title: Performance comparison of an in-house integrase genotyping assay versus the ViroSeq™ Integra48, and study of HIV-1 integrase polymorphisms in Hong Kong.
abstract: BACKGROUND
  Integrase inhibitors are recently prescribed to multi-class drug resistant HIV-1 patients in Hong Kong. Unlike pol gene, there are no FDA-approved genotypic resistance tests available for int. Limited studies compared the performance between an in-house and commercial integrase genotyping system. Information on baseline polymorphisms was also insufficient in our region.
  
  
  OBJECTIVE
  To compare integrase genotyping data obtained from an in-house and ViroSeq™ Integra48 assay, and to illustrate integrase polymorphisms on HIV-1 B and non-B subtypes in Hong Kong.
  
  
  METHODS
  A total of 283 HIV-1 patients were recruited during 2006-2012 in Hong Kong. All samples were genotyped by an in-house assay for pol and int separately, and 46 of them were further genotyped by ViroSeq™ Integra48. Polymorphisms and resistance mutations were analyzed by Stanford HIV Drug Resistance Database.
  
  
  RESULTS
  The included patients were mainly infected by HIV-1 subtype B (38.9%) and CRF01_AE (43.1%), followed by CRF07_BC (5.3%), C (3.9%), CRF02_AG (2.8%), D (1.4%), CRF08_BC (1.1%) or others (3.5%). Of 46 samples genotyped by ViroSeq™ and the in-house assays, all major and minor resistance mutations were concordant. Integrase major resistance mutations were identified in two CRF01_AE raltegravir-treated patients. Integrase minor resistance mutations were observed in subtypes B and CRF01_AE.
  
  
  CONCLUSIONS
  With 25% of the commercial cost, the in-house integrase genotyping assay managed to regenerate over 96% concordant results as good as the RUO ViroSeq™ assay. Further investigations are required to understand the effect on integrase minor mutations, which are present in many subtype B and CRF01_AE samples.
authors.affiliation: Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region.
authors.forename: Sabrina Wai-Chi
authors.initials: SW
authors.lastname: To
authors.forename: Jonathan Hon-Kwan
authors.initials: JH
authors.lastname: Chen
authors.forename: Ka-Hing
authors.initials: KH
authors.lastname: Wong
authors.forename: Kenny Chi-Wai
authors.initials: KC
authors.lastname: Chan
authors.forename: Hon-Man
authors.initials: HM
authors.lastname: Ng
authors.forename: Hao
authors.initials: H
authors.lastname: Wu
authors.forename: Jason Tszhin
authors.initials: JT
authors.lastname: Lam
authors.forename: Wing-Cheong
authors.initials: WC
authors.lastname: Yam
mesh_terms: D000328:Adult; D000368:Aged; D024882:Drug Resistance, Viral; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D019427:HIV Integrase / Q000235:genetics*; D015497:HIV-1 / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D006723:Hong Kong; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D020125:Mutation, Missense; D014773:Virology / Q000379:methods*; D055815:Young Adult
chemical_list: D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1
keywords: CRF01_AE; In-house; Integrase genotyping; Integrase polymorphisms; Integrase resistance; Versus ViroSeq Integra48