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

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 & 22 others 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

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)234-243
Number of pages10
JournalJournal of Medical Virology
Volume88
Issue number2
DOIs
Publication statusPublished - Feb 1 2016
Externally publishedYes

Fingerprint

Drug Resistance
Area Under Curve
HIV
Didanosine
Phenotype
HIV-1
Databases
Gold
Mutation

Keywords

  • Algorithm
  • Drug resistance
  • Subtype

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Jiamsakul, A., Chaiwarith, R., Durier, N., Sirivichayakul, S., Kiertiburanakul, S., Van Den Eede, P., ... Boettiger, D. C. (2016). Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals. Journal of Medical Virology, 88(2), 234-243. https://doi.org/10.1002/jmv.24320

Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals. / Jiamsakul, Awachana; Chaiwarith, Romanee; Durier, Nicolas; Sirivichayakul, Sunee; Kiertiburanakul, Sasisopin; Van Den Eede, Peter; Ditangco, Rossana; Kamarulzaman, Adeeba; Li, Patrick Ck; Ratanasuwan, Winai; Sirisanthana, Thira; Li, P. C.K.; Lee, M. P.; Kumarasamy, N.; Saghayam, S.; Pujari, S.; Joshi, K.; Merati, T. P.; Yuliana, F.; Lee, C. K.C.; Sim, B. L.H.; Ong, L. Y.; Mustafa, M.; Nordin, N.; Bantique, R. O.; Chen, Y. M.A.; Lin, Y. T.; Phanuphak, P.; Sirivichayakul, S.; Sungkanuparph, S.; Chumla, L.; Sanmeema, N.; Praparattanapan, J.; Kantipong, P.; Kambua, P.; Sriondee, R.; Kantor, R.; Sohn, A. H.; Singtoroj, T.; Cooper, D. A.; Law, M. G.; Boettiger, D. C.

In: Journal of Medical Virology, Vol. 88, No. 2, 01.02.2016, p. 234-243.

Research output: Contribution to journalArticle

Jiamsakul, A, Chaiwarith, R, Durier, N, Sirivichayakul, S, Kiertiburanakul, S, Van Den Eede, P, Ditangco, R, Kamarulzaman, A, Li, PC, Ratanasuwan, W, Sirisanthana, T, Li, PCK, Lee, MP, Kumarasamy, N, Saghayam, S, Pujari, S, Joshi, K, Merati, TP, Yuliana, F, Lee, CKC, Sim, BLH, Ong, LY, Mustafa, M, Nordin, N, Bantique, RO, Chen, YMA, Lin, YT, Phanuphak, P, Sirivichayakul, S, Sungkanuparph, S, Chumla, L, Sanmeema, N, Praparattanapan, J, Kantipong, P, Kambua, P, Sriondee, R, Kantor, R, Sohn, AH, Singtoroj, T, Cooper, DA, Law, MG & Boettiger, DC 2016, 'Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals', Journal of Medical Virology, vol. 88, no. 2, pp. 234-243. https://doi.org/10.1002/jmv.24320
Jiamsakul, Awachana ; Chaiwarith, Romanee ; Durier, Nicolas ; Sirivichayakul, Sunee ; Kiertiburanakul, Sasisopin ; Van Den Eede, Peter ; Ditangco, Rossana ; Kamarulzaman, Adeeba ; Li, Patrick Ck ; Ratanasuwan, Winai ; Sirisanthana, Thira ; Li, P. C.K. ; Lee, M. P. ; Kumarasamy, N. ; Saghayam, S. ; Pujari, S. ; Joshi, K. ; Merati, T. P. ; Yuliana, F. ; Lee, C. K.C. ; Sim, B. L.H. ; Ong, L. Y. ; Mustafa, M. ; Nordin, N. ; Bantique, R. O. ; Chen, Y. M.A. ; Lin, Y. T. ; Phanuphak, P. ; Sirivichayakul, S. ; Sungkanuparph, S. ; Chumla, L. ; Sanmeema, N. ; Praparattanapan, J. ; Kantipong, P. ; Kambua, P. ; Sriondee, R. ; Kantor, R. ; Sohn, A. H. ; Singtoroj, T. ; Cooper, D. A. ; Law, M. G. ; Boettiger, D. C. / Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals. In: Journal of Medical Virology. 2016 ; Vol. 88, No. 2. pp. 234-243.
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AU - Durier, Nicolas

AU - Sirivichayakul, Sunee

AU - Kiertiburanakul, Sasisopin

AU - Van Den Eede, Peter

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AU - Lin, Y. T.

AU - Phanuphak, P.

AU - Sirivichayakul, S.

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