M gene analysis of atypical strains of feline and canine coronavirus circulating in an Austrian animal shelter

Coronavirus-positive samples of faeces collected in an Austrian animal shelter from 12 cats and 10 dogs were analysed by reverse transcriptase-PCR With primers amplifying a segment of the M protein gene, and by sequence analysis. in addition, the samples were subjected to S gene typing, using primers that differentiated between feline coronavirus (Kov) types I and II. A phylogenetic analysis of the M gene sequences revealed not only clearly segregating canine coronavirus (CCoV) in the dogs, typical CCoV sequences and the recently described FCoV-Iike CCoV, but also at least two genetic clusters Of FCoV in the cats, one species-specific, the other more closely related to FCoV-Iike CCoV. The M gene sequences of these new feline strains had at most 88 per cent identity with the FCoV-like CCoV strain 259/01 and only up to 85 per cent with any FCoV sequence available in GenBank. In the phylogenetic tree they occupy an intermediate position between feline and canine coronaviruses.