Article Figures & Data
Figures
- FIG. 1.
Phylogenetic tree analysis of full-length sequences of 13 Paharia HBV isolates, along with reference sequences of HBV strains belonging to different genotypes (A to J) derived from GenBank, including 3 sequences of HBV strains from nonhuman primates. HBV sequences from GenBank are indicated by their genotypes, followed by accession numbers and countries of origin, while the sequences determined in this study are indicated by isolate numbers starting with “T.” Bootstrap values are given at the internal nodes.
- FIG. 2.
Phylogenetic tree showing the subgenotypic distribution of HBV strains belonging to genotype D. The tree was formed by 52 full-length reference sequences of HBV strains belonging to different subgenotypes of D, namely, D1 to D7, as indicated by their accession numbers followed by countries of origin. Thirteen Paharia HBV sequences determined in the study are indicated by respective isolate numbers beginning with “T.”
- FIG. 3.
Estimation of divergence times of subgenotypes D1 to D5 of HBV. The tree was constructed by the DNAMLK program of the PHYLIP package, using 64 indel-free HBV sequences of different subgenotypes of D, derived from GenBank, along with 13 Paharia HBV sequences. Reference sequences are indicated by their specific subgenotypes followed by accession numbers, and the tribal sequences are indicated by respective isolate numbers beginning with “T.”
Tables
- TABLE 1.
Primers used in this study
Primer Sequence (5′-3′) Location (nt) F1 CACAAGAGGACTCTTGGACT 1653-1672a F2 CTGCACTCAGGCAAGCAATT 2058-2077a F3 CGCCTCATTTTGTGGGTCAC 2801-2820a F4 CTCAGGCCATGCAGTGGAA 3164-3182a F6 TGCCGATCCATACTGCGGAA 1259-1278a F9 TTTACCTCTATTACCAATTTTC 789-810b F10 GACCACCAAATGCCCCTATC 2298-2317b R1 CCACCTTATGAGTCCAAGG 2457-2475a R2 AAATTACCACCCACCCAGG 2109-2127a R3 AACTGGAGCCACCAGCAG 57-74a R4 AGAGGACAAACGGGCAACA 462-480a R5 AAAGCCCAAAAGACCCACAAT 997-1017a - TABLE 2.
Baseline characteristics of HBsAg-positive Paharia individuals participating in the study
ID Age (yr) Sexa ALT level (IU/liter) AST level (IU/liter) HBV DNA concn (copies/ml) Presence of HBeAg Presence of anti-HBeAg T1029 35 F 26 38 <250 Negative Positive T1159 38 M 38 54 <250 Negative Positive T1178 61 F 24 41 14,100 Negative Negative T1181 38 F 26 44 9,190 Negative Positive T1195 19 M 54 80 <250 Negative Positive T1234 40 M 62 52 1.42 × 107 Positive Negative T1245 21 M 31 55 1,967 Negative Negative T1258 35 M 16 27 <250 Negative Positive T1360 60 M 31 93 5.05 × 106 Positive Negative T1434 20 M 31 50 2.25 × 107 Positive Negative T1469 10 M 14 28 2.31 × 106 Negative Negative T1503 64 M 23 52 2.40 × 107 Negative Negative T1545 70 F 22 37 4.59 × 107 Positive Negative T1562 14 M 19 38 1.90 × 104 Negative Negative T1667 35 M 31 44 1.60 × 104 Negative Negative ↵ a F, female; M, male.
- TABLE 3.
Mean intersubgenotypic divergence among the subgenotypes of HBV genotype D
Subgenotype Intersubgenotype divergence (%)a D1 D2 D3 D4 D5 D6 D1 D2 2.53 D3 3.19 3.39 D4 3.88 4.05 3.89 D5 4.68 4.82 4.85 4.81 D6 3.55 3.73 2.5 4.19 5.16 D7 4.25 4.61 4.52 3.51 5.38 4.94 ↵ a The genetic distances of D5 from the other subgenotypes of D are indicated in bold. There was no divergence for the D7 column.
- TABLE 4.
Conserved amino acid residues in four ORFs of Paharia HBV isolates compared with the previously reported residues at the same positions in different subgenotypes of D (D1 to D7)
a D5 subgenotype-specific residues are shaded.
b The conserved domains of the HBV polymerase open reading frame are indicated as follows: tp, terminal protein domain; sp, spacer region; rt, reverse transcriptase domain; rh, RNase H region.
c The maxsjor amino acid is indicated in bold.
