{"doi":"10.17615/6cvc-1112","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 Assay","abstract":"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.","journal":"UNC Libraries","year":2020,"id":117819,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9626,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":548517,"name":"Zhiyong Zhou","orcid":"0000-0002-1546-7741","position":1,"is_corresponding":false},{"id":248972,"name":"Jeffrey S. A. Stringer","orcid":"0000-0002-9590-7216","position":2,"is_corresponding":false},{"id":549313,"name":"Abdoulaye Dieng Sarr","orcid":null,"position":3,"is_corresponding":false},{"id":548518,"name":"Joshua DeVos","orcid":"0000-0002-3306-1462","position":4,"is_corresponding":false},{"id":549314,"name":"Isaac Zulu","orcid":null,"position":5,"is_corresponding":false},{"id":549315,"name":"Fangping Cai","orcid":null,"position":6,"is_corresponding":false},{"id":500298,"name":"Paul J. Weidle","orcid":null,"position":7,"is_corresponding":false},{"id":549316,"name":"Nick Wagar","orcid":null,"position":8,"is_corresponding":false},{"id":548519,"name":"Karidia Diallo","orcid":"0000-0001-7767-9638","position":9,"is_corresponding":false},{"id":388629,"name":"John N. Nkengasong","orcid":"0000-0001-6047-0184","position":10,"is_corresponding":false},{"id":548520,"name":"Feng Gao","orcid":"0000-0002-8853-0123","position":11,"is_corresponding":false},{"id":549317,"name":"Matthew Kagoli","orcid":null,"position":12,"is_corresponding":false},{"id":299399,"name":"Izukanji Sikazwe","orcid":"0000-0002-3898-2607","position":13,"is_corresponding":false},{"id":388626,"name":"Guoqing Zhang","orcid":"0000-0001-8827-7546","position":14,"is_corresponding":false},{"id":549318,"name":"Nellie Wadonda-Kabondo","orcid":null,"position":15,"is_corresponding":false},{"id":36891,"name":"Chunfu Yang","orcid":"0000-0002-3331-0991","position":16,"is_corresponding":false},{"id":548516,"name":"Clement B. Ndongmo","orcid":"0000-0003-0177-8458","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-18T23:13:54.951170Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}