University of Manitoba
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University of Manitoba and at National Centre for Foreign Animal Diseases, Canadian Food Inspection Agency
Genomic characterization of viruses in the Arctic and red fox feces from Canadian Arctic regions
In North America, global warming resulted in the expansion of red fox (Vulpes vulpes) in Arctic regions and led to changes in its ecology and diet. Climate change and the northern range expansion of red foxes may impact prey availability and habitat of Arctic foxes (V. lagopus). These carnivorous species harbor infectious disease agents, including the rabies virus. However, viral diversity data in Arctic and red foxes are limited. Since many viral outbreaks in humans were of animal origin, determining the diversity of viruses in non-human animal hosts will expand our knowledge on ecology, evolution, and potential host ranges of known and novel viruses. We performed whole-genome sequencing and virome analysis of feces and fecal swabs from 20 Arctic and 11 red foxes collected in Churchill, Manitoba between 2018-2020. Metagenomics followed by a targeted capture-probe enrichment was performed. Viruses belonging to Picornaviridae, Paramyxoviridae, Adenoviridae, Circoviridae, Parvoviridae, Anelloviridae, and Astroviridae families were discovered. Arctic foxes have more viral diversity than red foxes, and canine kobuviruses are the most prevalent, detected in 13 out of 31 foxes. To our knowledge, this is the first report of canine kobuvirus in Arctic foxes. The kobuvirus genome from Arctic fox shows 94% identity to a strain found in the USA, which suggests potential cross-species transmission between domestic dogs and foxes. Phylogenetic analysis of amino acid sequences derived from assembled genomes show clustering with rodent circovirus and seal parvovirus from rodents and seals, suggesting these viruses were likely acquired from the diet.