title: Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.
abstract: BACKGROUND
  It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown.
  
  
  RESULTS
  Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004-2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85-5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5-74.3, p = 0.0016).
  
  
  CONCLUSIONS
  Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.
authors: Yale University School of Medicine, New Haven, CT, USA. Thuy.Le@yale.edu
authors: Thuy
authors: T
authors: Le
authors: Jennifer
authors: J
authors: Chiarella
authors: Birgitte B
authors: BB
authors: Simen
authors: Bozena
authors: B
authors: Hanczaruk
authors: Michael
authors: M
authors: Egholm
authors: Marie L
authors: ML
authors: Landry
authors: Kevin
authors: K
authors: Dieckhaus
authors: Marc I
authors: MI
authors: Rosen
authors: Michael J
authors: MJ
authors: Kozal
mesh_terms: D000465:Algorithms; D019380:Anti-HIV Agents / Q000494:pharmacology*; D044966:Anti-Retroviral Agents / Q000494:pharmacology*; D018076:DNA, Complementary / Q000378:metabolism; D024882:Drug Resistance, Viral; D005838:Genotype; D015658:HIV Infections / Q000175:diagnosis* / Q000188:drug therapy* / Q000821:virology*; D006801:Humans; D009154:Mutation; D016017:Odds Ratio; D015995:Prevalence; D012367:RNA, Viral; D014779:Virus Replication
chemical_list: D019380:Anti-HIV Agents; D044966:Anti-Retroviral Agents; D018076:DNA, Complementary; D012367:RNA, Viral