{"doi":"10.1093/jac/dkaa352","title":"Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load","abstract":"OBJECTIVES: To evaluate the performance of a high-throughput research assay for HIV drug resistance testing based on whole genome next-generation sequencing (NGS) that also quantifies HIV viral load. METHODS: Plasma samples (n = 145) were obtained from HIV-positive MSM (HPTN 078). Samples were analysed using clinical assays (the ViroSeq HIV-1 Genotyping System and the Abbott RealTime HIV-1 Viral Load assay) and a research assay based on whole-genome NGS (veSEQ-HIV). RESULTS: HIV protease and reverse transcriptase sequences (n = 142) and integrase sequences (n = 138) were obtained using ViroSeq. Sequences from all three regions were obtained for 100 (70.4%) of the 142 samples using veSEQ-HIV; results were obtained more frequently for samples with higher viral loads (93.5% for 93 samples with >5000 copies/mL; 50.0% for 26 samples with 1000-5000 copies/mL; 0% for 23 samples with <1000 copies/mL). For samples with results from both methods, drug resistance mutations (DRMs) were detected in 33 samples using ViroSeq and 42 samples using veSEQ-HIV (detection threshold: 5.0%). Overall, 146 major DRMs were detected; 107 were detected by both methods, 37 were detected by veSEQ-HIV only (frequency range: 5.0%-30.6%) and two were detected by ViroSeq only. HIV viral loads estimated by veSEQ-HIV strongly correlated with results from the Abbott RealTime Viral Load assay (R2 = 0.85; n = 142). CONCLUSIONS: The NGS-based veSEQ-HIV method provided results for most samples with higher viral loads, was accurate for detecting major DRMs, and detected mutations at lower levels compared with a method based on population sequencing. The veSEQ-HIV method also provided HIV viral load data.","journal":"Journal of Antimicrobial Chemotherapy","year":2020,"id":104147,"datarank":0.48283137373023016,"base_score":3.2188758248682006,"endowment":3.2188758248682006,"self_citation_contribution":0.48283137373023016,"citation_network_contribution":0.0,"self_endowment_contribution":0.48283137373023016,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":24,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8056,"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":395919,"name":"David Bonsall","orcid":"0000-0003-2187-0550","position":1,"is_corresponding":false},{"id":443217,"name":"Vanessa Cummings","orcid":"0000-0001-7325-1837","position":2,"is_corresponding":false},{"id":438192,"name":"Rory Bowden","orcid":"0000-0001-8596-0366","position":3,"is_corresponding":false},{"id":395920,"name":"Tanya Golubchik","orcid":"0000-0003-2765-9828","position":4,"is_corresponding":false},{"id":506459,"name":"Mariateresa de Cesare","orcid":"0000-0002-9847-1526","position":5,"is_corresponding":false},{"id":440379,"name":"Ethan Wilson","orcid":"0000-0002-9120-3182","position":6,"is_corresponding":false},{"id":340352,"name":"Theresa Gamble","orcid":"0000-0002-2515-0828","position":7,"is_corresponding":false},{"id":294608,"name":"Carlos del Rı́o","orcid":"0000-0002-0153-3517","position":8,"is_corresponding":false},{"id":394768,"name":"D. Scott Batey","orcid":"0000-0002-2422-5787","position":9,"is_corresponding":false},{"id":305156,"name":"Kenneth H. Mayer","orcid":"0000-0001-7460-733X","position":10,"is_corresponding":false},{"id":299160,"name":"Jason E. Farley","orcid":"0000-0002-6896-0134","position":11,"is_corresponding":false},{"id":316704,"name":"James P. Hughes","orcid":"0000-0001-5034-3157","position":12,"is_corresponding":false},{"id":374739,"name":"Robert H. Remien","orcid":"0000-0002-3963-3273","position":13,"is_corresponding":false},{"id":241510,"name":"Chris Beyrer","orcid":"0000-0003-0665-9124","position":14,"is_corresponding":false},{"id":392159,"name":"Christophe Fraser","orcid":"0000-0003-2399-9657","position":15,"is_corresponding":false},{"id":36851,"name":"Susan H. Eshleman","orcid":"0000-0002-4587-791X","position":16,"is_corresponding":false},{"id":432556,"name":"Jessica M. Fogel","orcid":"0000-0003-3143-9000","position":0,"is_corresponding":true}],"reference_count":14,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T22:43:22.755723Z","pmid":"32772080","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":[]}