Sequence analysis of passages viruses in the presence or absence of CQ. HIV-1 RNA was isolated from culture supernatant and viral RNA was converted to cDNA and then subjected to a nested PCR in order to amplify a fragment covering the V1V2 – C4 region of the gp120 gene. Sequence analysis was performed on several clones of the CQ and control passages. The sequence of the original virus 293.10 is shown. A) the V1V2 region. B) the V3 region including the PNG site at the base of the loop. C) the V4 region. The black lines above the original sequence represent PNG sites.