title: Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients.
abstract: BACKGROUND
  The Maraviroc versus Optimized Therapy in Viremic Antiretroviral Treatment-Experienced Patients (MOTIVATE) studies compared maraviroc versus placebo in treatment-experienced patients with CCR5-using (R5) human immunodeficiency virus type 1 (HIV-1), screened using the original Trofile assay. A subset with non-R5 HIV infection entered the A4001029 trial. We retrospectively examined the performance of a genotypic tropism assay based on deep sequencing of the HIV env V3 loop in predicting virologic response to maraviroc in these trials.
  
  
  METHODS
  V3 amplicons were prepared from 1827 screening plasma samples and sequenced on a Roche/454 GS-FLX to a depth of >3000 sequences/sample. Samples were considered non-R5 if ≥2% of their viral population scored greater than or equal to -4.75 or ≤3.5 using the PSSM(x4/R5) or geno2pheno algorithms, respectively.
  
  
  RESULTS
  Deep sequencing identified more than twice as many maraviroc recipients as having non-R5 HIV, compared with the original Trofile. With use of genotyping, we determined that 49% of maraviroc recipients with R5 HIV at screening had a week 48 viral load <50 copies/mL versus 26% of recipients with non-R5. Corresponding percentages were 46% and 23% with screening by Trofile. In cases in which screening assays differed, median week 8 log₁₀ copies/mL viral load decrease favored 454. Other parameters predicted by genotyping included likelihood of changing to non-R5 tropism.
  
  
  CONCLUSIONS
  This large study establishes deep V3 sequencing as a promising tool for identifying treatment-experienced individuals who could benefit from CCR5-antagonist-containing regimens.
authors.affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.
authors.forename: Luke C
authors.initials: LC
authors.lastname: Swenson
authors.forename: Theresa
authors.initials: T
authors.lastname: Mo
authors.forename: Winnie W Y
authors.initials: WW
authors.lastname: Dong
authors.forename: Xiaoyin
authors.initials: X
authors.lastname: Zhong
authors.forename: Conan K
authors.initials: CK
authors.lastname: Woods
authors.forename: Mark A
authors.initials: MA
authors.lastname: Jensen
authors.forename: Alexander
authors.initials: A
authors.lastname: Thielen
authors.forename: Douglass
authors.initials: D
authors.lastname: Chapman
authors.forename: Marilyn
authors.initials: M
authors.lastname: Lewis
authors.forename: Ian
authors.initials: I
authors.lastname: James
authors.forename: Jayvant
authors.initials: J
authors.lastname: Heera
authors.forename: Hernan
authors.initials: H
authors.lastname: Valdez
authors.forename: P Richard
authors.initials: PR
authors.lastname: Harrigan
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D002986:Clinical Trials as Topic; D003510:Cyclohexanes / Q000494:pharmacology*; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D000077592:Maraviroc; D012367:RNA, Viral / Q000235:genetics; D019713:Receptors, CCR5 / Q000378:metabolism; D015728:Receptors, HIV / Q000378:metabolism*; D012189:Retrospective Studies; D014230:Triazoles / Q000494:pharmacology*; D056189:Viral Tropism; D014773:Virology / Q000379:methods*; D053585:Virus Attachment; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics / Q000378:metabolism
chemical_list: D019380:Anti-HIV Agents; D003510:Cyclohexanes; D012367:RNA, Viral; D019713:Receptors, CCR5; D015728:Receptors, HIV; D014230:Triazoles; D054299:env Gene Products, Human Immunodeficiency Virus; D000077592:Maraviroc