Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam

Van Nguyen, Dung; Van Nguyen, Cuong; Bonsall, David; Ngo, Tue Tri; Carrique-Mas, Juan; Pham, Anh Hong; Bryant, Juliet E.; Thwaites, Guy; Baker, Stephen; Woolhouse, Mark; Simmonds, Peter

The two Vietnamese pegivirus sequences from Rattus tanezumi grouped with a sequence previously reported from Rattus norvegicus (Figure 5a ). The amino acid p-distance between the obtained rodent pegivirus sequence and KJ950934 in the region 888-1635 (numbered relative to U22303) was 17.8% and the two viruses could be classified as members of species Pegivirus J (Figure 5b) , according in the update to the taxonomy of the Pegivirus genus [32] . The three HBV variants (from bat species Hipposideros pomona and Hipposideros larvatus) clustered with known bat HBV sequences (Figure 4) . The two bat HBV complete genome sequences comprised 3275 and 3302 nucleotides. As with other hepadnaviruses, the bat HBV genomes have four open reading frames (ORFs) encoding the surface (S), polymerase (P), core (C), and X proteins. A detailed comparison of the ORFs of these viruses with their closest sequences is shown in Table 2 . Bat031 consistently showed greatest sequence identity to KY905324 in all 4 ORFs. In contrast, Bat033 shared highest identity to KY905328 in the P and S ORFs, but was more similar to KY905324 and KY905327 in the ORFs encoding for X and C, respectively.