title: Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo.
abstract: 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.
authors.affiliation: Massachusetts General Hospital, Boston, Massachusetts, United States of America.
authors.forename: Athe M N
authors.initials: AM
authors.lastname: Tsibris
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Ramy
authors.initials: R
authors.lastname: Arnaout
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Chien-Chi
authors.initials: CC
authors.lastname: Lo
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
authors.forename: Brian
authors.initials: B
authors.lastname: Gaschen
authors.forename: James
authors.initials: J
authors.lastname: Theiler
authors.forename: Roger
authors.initials: R
authors.lastname: Paredes
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Su
authors.forename: Michael D
authors.initials: MD
authors.lastname: Hughes
authors.forename: Roy M
authors.initials: RM
authors.lastname: Gulick
authors.forename: Wayne
authors.initials: W
authors.lastname: Greaves
authors.forename: Eoin
authors.initials: E
authors.lastname: Coakley
authors.forename: Charles
authors.initials: C
authors.lastname: Flexner
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Kuritzkes
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D065100:CCR5 Receptor Antagonists; D019277:Entropy; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000502:physiology*; D006801:Humans; D016013:Likelihood Functions; D009690:Nucleic Acid Conformation; D010879:Piperazines / Q000494:pharmacology* / Q000627:therapeutic use; D011743:Pyrimidines / Q000494:pharmacology* / Q000627:therapeutic use; D012367:RNA, Viral / Q000097:blood / Q000737:chemistry; D015203:Reproducibility of Results; D012641:Selection, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D013997:Time Factors; D017211:Treatment Failure
chemical_list: D065100:CCR5 Receptor Antagonists; D010879:Piperazines; D011743:Pyrimidines; D012367:RNA, Viral; C486781:vicriviroc