Fig. 4.

Participant B population HIV-1 env V3 loop amino acid sequences and results of the phenotypic coreceptor usage assay. Envelope sequences were obtained from plasma RNA prior to virologic escape (2008) and from cell-associated DNA from 2011 and 2012, after rising viral loads. The geno2pheno (G2P) algorithm predicted that all virus or proviruses would use CXCR4 given low FPRs and positively charged amino acids in V3 position 11 (arginine). However, pseudoviruses incorporating population envelope sequences from 2008 RNA used only CCR5 for entry. HIV-1 RNA was unable to be recovered or amplified from post-virologic escape time points but pseudoviruses incorporating cell-associated DNA envelope sequences from 2012 were able to use CXCR4 and CCR5 (dual/mixed tropic), but at lower levels than viruses derived from RNA. AMD3100 either incompletely suppressed or potentiated entry in CXCR4-expressing U87 cells. Pseudovirsues derived from DNA in 2008 and 2011 were unable to enter U87 cells expressing either CXCR4 or CCR5.