Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events

Zhizhou Tan; Gabriel Gonzalez; Jinliang Sheng; Jianmin Wu; Fuqiang Zhang; Lin Xu; Peisheng Zhang; Aiwei Zhu; Yonggang Qu; Changchun Tu; Michael J. Carr; Biao He

VP1 genes of PyV were amplified using broad-spectrum primers from 186 positive samples and 151 then cloned into vectors. Four clones derived from each amplicon were sequenced to detect 152 potential co-infection of multiple PyVs in each positive sample. As a result, 180 of 186 bats were 153 confirmed to harbor one PyV, while the remaining 6 had a co-infection with two distinct PyVs 154 (detailed in S1 Table) . A total of 192 non-redundant partial VP1 sequences were obtained and 155 phylogenetically compared with VP1 sequences of known PyVs. Results showed that the 192 156 VP1 sequences had extensive diversity and could be classified into 44 clusters within the Alpha- 157 and Betapolyomavirus genera (Fig 2 and S1 Fig), 198 Among the newly identified single-host PyVs (Fig 3) , 19 PyVs shared 68-83% nt sequence 199 identities with the closest-known species or with each other in the LTAg coding sequences, Table) . They could therefore be considered novel PyV species, a proposal 206 further reinforced by additional correlation provided by the genetic selection analysis described The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/627158 doi: bioRxiv preprint Fig 1, with detailed information in S1 Table. 214 b Similarity in percentage of amplified bat cytb genes with the closest GenBank hit. The GenBank accession numbers of amplified bat 215 cytb genes are shown in S4 Table. 216 Phylogenetic analysis and identification of host-switching events. 217 In order to verify the host-switching events, an LTAg amino acid tree was constructed to and Rhinolophidae), indicative of another inter-family host-switching event (HS3 in Fig 4) .