Figure 2.

Phylogenetic associations between intact proviruses isolated from individual subsets from blood and tissues (lymph nodes [LNs]). Figure shows neighborhood-joining phylogenetic tree of all intact proviral sequences (n = 62) isolated from indicated CD4 T-cell subsets from blood and tissue from 3 persons living with human immunodeficiency virus (HIV) 1. Clusters of completely identical HIV-1 sequences are highlighted with boxes; within each cluster, proportions of sequences derived from given CD4 T-cell subsets are shown in pie charts. If a near-full-length sequence showed a mapped 5’ long terminal repeat deletion with an absent or incomplete primer binding site, but otherwise displayed no lethal sequence defects, the missing 5’ long terminal repeat region was inferred to be present, and the sequence was termed “inferred intact.” Abbreviations: PD-1, programmed cell death 1; Tfh, T follicular helper; Th1, Th2, and Th17, T-helper 1, 2, and 17.