Metaviromics reveals a high diversity of viruses belonging to the Caliciviridae family in seal feces

Abstract Investigating potential zoonotic viruses in animal reservoirs is crucial to anticipate viral emergence. Seals can represent large populations of coastal mammals with unknown consequences on the microbiological quality of their surrounding environment. To assess this, we conducted a metaviromics analysis of feces collected from two species of seals in the North-Western Atlantic (Saint-Pierre et Miquelon archipelago). We focused on the Caliciviridae family, which regroups several genera with viruses infecting humans and other mammals, including marine mammals, but none identified in seals (Phocidae). Among the assembled sequences identified as Caliciviridae, there were four known genera (norovirus, sapovirus, vesivirus, and salovirus) and unknown, distantly related viruses. Complete or nearly-complete genomes could be assembled for each genus. Norovirus and sapovirus sequences from seals were diverse and likely represent several new genogroups or genotypes. Seal vesivirus formed a monophyletic group, representing a potential new species related to the canine vesivirus. Salovirus, which are fish viruses, were likely diet-derived, like the distant sequences which exhibited the hallmarks of caliciviruses and were more closely related to fish and reptile viruses. In conclusion, seals are a reservoir for a large diversity of Caliciviridae, some related to norovirus or sapovirus genotypes known to infect humans, and their impact on the quality of coastal water or shellfish should be further assessed. This study expands the knowledge on Caliciviridae genetic diversity and circulation in marine mammals.