Abstract
Coronaviruses (CoVs) can cross species barriers and endanger public health. Despite reports on their circulation and evolution in companion animals during the pandemic, postpandemic surveillance remains crucial. Therefore, during the first postpandemic year, 309 samples from 263 companion animals (cats and dogs) in Chengdu, China, were detected for CoVs using a universal assay based on Rdrp genes combined with one-generation sequencing. Four kinds of CoVs, including feline CoV (FCoV), canine CoV (CCoV), CRCoV, and SARS-CoV-2 (the first reported case of SARS-CoV-2 in a dog in mainland China, confirmed by viral nucleic acid detection and analysis), were detected with an overall positive rate of 21.7% (57/263); FCoV-I and CCoV-IIa were the dominant genotypes, and of these 57 positive cases, 71.9% (41/57) were in pets ≤12 months old. In CCoV-positive dogs, 72.2% (13/18) were coinfected with other viruses (primarily canine parvovirus [CPV], 76.9%; 10/13), while 13.9% (5/36) codetection with feline parvovirus (FPV). A 21-nt deletion in two FCoV S genes and a 145-nt deletion in one FCoV ORF3abc gene were identified, and recombination events at positions 919 and 1639 nt in two S genes were noticed. Notably, the amino acid variations in FCoV and CCoV S genes revealed distinct regional adaptations: FCoV strains showed unique substitutions (e.g., Ala/Ser129Leu) and a shift from RSRR to RARR furin cleavage motifs; CCoV strains in China exhibited significant differences from those in other countries. Phylogenetic analysis demonstrated that the S genes of FCoV and CCoV were closely related to those of the prevalent strains in China, whereas the S genes of CRCoV were closely related to that of human CoV (HCoV) OC43. These findings highlight the need for continued surveillance of CoV infection in companion animals (especially ≤12 months old) in the postpandemic era.