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

© 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 subtyp...

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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
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Published: 2018
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spelling th-cmuir.6653943832-559072018-09-05T03:10:32Z 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 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 Immunology and Microbiology Medicine © 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. 2018-09-05T03:03:36Z 2018-09-05T03:03:36Z 2016-02-01 Journal 10969071 01466615 2-s2.0-84954399287 10.1002/jmv.24320 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84954399287&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/55907
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Immunology and Microbiology
Medicine
spellingShingle Immunology and Microbiology
Medicine
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
Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
description © 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.
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author 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
author_facet 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
author_sort Awachana Jiamsakul
title Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
title_short Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
title_full Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
title_fullStr Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
title_full_unstemmed Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals
title_sort comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among crf01_ae and subtype b hiv-infected individuals
publishDate 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84954399287&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/55907
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