Figure 3

Phylogenetic analysis of intra-host viral quasispecies. A phylogenetic analysis of HBV haplotypes identified by BAsE-Seq identified six distinct clades (numbered 1 to 6) in S7.1. The black scale bar represents the expected number of substitutions per site and the blue scale bar represents the frequency at which a particular haplotype was identified in the sample. Amino acid changes that are found in ≥70% of clade members are listed within each clade. Amino acid changes that are unique to each clade are listed with an asterisk. Five out of six clades contain at least one amino acid change (red) that is likely to confer the ability to escape immune detection.