Faecal virome of cats in an animal shelter

Abstract

We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.

Fig. 1.

Distribution of sequence reads to different viral families in six cat faecal pools.

Fig. 2.

(a) Genomic organization of feline astroviruses (FAstV-D1, -D2 and -D3) (distance in nt). (b, c) Neighbour-joining phylogenetic analysis based on amino acid sequences of Cap (b) and RdRp (c) regions of feline astroviruses. Feline astroviruses identified in this study are marked with black diamonds.

Fig. 3.

(a) Genomic organization of feline bocaviruses (distance in nt). (b, c) Neighbour-joining phylogenetic analysis based on amino acid sequences of NS1 (b) and VP1 (c) regions of feline bocavirus. Feline bocaviruses identified in this study are marked with black diamonds.

Fig. 4.

(a) Genomic organizations of the novel feline cylcovirus. The locations of putative Rep and Cap genes are indicated by arrows. The stem–loop is also shown. (b) Neighbour-joining phylogenetic analysis based on amino acid sequences of Rep of feline bocavirus. CSF, cerebrospinal fluid. Feline cyclovirus identified in this study is marked with a black diamond.

Fig. 5.

Genomic organization showing the ORFs and conserved protein domains of fesavirus-1 and -4, and other RNA viruses with related genomic organization. CPro, cysteine protease; S3H, superfamily 3 helicase. CrPV, cricket paralysis virus; RHDV, rabbit haemorrhagic disease virus; SJNNV, striped jack nervous necrosis virus. Fesavirus-1 and -4 in this study are marked with arrows.

Fig. 6.

Maximum-likelihood phylogenetic analysis based on the divergent amino acid sequences of RdRp in the present study and the members of the picorna-like virus supergroup presented in a previous study (Koonin et al., 2008). The best blastp hits of the RdRp sequences in this study and five RdRp representative sequences from the family Hepeviridae were also included in the alignment. The six main clades identified and abbreviations of viruses are labelled according to their previous designations (Koonin et al., 2008). Bootstrap values >50 are indicated on the tree.