{"doi":"10.3390/v14081673","title":"Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa","abstract":"The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 incidence. Here, we quantify breakthrough HIV-1 transmissions occurring during the trial from population-based, dried blood spot samples. Between 2013 and 2017, we obtained 549 gag and 488 pol HIV-1 consensus sequences from 745 participants: 469 participants infected prior to trial commencement and 276 SEARCH-incident infections. Putative transmission clusters, with a 1.5% pairwise genetic distance threshold, were inferred from maximum likelihood phylogenies; clusters arising after the start of SEARCH were identified with Bayesian time-calibrated phylogenies. Our phylodynamic approach identified nine clusters arising after the SEARCH start date: eight pairs and one triplet, representing mostly opposite-gender linked (6/9), within-community transmissions (7/9). Two clusters contained individuals with non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, both linked to intervention communities. The identification of SEARCH-incident, within-community transmissions reveals the role of unsuppressed individuals in sustaining the epidemic in both arms of a UTT trial setting. The presence of transmitted NNRTI resistance, implying treatment failure to the efavirenz-based antiretroviral therapy (ART) used during SEARCH, highlights the need to improve delivery and adherence to up-to-date ART recommendations, to halt HIV-1 transmission.","journal":"Viruses","year":2022,"id":283808,"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":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.6486,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":325082,"name":"Jesus F. Salazar-Gonzalez","orcid":"0000-0003-4626-6448","position":1,"is_corresponding":false},{"id":36881,"name":"Deogratius Ssemwanga","orcid":"0000-0001-9675-4234","position":2,"is_corresponding":false},{"id":255274,"name":"Edwin D. Charlebois","orcid":"0000-0001-7237-2119","position":3,"is_corresponding":false},{"id":255275,"name":"James Ayieko","orcid":"0000-0002-0324-4006","position":4,"is_corresponding":false},{"id":499542,"name":"Heather E. Grant","orcid":"0000-0001-9500-1644","position":5,"is_corresponding":false},{"id":412903,"name":"Teri Liegler","orcid":null,"position":6,"is_corresponding":false},{"id":960666,"name":"Katherine E. Atkins","orcid":"0000-0001-5250-0558","position":7,"is_corresponding":false},{"id":36860,"name":"Pontiano Kaleebu","orcid":"0000-0001-9706-2977","position":8,"is_corresponding":false},{"id":242453,"name":"Moses R. Kamya","orcid":"0000-0001-9106-4234","position":9,"is_corresponding":false},{"id":255295,"name":"Maya L. Petersen","orcid":"0000-0002-5505-153X","position":10,"is_corresponding":false},{"id":58746,"name":"Diane V. Havlir","orcid":"0000-0003-0761-3136","position":11,"is_corresponding":false},{"id":438195,"name":"Andrew Brown","orcid":"0000-0002-5700-3128","position":12,"is_corresponding":false},{"id":960665,"name":"Emma Pujol-Hodge","orcid":"0000-0001-8861-6608","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T00:29:28.452697Z","pmid":"36016295","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":[]}