title: Evaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping.
abstract: BACKGROUND
  The human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) has been considered essential for HIV-1 drug resistance monitoring. However, it is not commonly used in some developing countries in Asia and Africa due to its high running cost.
  
  
  OBJECTIVE
  This study aims to evaluate a new low-cost in-house GRT for both subtype B and non-B HIV-1.
  
  
  METHODS
  The in-house GRT sequenced the entire protease and 410 codons of reverse transcriptase (RT) in the pol gene. Its performance on drug resistance interpretation was evaluated against the FDA-approved ViroSeq HIV-1 Genotyping System. Particularly, a panel of 235 plasma samples from 205 HIV-1-infected patients in Hong Kong was investigated. The HIV-1 drug resistance-related mutations detected by the two systems were compared. The HIV-1 subtypes were analyzed through the REGA HIV-1 Genotyping Tool and env phylogenetic analysis.
  
  
  RESULTS
  Among the 235 samples, 229 (97.4%) were successfully amplified by both in-house and ViroSeq systems. All PCR-negative samples harbored viral RNA at <400 copies/mL. The in-house and ViroSeq system showed identical drug resistance-related mutation patterns in 216 out of 229 samples (94.3%). The REGA pol genotyping results showed 93.9% (215/229) concordance with the env phylogenetic results including HIV-1 subtype A1, B, C, D, G, CRF01_AE, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC, CRF15_01B and other recombinant strains. The cost of running the in-house GRT is only 25% of that for the commercial system, thus making it suitable for the developing countries in Asia and Africa.
  
  
  CONCLUSIONS
  Overall, our in-house GRT provided comparable results to those of the commercial ViroSeq genotyping system on diversified HIV-1 subtypes at a more affordable price which make it suitable for HIV-1 monitoring in developing countries.
authors: Department of Microbiology, The University of Hong Kong, Hong Kong, SAR, China.
authors: J H K
authors: JH
authors: Chen
authors: K H
authors: KH
authors: Wong
authors: K
authors: K
authors: Chan
authors: H Y
authors: HY
authors: Lam
authors: S S
authors: SS
authors: Lee
authors: P
authors: P
authors: Li
authors: M P
authors: MP
authors: Lee
authors: D N
authors: DN
authors: Tsang
authors: B J
authors: BJ
authors: Zheng
authors: K Y
authors: KY
authors: Yuen
authors: W C
authors: WC
authors: Yam
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D023241:Antiretroviral Therapy, Highly Active / Q000145:classification / Q000379:methods; D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics*; D005821:Genetic Techniques; D005838:Genotype; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D006723:Hong Kong; D006801:Humans; D008826:Microbial Sensitivity Tests; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity
chemical_list: D019380:Anti-HIV Agents