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Between-host HIV phylogeny. Shown is the maximum likelihood phylogeny inferred from 546 plasma HIV RNA sequences (circles) and 267 proviral DNA sequences (open diamonds) isolated from participants. Numbers on internal branches indicate bootstrap values supporting within-host monophyletic clades. The scale is in estimated substitutions per nucleotide site. The phylogeny is midpoint rooted. The black dot represents the HIV-1 subtype B reference strain HXB2.
