FIG 2.

Maximum likelihood phylogeny of 185 FL HIV-env sequences obtained from postmortem brain and lymphoid tissues from 14 PWH donors enrolled as part of the NNTC cohort. Each taxon is an individual env sequence. Each sequence is labeled with the participant’s number, followed by the tissue type (FC, frontal cortex; OCC, occipital cortex; LN, lymph node; SP, spleen). Individual participants are also represented by colors, and different tissues within a participant are represented by a shade of that color. Nonintact env sequences are indicated for APOBEC hypermutations (HM), deletions (DEL), and frameshifts due to stop codon (STOP), following the sequence name. Sequence nodes are colored based on in silico Geno2Pheno predictions of coreceptor tropism (see Materials and Methods). Cutoffs for classifying sequences based on the X4 FPR were defined as follows: less than 2% for likely CXCR4-tropic, 2% to 10% for an “indeterminate” range, and greater than or equal to 10% as likely CCCR5-tropic. A missing node indicates the V3 loop was not identifiable by the Geno2Pheno tool (FPR, false-positive rate).