Full-length genome analysis of canine coronavirus type I

Abstract

Canine coronavirus types I (CCoV-I) and II (CCoV-II) are usually responsible for mild enteritis in dogs. While the CCoV-II genome has been completely sequenced, to date there are no complete genomic sequence data available publicly for CCoV-I. Thus, the aim of the present study was to analyze the full-length genome of a CCoV-I prototype strain that had been recovered from a dog with diarrhea in Italy. CCoV-I strain 23/03 has a genome of 30,000 nucleotides, excluding the 3' poly(A) tail, displaying the typical Alphacoronavirus-1 organization and the highest genetic relatedness to CCoV-II. However, two distinct features were observed in the CCoV-I genome: (i) the presence of an additional ORF between the spike (S) protein gene and ORF3a; (ii) the diversity of the S protein, which is more closely related to that of feline coronavirus type I and presents a furin cleavage site. The present study may contribute to a better understanding of the Alphacoronavirus-1 evolutionary pattern and may be paradigmatic of how coronaviruses evolve through gene losses, acquisition and exchanges among different members.

Keywords: Canine coronavirus type I; Dog; Genomic analysis.

Fig. 1

Schematic representation of the genomes of Alphacoronavirus-1 members depicting the genetic differences among the CCoV genotypes. Genes encoding for structural and non-structural proteins are shown in gray and white, respectively. ORF sizes are not drawn to scale. The arrows indicate the transcription regulating sequences preceding each CoV gene.

Fig. 2

Phylogenetic analysis of CCoV-I strain 23/03 and other members of the species Alphacoronavirus-1. Neighbor-joining trees are based on the 23,106-nt fragment spanning from the 3′ end of ORF3a to the very 3′ end of the viral genome (A), and on the spike (B), membrane (C) and nucleocapsid (N) proteins. For phylogenetic tree construction, the reference strains and GenBank accession numbers are as reported in Table 3. The distantly-related Betacoronavirus-1 canine respiratory coronavirus (CRCoV) K37 (JX860640) was used as outgroup. A statistical support was provided by bootstrapping over 1000 replicates. The scale bars indicate the estimated numbers of nucleotide (A) or amino acid (B–D) substitutions.