TY - JOUR
T1 - Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo
AU - Tsibris, Athe M.N.
AU - Korber, Bette
AU - Arnaout, Ramy
AU - Russ, Carsten
AU - Lo, Chien Chi
AU - Leitner, Thomas
AU - Gaschen, Brian
AU - Theiler, James
AU - Paredes, Roger
AU - Su, Zhaohui
AU - Hughes, Michael D.
AU - Gulick, Roy M.
AU - Greaves, Wayne
AU - Coakley, Eoin
AU - Flexner, Charles
AU - Nusbaum, Chad
AU - Kuritzkes, Daniel R.
PY - 2009/5/25
Y1 - 2009/5/25
N2 - High-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. © 2009 Tsibris et al.
AB - High-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. © 2009 Tsibris et al.
U2 - 10.1371/journal.pone.0005683
DO - 10.1371/journal.pone.0005683
M3 - Article
VL - 4
IS - 5
M1 - e5683
ER -