Phylogenetic analysis of feline coronavirus strains in an epizootic outbreak of feline infectious peritonitis

Abstract

Background: Feline coronavirus (FCoV) infection is common. In a small percentage of cats, FCoV infection is associated with the fatal disease feline infectious peritonitis (FIP). Genetically distinct virulent and avirulent strains of FCoV might coexist within a cat population.

Objectives: To determine whether the strains of FCoV in FIP-affected cats are closely related or genetically distinct from the fecally derived strains of FCoV in contemporary-asymptomatic cats during an epizootic outbreak of FIP.

Animals: Four cats euthanized because of FIP and 16 asymptomatic cats.

Methods: This prospective outbreak investigation was initiated during an outbreak of FIP in cats within or rehomed from a rescue/rehoming center. Postmortem samples were collected from cats with FIP and contemporaneous fecal samples from asymptomatic cats. RNA was purified from tissue and fecal samples, FCoV gene fragments were reverse transcribed, PCR-amplified using novel primers, and sequenced. Sequences were aligned with ClustalW and compared with published FCoV sequences.

Results: FCoV RNA was detected in all 4 FIP cat postmortem samples and in 9 of the 16 fecal samples from contemporary-asymptomatic cats. Novel primers successfully amplified fragments from 4 regions of the genome for all FCoV-positive samples. Phylogenetic analysis showed that the FIP-associated strains of FCoV from the outbreak were very closely related to the fecally derived strains of FCoV from contemporary-asymptomatic cats.

Conclusions and clinical importance: Sequence analysis provided no evidence that genetically distinct virulent and avirulent strains of FCoV were present during this FIP outbreak.

Figure 1

Feline coronavirus genome with component genes, nucleotide scale, and for each of the 4 primer pairs their approximate binding sites, their target gene fragment, and the predicted amplicon size.

Figure 2

Phylogenetic analysis of nsp3 (A), nsp12 (B), nsp16 and surface glycoprotein (C), and small envelope protein and membrane glycoprotein (D) gene fragments for feline coronavirus strains analyzed in this study (in bold) and published feline coronavirus genome sequences (as NC_002306 is identical to AY994055 it was excluded from the analyzes) http://veb.lumc.nl/SARGENS/ accessed 28 May 2011. Phylogenetic trees were constructed by the neighbor‐joining method. Evolutionary distances are to the scales shown (number of substitutions per nucleotide). The data set was resampled 1,000 times to generate bootstrap percentage values, and values greater than 80% are given at the nodes of the tree. GenBank accession numbers are shown for all sequences. Fecal sample derived FCoV sequences from cats that were subsequently euthanized are marked with an asterix. CCoV, canine coronavirus; FCoV, Feline coronavirus; CLN, colonic lymph node.