 51.3%, CCoV-IIa: 20.5%) or in copresence (CCoV-I and CCoV-IIa, 23.1%); surprisingly, CCoV-IIb was not identified in this study. Five clusters of CCoV-I were detected, and their spike gene sequences showed the highest nucleotide identities with CCoV-I strains collected from Greece in 2008/2009 and from China in 2021. CCoV-IIa spike gene sequences (three variants) had the highest nucleotide identities with CCoV-IIa strains collected in Greece in 2008/2009 and in Italy in 2009/2011. Given the high CCoV diversity and the variable pathogenicity potential, we underline the need of further surveillance studies to increase our understanding of the epidemiology and evolution of these viruses.