Table 1.
PCR primers.
Figure 1.
Phylogenetic tree of the partial S-gene sequences (378bp) from 55 Nigerian HBV isolates identified in this study (marked •) and sequences recovered from GenBank (not marked).
Sequences retrieved from GenBank are denoted by their accession numbers and the source country of the isolates. Bootstrap values of major branches are shown.
Figure 2.
Phylogenetic tree of the 47 HBV/E and 2-HBV/A3 whole genome sequences from Nigeria (marked •) and GenBank references (not marked).
Sequences retrieved from GenBank are denoted by their accession numbers and the source country of the isolates. Bootstrap values of major branches are shown.
Figure 3.
Median joining network of the intra-host S-gene sequence variants identified in 22 individuals infected with HBV/E.
Each node represents a single sequence variant. Each color represents a single individual. The size of the node reflects frequency of the corresponding variant in the population.
Figure 4.
Phylogenetic tree of HBV sequence variants identified in 5 individuals with mixed genotype infections.
Sequences identified in this study are colored. Reference sequences retrieved from GenBank for genotypes HBV/E, HBV/G and HBV/D are shown in black. The consensus S-gene sequences for each individual are indicated with white arrows. All sequences that obtained from a single individual are shown using same color.
Table 2.
Divergence within the HBV S-gene quasispecies.
Figure 5.
Network of individuals sharing identical sequences.
Each node represents an individual and the link connects individuals that share at least one HBV variant. Blue nodes belong to village 1 (light for females, dark for males) and yellow nodes belong to village 2 (light for females, dark for males).
Figure 6.
Median joining network of the intra-host S-gene sequence variants identified in 2 individuals infected with HBV/A3.
Each node represents a single sequence variant. Each color represents a single individual. The size of the node reflects frequency of the corresponding variant in the population.
Table 3.
The number of negatively selected sites and specific sites under positive selection.
Figure 7.
Bayesian skyline plot showing the epidemic history estimated from the Nigerian HBV genotype E dataset.
The middle line is the median estimate of effective population size (log10) and the grey area shows the 95% highest posterior density intervals for this estimate. The most recent time is the time of collection for the most recently collected sequences (2007) and the oldest time shown is the lower limit of the 95% highest posterior probability density for the root height for all the sequences (1959).