Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals

• Main Authors: Awachana Jiamsakul, Romanee Chaiwarith, Nicolas Durier, Sunee Sirivichayakul, Sasisopin Kiertiburanakul, Peter Van Den Eede, Rossana Ditangco, Adeeba Kamarulzaman, Patrick Ck Li, Winai Ratanasuwan, Thira Sirisanthana, P. C.K. Li, M. P. Lee, N. Kumarasamy, S. Saghayam, S. Pujari, K. Joshi, T. P. Merati, F. Yuliana, C. K.C. Lee, B. L.H. Sim, L. Y. Ong, M. Mustafa, N. Nordin, R. O. Bantique, Y. M.A. Chen, Y. T. Lin, P. Phanuphak, S. Sirivichayakul, S. Sungkanuparph, L. Chumla, N. Sanmeema, J. Praparattanapan, P. Kantipong, P. Kambua, R. Sriondee, R. Kantor, A. H. Sohn, T. Singtoroj, D. A. Cooper, M. G. Law, D. C. Boettiger
• Other Authors: University of New South Wales (UNSW) Australia
• Format: Article
• Published: 2018
• Subjects: Immunology and Microbiology
• Online Access: https://repository.li.mahidol.ac.th/handle/123456789/40884
• Institution: Mahidol University

© 2016 Wiley Periodicals, Inc. 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 vircoTypeTMHIV-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. © 2015 Wiley Periodicals, Inc.