{"doi":"10.1101/2021.06.19.21259186","title":"Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial","abstract":"Abstract Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV- intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly-aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] versus 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] versus 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention. Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies.","journal":"medRxiv","year":2021,"id":219029,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9449,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":548686,"name":"Yinfeng Zhang","orcid":"0000-0003-2457-7712","position":1,"is_corresponding":false},{"id":395920,"name":"Tanya Golubchik","orcid":"0000-0003-2765-9828","position":2,"is_corresponding":false},{"id":529228,"name":"Victor De Gruttola","orcid":null,"position":3,"is_corresponding":false},{"id":546382,"name":"Eric Tchetgen Tchetgen","orcid":null,"position":4,"is_corresponding":false},{"id":439048,"name":"Vlad Novitsky","orcid":null,"position":5,"is_corresponding":false},{"id":257502,"name":"Janet Moore","orcid":"0009-0008-9727-701X","position":6,"is_corresponding":false},{"id":503007,"name":"Pamela Bachanas","orcid":"0000-0001-9408-9904","position":7,"is_corresponding":false},{"id":817579,"name":"Tebogo Segolodi","orcid":null,"position":8,"is_corresponding":false},{"id":503006,"name":"Refeletswe Lebelonyane","orcid":"0000-0002-9838-2419","position":9,"is_corresponding":false},{"id":439057,"name":"Molly Pretorius Holme","orcid":null,"position":10,"is_corresponding":false},{"id":425983,"name":"Sikhulile Moyo","orcid":"0000-0003-3821-4592","position":11,"is_corresponding":false},{"id":393322,"name":"Joseph Makhema","orcid":"0000-0003-0017-2438","position":12,"is_corresponding":false},{"id":257497,"name":"Shahin Lockman","orcid":"0000-0002-5384-9716","position":13,"is_corresponding":false},{"id":392159,"name":"Christophe Fraser","orcid":"0000-0003-2399-9657","position":14,"is_corresponding":false},{"id":425982,"name":"Max Essex","orcid":"0000-0002-4576-7841","position":15,"is_corresponding":false},{"id":106022,"name":"Marc Lipsitch","orcid":"0000-0003-1504-9213","position":16,"is_corresponding":false},{"id":817164,"name":"Lerato E Magosi","orcid":"0000-0002-3388-9892","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-18T23:53:33.915158Z","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":[]}