Molecular characterisation of the virulent canine coronavirus CB/05 strain

Abstract

This paper characterises a virulent strain (CB/05) of canine coronavirus (CCoV) isolated from the internal organs of pups that had died of a systemic disease without evidence of other common canine pathogens. High viral RNA titres were detected in the internal organs by a real-time RT-PCR assay specific for CCoV type II. Sequence analysis of the 3' end (8.7kb) of the genomic RNA of strain CB/05 revealed conserved structural as well as non-structural proteins, with the exception of a truncated form of non-structural protein 3b. The exceptional form was due to a 38-nucleotide deletion and a frame shift in ORF3b that introduced an early stop codon. By phylogenetic analysis of the structural proteins, the spike (S) protein was found to cluster with feline coronavirus type II strain 79-1683, whereas, the envelope (E), membrane (M) and nucleocapsid (N) proteins segregated together with the reference strain Purdue of transmissible gastroenteritis virus of swine.

Fig. 1

Neighbor-joining trees based on the S (a), E, (b), M (c) and N (d) proteins of group I coronaviruses. Accession numbers of the strains used for phylogeny are reported in Table 2. The trees are rooted on the distantly related group I coronavirus HCoV-NL63 (accession no. NC_005831) and drawn to scale. A statistical support was provided by bootstrapping over 100 replicates. The scale bars represent the numbers of amino acid substitutions.

Fig. 2

(A) Schematic representation of the 3′ end of the viral genome of CCoV strains CB/05 and BGF10. The 38-nt deletion in ORF3b of strain CB/05 is reported. (B) Comparison between the amino acid sequences of nsp3b of strains CB/05 and BGF10.