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 Article Swipe
Guoqing Zhang
,
Fangping Cai
,
Zhiyong Zhou
,
Joshua DeVos
,
Nick Wagar
,
Karidia Diallo
,
Isaac Zulu
,
Nellie Wadonda-Kabondo
,
Jeffrey S. A. Stringer
,
Paul J. Weidle
,
Clement B. Ndongmo
,
Izukanji Sikazwe
,
Abdoulaye Dieng Sarr
,
Matthew Kagoli
,
John N. Nkengasong
,
Feng Gao
,
Chunfu Yang
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.17615/6cvc-1112
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.17615/6cvc-1112
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.
Related Topics
Concepts
Reverse transcriptase
Multiplex
Virology
Variants of PCR
Gene
Multiplex polymerase chain reaction
Biology
Drug resistance
Protease
Human immunodeficiency virus (HIV)
Allele
Genetics
Polymerase chain reaction
Molecular biology
Enzyme
Biochemistry
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.17615/6cvc-1112
- OA Status
- green
- Cited By
- 1
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4300520632
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4300520632Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.17615/6cvc-1112Digital Object Identifier
- Title
-
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 AssayWork title
- Type
-
articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2020Year of publication
- Publication date
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2020-11-04Full publication date if available
- Authors
-
Guoqing Zhang, Fangping Cai, Zhiyong Zhou, Joshua DeVos, Nick Wagar, Karidia Diallo, Isaac Zulu, Nellie Wadonda-Kabondo, Jeffrey S. A. Stringer, Paul J. Weidle, Clement B. Ndongmo, Izukanji Sikazwe, Abdoulaye Dieng Sarr, Matthew Kagoli, John N. Nkengasong, Feng Gao, Chunfu YangList of authors in order
- Landing page
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https://doi.org/10.17615/6cvc-1112Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.17615/6cvc-1112Direct OA link when available
- Concepts
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Reverse transcriptase, Multiplex, Virology, Variants of PCR, Gene, Multiplex polymerase chain reaction, Biology, Drug resistance, Protease, Human immunodeficiency virus (HIV), Allele, Genetics, Polymerase chain reaction, Molecular biology, Enzyme, BiochemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
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2016: 1Per-year citation counts (last 5 years)
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.K101E, | 146 |
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| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
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| sustainable_development_goals[0].display_name | Good health and well-being |
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| citation_normalized_percentile.is_in_top_10_percent | False |