Identification of four novel subgenotypes (C13–C16) and two inter-genotypic recombinants (C12/G and C13/B3) of hepatitis B virus in Papua Province, Indonesia

► In this study, we identified and characterized four novel HBV subgenotypes (C13−C16) in Papua, Indonesia. ► Two inter-genotypic recombinants (C12/G and C13/B3), displaying recombination breakpoints in the 5′-terminus of the P gene, were also found. ► The distribution of indigenous subgenotypes C11−C16 was associated with particular language speakers in Papua. Four novel subgenotypes (C6, C11, C12, and D6) of hepatitis B virus (HBV) were identified in Papua, a multiethnic province of Indonesia. To characterize the HBV strains in Papua, serum samples collected from 515 indigenous inhabitants (mean age: 26.6±9.6years) in a previously unexamined area, Nabire, located in northern Papua, were used in the present study. Among 46 samples whose 1.6-kilobase (kb) HBV DNA sequence was amplified, 38 (83%) were typeable into known subgenotypes [B3 (n=4), C1 (n=2), C5, (n=1), C6 (n=5), C12 (n=13), and D6 (n=13)]. An analysis of the full-length sequence of the eight remaining HBV/C isolates whose sequence was either unclassifiable or uncertain within the 1.6-kb sequence showed no significant evidence of recombination in six isolates, and inter-genotypic recombination in two isolates (NAB20 and NAB46). By pairwise comparisons and a maximum-likelihood phylogenetic analysis, six non-recombinant isolates were considered significantly remote from known HBV/C isolates of subgenotypes C1−C12, and were classifiable into four novel subgenotypes (tentatively designated C13–C16). NAB20 and NAB46 were hybrids of C13/B3 and C12/G, respectively, displaying recombination breakpoints in the 5′-terminus of the P gene. Notably, the distribution of presumably indigenous subgenotypes C11−C16 was associated with particular language speakers in Papua.