Korber, BetteRuss, CarstenLo, Chien-ChiLeitner, ThomasGaschen, BrianTheiler, JamesParedes, RogerSu, ZhaohuiGulick, Roy M.Greaves, WayneCoakley, EoinFlexner, CharlesNusbaum, ChadTsibris, AtheArnaout, RamyHughes, MichaelKuritzkes, Daniel2011-04-232009Tsibris, Athe M. N., Bette Korber, Ramy Arnaout, Carsten Russ, Chien-Chi Lo, Thomas Leitner, Brian Gaschen, et al. 2009. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS ONE 4(5): e5683.1932-6203http://nrs.harvard.edu/urn-3:HUL.InstRepos:4874827High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected from 4 chronically HIV-infected subjects in whom CCR5 antagonist (vicriviroc [VVC]) therapy failed. Between 25,000–140,000 amplified sequences were obtained per sample. Profound baseline V3 loop sequence heterogeneity existed; predicted CXCR4-using populations were identified in a largely CCR5-using population. The V3 loop forms associated with subsequent virologic failure, either through CXCR4 use or the emergence of high-level VVC resistance, were present as minor variants at 0.8–2.8% of baseline samples. Extreme, rapid shifts in population frequencies toward these forms occurred, and deep sequencing provided a detailed view of the rapid evolutionary impact of VVC selection. Greater V3 diversity was observed post-selection. This previously unreported degree of V3 loop sequence diversity has implications for viral pathogenesis, vaccine design, and the optimal use of HIV-1 CCR5 antagonists.en-USgenetics and genomicsmicrobial evolution and genomicsvirologyhost invasion and cell entrymechanisms of resistance and susceptibility, including host geneticsvirus evolution and symbiosisinfectious diseasesHIV infection and AIDSJournal Article2011-04-2310.1371/journal.pone.0005683