Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE

Methods based on genetic sequencing to monitor drug-resistance mutations in human immunodeficiency virus type 1 (HIV-1) require expensive instruments and are only capable of detecting mutant strains comprising > 20% of virus populations. The National Institutes of Health's AIDS Research and...

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Main Authors: Sirikwan Dokuta, Utaiwan Utaipat, Jutarat Praparattanapan, Jeitsada Keitkarn, Niwat Maneekarn, Thira Sirisanthana, Khuanchai Supparatpinyo
Format: Journal
Published: 2018
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http://cmuir.cmu.ac.th/jspui/handle/6653943832/47885
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Institution: Chiang Mai University
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spelling th-cmuir.6653943832-478852018-04-25T08:45:09Z Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE Sirikwan Dokuta Utaiwan Utaipat Jutarat Praparattanapan Jeitsada Keitkarn Niwat Maneekarn Thira Sirisanthana Khuanchai Supparatpinyo Methods based on genetic sequencing to monitor drug-resistance mutations in human immunodeficiency virus type 1 (HIV-1) require expensive instruments and are only capable of detecting mutant strains comprising > 20% of virus populations. The National Institutes of Health's AIDS Research and Reference Reagent Program (NIH ARRRP) makes available a probe-based method, an oligonucleotide ligation assay (OLA-ARRRP), which is less expensive and more sensitive than sequencing to detect such mutations for HIV-1 subtype B.In this study, an OLA was designed to detect the Methionine to Valine mutation at codon 184 (M184V) of the reverse transcriptase (RT) gene in the circulating recombinant form AE strain of HIV-1 (HIV-1 CRF01_AE) common in Thailand, and was evaluated in Thai patients experiencing treatment failure. The subtype-specific OLA-CRF01_AE proved superior to OLA-ARRRP in detecting M184V, although this mutation existed in the genome of the multiple-drug-resistant virus at lower minimal detection levels of 3% prevalence of mutated virus, compared to 50% for OLA-ARRRP.On evaluation using clinical specimens, OLA-CRF01_AE showed excellent agreement with nucleotide sequencing (95.1% overall concordance, kappa. > . 0.79), and the sensitivity was 100% for wild-type and 93.9% for mutant detection at codon 184. The OLA-CRF01_AE also detected M184V mutations in 2.4% (1/42) of specimens that were not detected by sequencing. The indeterminate detection by OLA-CRF01_AE was decreased, from 16.7% to 4.8%, in the samples containing mutant genotype when the strategy using unmodified- as a substitute of the modified-mutant detector probe was applied. Because of their low cost, sensitivity, and ease of use, the OLA-CRF01_AE is an attractive alternative to standard sequencing in resource-limited countries affected by this subtype of HIV-1. © 2013 Elsevier B.V. 2018-04-25T08:45:09Z 2018-04-25T08:45:09Z 2013-06-01 Journal 18790984 01660934 2-s2.0-84876984572 10.1016/j.jviromet.2013.03.016 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84876984572&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/47885
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
description Methods based on genetic sequencing to monitor drug-resistance mutations in human immunodeficiency virus type 1 (HIV-1) require expensive instruments and are only capable of detecting mutant strains comprising > 20% of virus populations. The National Institutes of Health's AIDS Research and Reference Reagent Program (NIH ARRRP) makes available a probe-based method, an oligonucleotide ligation assay (OLA-ARRRP), which is less expensive and more sensitive than sequencing to detect such mutations for HIV-1 subtype B.In this study, an OLA was designed to detect the Methionine to Valine mutation at codon 184 (M184V) of the reverse transcriptase (RT) gene in the circulating recombinant form AE strain of HIV-1 (HIV-1 CRF01_AE) common in Thailand, and was evaluated in Thai patients experiencing treatment failure. The subtype-specific OLA-CRF01_AE proved superior to OLA-ARRRP in detecting M184V, although this mutation existed in the genome of the multiple-drug-resistant virus at lower minimal detection levels of 3% prevalence of mutated virus, compared to 50% for OLA-ARRRP.On evaluation using clinical specimens, OLA-CRF01_AE showed excellent agreement with nucleotide sequencing (95.1% overall concordance, kappa. > . 0.79), and the sensitivity was 100% for wild-type and 93.9% for mutant detection at codon 184. The OLA-CRF01_AE also detected M184V mutations in 2.4% (1/42) of specimens that were not detected by sequencing. The indeterminate detection by OLA-CRF01_AE was decreased, from 16.7% to 4.8%, in the samples containing mutant genotype when the strategy using unmodified- as a substitute of the modified-mutant detector probe was applied. Because of their low cost, sensitivity, and ease of use, the OLA-CRF01_AE is an attractive alternative to standard sequencing in resource-limited countries affected by this subtype of HIV-1. © 2013 Elsevier B.V.
format Journal
author Sirikwan Dokuta
Utaiwan Utaipat
Jutarat Praparattanapan
Jeitsada Keitkarn
Niwat Maneekarn
Thira Sirisanthana
Khuanchai Supparatpinyo
spellingShingle Sirikwan Dokuta
Utaiwan Utaipat
Jutarat Praparattanapan
Jeitsada Keitkarn
Niwat Maneekarn
Thira Sirisanthana
Khuanchai Supparatpinyo
Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
author_facet Sirikwan Dokuta
Utaiwan Utaipat
Jutarat Praparattanapan
Jeitsada Keitkarn
Niwat Maneekarn
Thira Sirisanthana
Khuanchai Supparatpinyo
author_sort Sirikwan Dokuta
title Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
title_short Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
title_full Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
title_fullStr Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
title_full_unstemmed Improvement of the oligonucleotide ligation assay for detection of the M184V drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype CRF01_AE
title_sort improvement of the oligonucleotide ligation assay for detection of the m184v drug-resistant mutation in patients infected with human immunodeficiency virus type 1 subtype crf01_ae
publishDate 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84876984572&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/47885
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