Affiliations 

  • 1 The Kirby Institute, UNSW Australia, Sydney, Australia
  • 2 Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
  • 3 TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
  • 4 Faculty of Medicine, Chulalongkorn University and HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand
  • 5 Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
  • 6 Janssen Diagnostics BVBA, Beerse, Belgium
  • 7 Research Institute for Tropical Medicine, Manila, Philippines
  • 8 University of Malaya Medical Center, Kuala Lumpur, Malaysia
  • 9 Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
  • 10 Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
J. Med. Virol., 2016 Feb;88(2):234-43.
PMID: 26147742 DOI: 10.1002/jmv.24320

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.