Identification of Novel Mammalian Viruses in Tree Shrews (Tupaia belangeri chinensis)

We used meta-transcriptomic sequencing to analyze plasma, oral and anal swab samples from 105 apparently healthy tree shrew individuals to identify potential zoonotic viruses. Eight mammalian viruses with complete genomes were identified, belonging to six viral families: Flaviviridae, Hepeviridae, Parvovirinae, Picornaviridae, Sedoreoviridae, and Spinareoviridae. We report, for the first time, a rotavirus in tree shrews. Of particular note were three viruses - hepacivirus1, parvovirus, and picornavirus - that exhibited low genetic similarity with previously reported viruses at the scale of whole genome and so were novel. Three other viruses - hepacivirus 2, hepatovirus A and hepevirus - exhibited high similarity to known viruses. Phylogenetic analyses revealed that the rotavirus and mammalian orthoreovirus identified in this study were closely related to known human and bat derived viruses, respectively.