title: Clinical evaluation of an in-house human immunodeficiency virus (HIV) genotyping assay for the detection of drug resistance mutations in HIV-1 infected patients in Singapore.
abstract: BACKGROUND
  Human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) is essential for monitoring HIV-1 drug resistance mutations (DRMs). High cost and HIV-1 genetic variability are challenges to assay availability in Singapore. An in-house Sanger sequencing-based GRT method was developed at the Communicable Disease Centre (CDC), Singapore's HIV national treatment reference centre for both subtype B and non-subtype B HIV-1.
  
  
  METHODS
  The in-house GRT sequenced the fi rst 99 codons of protease (PR) and 244 codons of reverse transcriptase (RT) in the pol gene. The results were compared with the Food and Drug Administration (FDA)-approved ViroSeq™ HIV-1 Genotyping System.
  
  
  RESULTS
  Subtype assignment for the 46 samples were as follows: 31 (67.4%) CRF01_AE, 14 (30.5%) subtype B and 1 (2.1%) subtype C. All 46 samples had viral load of ≥500 copies/mL, and were successfully amplified by the in-house primer sets. Compared to the ViroSeq™ test, our in-house assay showed drug-resistance conferring codon concordance of 99.9% at PR and 98.9% at RT, and partial concordance of 0.1% at PR and 1.1% at RT. No discordant result was observed.
  
  
  CONCLUSIONS
  The assay successfully identified DRMs in both subtype AE and B, making it suitable for the efficient treatment monitoring in genetically diverse population. At less than half of the running cost compared to the ViroSeq™ assay, the broadly sensitive in-house assay could serve as a useful addition to the currently limited HIV genotyping assay options for resource-limited settings, thereby enhancing the DRM surveillance and monitoring in the region.
authors.affiliation: Department of Infectious Disease, Tan Tock Seng Hospital, Singapore.
authors.forename: Kuan Kiat
authors.initials: KK
authors.lastname: Chew
authors.forename: Kah Ying
authors.initials: KY
authors.lastname: Ng
authors.forename: Wei Xin
authors.initials: WX
authors.lastname: Khong
authors.forename: Palvinder
authors.initials: P
authors.lastname: Kaur
authors.forename: Joe Kwan
authors.initials: JK
authors.lastname: Yap
authors.forename: Arlene
authors.initials: A
authors.lastname: Chua
authors.forename: Mei Ting
authors.initials: MT
authors.lastname: Tan
authors.forename: Yin Ling
authors.initials: YL
authors.lastname: Koh
authors.forename: Koh Cheng
authors.initials: KC
authors.lastname: Thoon
authors.forename: Yee Sin
authors.initials: YS
authors.lastname: Leo
authors.forename: Oon Tek
authors.initials: OT
authors.lastname: Ng
mesh_terms: D044966:Anti-Retroviral Agents / Q000494:pharmacology; D024882:Drug Resistance, Viral / Q000235:genetics*; D015751:Genes, pol / Q000235:genetics*; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D009154:Mutation; D017422:Sequence Analysis, DNA / Q000379:methods; D012846:Singapore
chemical_list: D044966:Anti-Retroviral Agents