title: HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China.
abstract: OBJECTIVE
  Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF).
  
  
  METHODS
  29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels.
  
  
  RESULTS
  DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×10(4) c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1-4% and 24 (60%) at levels of 5-19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS.
  
  
  CONCLUSIONS
  DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
authors.affiliation: Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
authors.forename: Xiaobai
authors.initials: X
authors.lastname: Zou
authors.affiliation: Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
authors.forename: Jianmei
authors.initials: J
authors.lastname: He
authors.affiliation: Hunan Provincial Center for Disease Control and Prevention, Changsha, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Yale School of Medicine, New Haven, United States of America.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Chiarella
authors.affiliation: Yale School of Medicine, New Haven, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Kozal
mesh_terms: D000328:Adult; D000368:Aged; D023241:Antiretroviral Therapy, Highly Active; D002681:China; D024882:Drug Resistance, Viral; D005260:Female; D015658:HIV Infections / Q000175:diagnosis / Q000188:drug therapy / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015994:Incidence; D008297:Male; D055118:Medication Adherence; D008875:Middle Aged; D009154:Mutation; D015995:Prevalence; D012307:Risk Factors; D017211:Treatment Failure; D019562:Viral Load; D055815:Young Adult