Characterization of the fecal virome in dogs with chronic enteropathy.

The fecal virome has been investigated in humans and various animal species using next generation sequencing. However, limited information is available about the fecal virome of dogs with chronic enteropathy (CE). We aimed to characterize the canine fecal virome of dogs with CE and compare it with the virome of previously analyzed healthy dogs.A total of 16 adult dogs; 8 healthy dogs (data from a parallel study) and 8 dogs with CE had fecal samples assessed by viral shotgun sequencing. Fecal samples were subjected to enrichment of viral nucleic acids prior to sequencing and metagenomic analyses. Characterization of the complete genome of a canine kobuvirus was performed by Sanger sequencing. An additional 21 healthy dogs and 14 dogs with CE were further analyzed for the prevalence of canine kobuvirus.Three fecal samples from dogs with CE contained in total 3 eukaryotic viral families. In contrast, 4/8 fecal samples previously identified from healthy dogs, contained 5 eukaryotic viral families with 2 families exclusive to this group. Bacteriophages were identified in all fecal samples from CE and healthy dogs. Canine kobuvirus was identified in one dog with CE, by shotgun sequencing, and the complete genome was then characterized. This kobuvirus was classified within canine kobuvirus group, being similar to strains from Korea and China. The larger prevalence study did not detect additional samples positive for canine kobuvirus. The fecal virome of dogs with CE differs in number and type of viral families from healthy dogs. The first Australian canine kobuvirus sequence was identified and characterized from a dog with CE.

Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics.

The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.