Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
Excerpts from the maximum credibility trees for HIV evolution within subjects DS2 and DS7 with reconstructed mutations mapped to individual branches (labels comprising the ancestral residue, position in the V3 loop, and the derived residue).
These excerpts emphasize the lineages that attained a CXCR4-using ancestral genotype (FPR3.5). Branches are coloured with respect to the predicted FPR value (see legend inset). Vertical lines indicate the times of the first serum sample (dashed) and first positive MT-2 assay (solid), respectively. Open circles indicate the start of the branch carrying mutations promoting CXCR4 usage, which otherwise cannot be distinguished because other branches that do not carry such mutations have been collapsed. Percentiles indicate the fraction of the most recent sample that descend from the corresponding lineage.