Identification and characterization of a novel rodent bocavirus from different rodent species in China

Members in the genus <i>Bocaparvovirus</i> are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (<i>Rattus norvegicus</i>, <i>Mus musculus</i>, <i>Apodemus agrarius</i>, <i>Cricetulus barabensis</i>, <i>Rattus flavipectus</i>, <i>Rattus rattus</i> and <i>Rhombomys opimus</i>). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of <i>Ungulate bocaparvovirus 4</i>, was the most related virus to RoBoV, with 92.1–92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.