title: Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals.
abstract: HIV drug resistance assessments and interpretations can be obtained from genotyping (GT), virtual phenotyping (VP) and laboratory-based phenotyping (PT). We compared resistance calls obtained from GT and VP with those from PT (GT-PT and VP-PT) among CRF01_AE and subtype B HIV-1 infected patients. GT predictions were obtained from the Stanford HIV database. VP and PT were obtained from Janssen Diagnostics BVBA's vircoType(TM) HIV-1 and Antivirogram®, respectively. With PT assumed as the "gold standard," the area under the curve (AUC) and the Bland-Altman plot were used to assess the level of agreement in resistance interpretations. A total of 80 CRF01_AE samples from Asia and 100 subtype B from Janssen Diagnostics BVBA's database were analysed. CRF01_AE showed discordances ranging from 3 to 27 samples for GT-PT and 1 to 20 samples for VP-PT. The GT-PT and VP-PT AUCs were 0.76-0.97 and 0.81-0.99, respectively. Subtype B showed 3-61 discordances for GT-PT and 2-75 discordances for VP-PT. The AUCs ranged from 0.55 to 0.95 for GT-PT and 0.55 to 0.97 for VP-PT. Didanosine had the highest proportion of discordances and/or AUC in all comparisons. The patient with the largest didanosine FC difference in each subtype harboured Q151M mutation. Overall, GT and VP predictions for CRF01_AE performed significantly better than subtype B for three NRTIs. Although discrepancies exist, GT and VP resistance interpretations in HIV-1 CRF01_AE strains were highly robust in comparison with the gold-standard PT.
authors.affiliation: The Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Awachana
authors.initials: A
authors.lastname: Jiamsakul
authors.affiliation: Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand.
authors.forename: Romanee
authors.initials: R
authors.lastname: Chaiwarith
authors.affiliation: TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Durier
authors.affiliation: Faculty of Medicine, Chulalongkorn University and HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand.
authors.forename: Sunee
authors.initials: S
authors.lastname: Sirivichayakul
authors.affiliation: Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Sasisopin
authors.initials: S
authors.lastname: Kiertiburanakul
authors.affiliation: Janssen Diagnostics BVBA, Beerse, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Van Den Eede
authors.affiliation: Research Institute for Tropical Medicine, Manila, Philippines.
authors.forename: Rossana
authors.initials: R
authors.lastname: Ditangco
authors.affiliation: University of Malaya Medical Center, Kuala Lumpur, Malaysia.
authors.forename: Adeeba
authors.initials: A
authors.lastname: Kamarulzaman
authors.affiliation: Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China.
authors.forename: Patrick C K
authors.initials: PC
authors.lastname: Li
authors.affiliation: Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors.forename: Winai
authors.initials: W
authors.lastname: Ratanasuwan
authors.affiliation: Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand.
authors.forename: Thira
authors.initials: T
authors.lastname: Sirisanthana
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D001208:Asia; D024882:Drug Resistance, Viral; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods; D010641:Phenotype
chemical_list: D019380:Anti-HIV Agents
keywords: algorithm; drug resistance; subtype