Strains recovered from Hanoi, Vietnam, 8 years ago and reported as aberrant strains (3 ) also group with subgenotype I1.
All recent serotine bat specimens clustered with genotype 5 (EBLV1) sequences, and homologies within subgenotypes EBLV1a and EBLV1b were 99.0%–100% and 99.2%100%%, respectively.
Direct sequencing of the RT-PCR amplified pRT-PCR amplified-nt coding region of the amino terminus of the nucleoproductsresulted in hofologies within subgenotypes EBLV1a (41 specimens) and EBLV1b (4 specimens) of 99.0%–100% and 99.2%–100%, respectively.
The phylogenetic trees show that the HBV 'CD1' isolates were grouped separately in one cluster within subgenotype C2, although the bootstrap values were relatively low (45% in Fig. 3A and 53% in Fig. 3B), reflecting the difference between the backbone sequence of the 'CD1' recombinant and that of the local subgenotype C2 strain.
The discrepant results could be attributed to cross-reactivity between the probes targeting IA and IB genomes due to high level of genetic sequence similarity shared by the two groups of subgenotype strains (Robertson et al. 1992).
When we phylogenetically analyzed the backbone sequences of 'CD1' and 'CD2' recombinants with the corresponding sequences of local subgenotype C2, we found that 'CD1' recombinants were grouped separately, instead of clustering among local C2 isolates within subgenotype C2 (Fig. 3).
In the part of the S gene (nt 155 832) encoding small surface protein (226 amino acid residues), HBsAg, two nucleotide substitutions were found in the B9 subgenotype isolate group that are not present in other isolate groups of B subgenotypes (Supplementary Figure 1).
In addition, the within subgenotype divergence of quasi-subgenotype B3 was 3.1 ± 0.1%, less than 4% to differentiate a subgenotype.
Furthermore, the within subgenotype divergences of these four subgenotypes were below 4% (Table 1).
The 3 and 2 strains were isolated from India and Japan, respectively, belonged to 2 distinct clusters within subgenotype IIIA.
One strain (strain 4) did not group with other subgenotypes but was closer to the BVDV1f.
