Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis

Abstract

Purpose: We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus.

Methods: Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms.

Results: Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified.

Conclusion: Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.

Figure 1

Phylogenetic analysis of the concatenated nsp12, nsp13, nsp14, S, 7b, and N gene sequences. The phylogenetic tree was reconstructed using the Bayesian method implemented in MrBayes 3.1. CCoV sequences were used as the outgroup for this analysis. Strains characterized in this study are labeled with triangles. Posterior probabilities are shown at the nodes of the phylogenetic tree. The branch to the CCoVs (outgroup) is shown with a dotted line, as it is very long and cannot be displayed at the same scale. Its branch length is 0.35 nucleotide substitutions per site and is indicated on the figure. Scale bar for the remaining branches is shown on the bottom length and represents 0.05 nucleotide substitutions per site.