title: HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing.
abstract: HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing.
  
  
  
  Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database.
  
  
  
  Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens.
  
  
  
  The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.
authors.affiliation: Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa. Electronic address: benjiechim@yahoo.com.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Chimukangara
authors.affiliation: Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe. Electronic address: bhavinivaryani@gmail.com.
authors.forename: Bhavini
authors.initials: B
authors.lastname: Varyani
authors.affiliation: Newlands Clinic, Newlands, Harare, Zimbabwe. Electronic address: TineiS@newlandsclinic.org.zw.
authors.forename: Tinei
authors.initials: T
authors.lastname: Shamu
authors.affiliation: Department of Molecular Biology, Biomedical Research and Training Institute, Harare, Zimbabwe. Electronic address: Jnr.mutsvangwa@gmail.com.
authors.forename: Junior
authors.initials: J
authors.lastname: Mutsvangwa
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: jmanasa@gmail.com.
authors.forename: Justen
authors.initials: J
authors.lastname: Manasa
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: betsyjohn@aol.com.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: White
authors.affiliation: Newlands Clinic, Newlands, Harare, Zimbabwe; Institute of Social and Preventive Medicine, University of Bern, Switzerland. Electronic address: cleophasc@newlandsclinic.org.zw.
authors.forename: Cleophas
authors.initials: C
authors.lastname: Chimbetete
authors.affiliation: Newlands Clinic, Newlands, Harare, Zimbabwe. Electronic address: RuediL@newlandsclinic.org.zw.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Luethy
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: davidkk@stanford.edu.
authors.forename: David
authors.initials: D
authors.lastname: Katzenstein
mesh_terms: D044966:Anti-Retroviral Agents / Q000494:pharmacology / Q000627:therapeutic use*; D023241:Antiretroviral Therapy, Highly Active; D024882:Drug Resistance, Viral; D060005:Genotyping Techniques / Q000379:methods*; D006678:HIV / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D017211:Treatment Failure; D014481:United States; D015030:Zimbabwe
chemical_list: D044966:Anti-Retroviral Agents
keywords: Genotyping; HIV drug resistance; SATuRN; Treatment failure; Zimbabwe