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Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay.

Publication ,  Journal Article
Zhang, G; Cai, F; Zhou, Z; DeVos, J; Wagar, N; Diallo, K; Zulu, I; Wadonda-Kabondo, N; Stringer, JSA; Weidle, PJ; Ndongmo, CB; Sikazwe, I ...
Published in: J Clin Microbiol
November 2013

High-throughput, sensitive, and cost-effective HIV drug resistance (HIVDR) detection assays are needed for large-scale monitoring of the emergence and transmission of HIVDR in resource-limited settings. Using suspension array technology, we have developed a multiplex allele-specific (MAS) assay that can simultaneously detect major HIVDR mutations at 20 loci. Forty-five allele-specific primers tagged with unique 24-base oligonucleotides at the 5' end were designed to detect wild-type and mutant alleles at the 20 loci of HIV-1 subtype C. The MAS assay was first established and optimized with three plasmid templates (C-wt, C-mut1, and C-mut2) and then evaluated using 148 plasma specimens from HIV-1 subtype C-infected individuals. All the wild-type and mutant alleles were unequivocally distinguished with plasmid templates, and the limits of detection were 1.56% for K219Q and K219E, 3.13% for L76V, 6.25% for K65R, K70R, L74V, L100I, K103N, K103R, Q151M, Y181C, and I47V, and 12.5% for M41L, K101P, K101E, V106A, V106M, Y115F, M184V, Y188L, G190A, V32I, I47A, I84V, and L90M. Analyses of 148 plasma specimens revealed that the MAS assay gave 100% concordance with conventional sequencing at eight loci and >95% (range, 95.21% to 99.32%) concordance at the remaining 12 loci. The differences observed were caused mainly by 24 additional low-abundance alleles detected by the MAS assay. Ultradeep sequencing analysis confirmed 15 of the 16 low-abundance alleles. This multiplex, sensitive, and straightforward result-reporting assay represents a new efficient genotyping tool for HIVDR surveillance and monitoring.

Duke Scholars

Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

November 2013

Volume

51

Issue

11

Start / End Page

3666 / 3674

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Mutation, Missense
  • Molecular Sequence Data
  • Molecular Diagnostic Techniques
  • Microbiology
  • Microbial Sensitivity Tests
  • Microarray Analysis
  • Humans
  • HIV-1
  • HIV Reverse Transcriptase
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Zhang, G., Cai, F., Zhou, Z., DeVos, J., Wagar, N., Diallo, K., … Yang, C. (2013). Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay. J Clin Microbiol, 51(11), 3666–3674. https://doi.org/10.1128/JCM.01669-13
Zhang, Guoqing, Fangping Cai, Zhiyong Zhou, Joshua DeVos, Nick Wagar, Karidia Diallo, Isaac Zulu, et al. “Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay.J Clin Microbiol 51, no. 11 (November 2013): 3666–74. https://doi.org/10.1128/JCM.01669-13.
Zhang, Guoqing, et al. “Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay.J Clin Microbiol, vol. 51, no. 11, Nov. 2013, pp. 3666–74. Pubmed, doi:10.1128/JCM.01669-13.
Zhang G, Cai F, Zhou Z, DeVos J, Wagar N, Diallo K, Zulu I, Wadonda-Kabondo N, Stringer JSA, Weidle PJ, Ndongmo CB, Sikazwe I, Sarr A, Kagoli M, Nkengasong J, Gao F, Yang C. Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay. J Clin Microbiol. 2013 Nov;51(11):3666–3674.

Published In

J Clin Microbiol

DOI

EISSN

1098-660X

Publication Date

November 2013

Volume

51

Issue

11

Start / End Page

3666 / 3674

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Mutation, Missense
  • Molecular Sequence Data
  • Molecular Diagnostic Techniques
  • Microbiology
  • Microbial Sensitivity Tests
  • Microarray Analysis
  • Humans
  • HIV-1
  • HIV Reverse Transcriptase