title: HIV drug resistance mutations in proviral DNA from a community treatment program.
abstract: BACKGROUND
  Drug resistance mutations archived in resting memory CD4+ cells may persist despite suppression of HIV RNA to <50 copies/ml. We sequenced pol gene from proviral DNA among viremic and suppressed patients to identify drug resistance mutations.
  
  
  METHODS
  The Peninsula AIDS Research Cohort study enrolled and followed over 2 years 120 HIV infected patients from San Mateo and San Francisco Counties. HIV-1 pol genotyping by bulk sequencing was performed on 38 DNA and RNA from viremic patients and DNA only among 82 suppressed patients at baseline. Antiretroviral susceptibility was predicted by HIVDB.stanford.edu.
  
  
  RESULTS
  Among 120 subjects, 81% were on antiretroviral therapy and had been treated for a median time of 7 years. Thirty-two viremic patients showed concordant RNA and DNA genotypes (84%); the discordant profiles were mainly observed in patients with low-level viremia. Among suppressed patients, 21 had drug resistance mutations in proviral DNA (26%) with potential resistance to one, two or three ARV classes in 16, 4 and 1 samples respectively.
  
  
  CONCLUSIONS
  The high level of genotype concordance between DNA and RNA in viremic patients suggested that DNA genotyping might be used to assess drug resistance in resource-limited settings, and further investigation of extracted DNA from dried blood spots is needed. Drug resistance mutations in proviral DNA in 26% of subjects with less than 50 copies/ml pose a risk for the transmission of drug resistant virus with virologic failure, treatment interruption or decreased adherence.
authors: Stanford University, Infectious Diseases Department /Medical School, Stanford, California, United States of America.
authors: Anne
authors: A
authors: Derache
authors: Center for Infectious Diseases National Medical Center, Seoul, South Korea.
authors: Hyoung-Shik
authors: HS
authors: Shin
authors: Stanford University, Infectious Diseases Department /Medical School, Stanford, California, United States of America.
authors: Maya
authors: M
authors: Balamane
authors: Stanford University, Infectious Diseases Department /Medical School, Stanford, California, United States of America.
authors: Elizabeth
authors: E
authors: White
authors: Stanford University, Infectious Diseases Department /Medical School, Stanford, California, United States of America.
authors: Dennis
authors: D
authors: Israelski
authors: University of California, Los Angeles, California, United States of America.
authors: Jeffrey D
authors: JD
authors: Klausner
authors: Kaiser Permanente San Francisco, California, United States of America.
authors: Alexandra H
authors: AH
authors: Freeman
authors: Stanford University, Infectious Diseases Department /Medical School, Stanford, California, United States of America.
authors: David
authors: D
authors: Katzenstein
mesh_terms: D000328:Adult; D023241:Antiretroviral Therapy, Highly Active; D004279:DNA, Viral / Q000235:genetics*; D003710:Demography; D024882:Drug Resistance, Viral / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics* / Q000276:immunology / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics*; D010802:Phylogeny; D011533:Proviruses / Q000235:genetics*; D012111:Residence Characteristics; D014766:Viremia / Q000821:virology
chemical_list: D004279:DNA, Viral
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