Fig. 4
From: Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA
Analysis of HIV-1 population structure in a clinical sample using uSGS for library construction. Neighbor joining trees of HIV-1 pol sequence from donor 1 sample 1 and blow up of NJ subtree, showing clustering and linkage of WT at RT position 106 (V106V blue squares) with 101Q (blue square with black outline). Numbers of identical sequences are shown in parentheses as this NJ tree was extracted from 1585 unique SGS, where identical sequences were collapsed. Within the highlighted subtree, note especially two sequences (2) in which WT RT codon 106, and rare mutations 101Q and 108I (blue square with black and orange out line) were found to be linked. Detection of such a rare linkage event would be virtually impossible using LP-PCR or conventional SGS. Data were obtained by NGS uSGS and rooted on Consensus B