{"doi":"10.3390/v13061174","title":"The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review","abstract":"<jats:p>To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995–2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.</jats:p>","journal":"Viruses","year":2021,"id":609287,"datarank":0.41588830833596724,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.0,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":509818,"name":"Jamirah Nazziwa","orcid":"0000-0001-9029-7976","position":1,"is_corresponding":false},{"id":707953,"name":"Amin S. 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Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995–2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.</jats:p>","is_dataset_classified":null,"base_score":2.772588722239781,"endowment":2.772588722239781,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"34205246","pmcid":"PMC8235305","openalex_id":"https://openalex.org/W3177277648","authors":[],"funders":[{"funder_name":"Sub-Saharan African Network for TB/HIV Research Excellence","grant_id":"-","title":null},{"funder_name":"DELTAS Africa Initiative","grant_id":"#DEL-15-006","title":null},{"funder_name":"Wellcome Trust","grant_id":"#107752/Z/15/Z","title":null},{"funder_name":"Swedish Research Council","grant_id":"#2016-01417","title":null},{"funder_name":"Swedish Society for Medical Research","grant_id":"#SA-2016","title":null},{"funder_name":"Wellcome Trust","grant_id":"107752/Z/15/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"209294/Z/17/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"107752","title":"Sub-Saharan African Network for TB/HIV research Excellence (SANTHE)"},{"funder_name":"Swedish Research Council","grant_id":"unidentified","title":"unidentified"}],"total_grants":9,"fwci":1.1604,"citation_percentile":0.68085106,"influential_citations":0,"citation_trend":[{"year":2021,"count":1},{"year":2022,"count":4},{"year":2023,"count":4},{"year":2024,"count":2},{"year":2025,"count":3},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/1999-4915/13/6/1174/pdf?version=1624080091","host_type":"journal"},{"url":"https://www.mdpi.com/1999-4915/13/6/1174/pdf?version=1624080091","host_type":"publisher"},{"url":"https://www.mdpi.com/1999-4915/13/6/1174/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/v13061174","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/34205246","host_type":"repository"},{"url":"https://pure.amsterdamumc.nl/en/publications/f6be5ddb-9d38-4919-9f00-5d7ca9841191","host_type":"repository"},{"url":"https://pure.amc.nl/en/publications/the-role-of-phylogenetics-in-discerning-hiv1-mixing-among-vulnerable-populations-and-geographic-regions-in-subsaharan-africa(e0e70edf-8d34-41ef-825e-18faac935c50).html","host_type":"repository"},{"url":"https://doaj.org/article/e0485b0f53e146b482d5c065b9e30f2b","host_type":"repository"},{"url":"https://lup.lub.lu.se/record/567bdd9b-162c-44a3-bf57-9364abfa410d","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/v13061174","host_type":"repository"},{"url":"https://ora.ox.ac.uk/objects/uuid:bc039e23-c6e0-4ca5-98d3-93d42daa3347","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8235305","host_type":"repository"},{"url":"https://pure.amsterdamumc.nl/ws/files/140647476/The-role-of-phylogenetics-in-discerning-hiv-1-mixing-among-vulnerable-populations-and-geographic-regions-in-sub-saharan-.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC8235305","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC8235305?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.3390/v13061174","host_type":""}],"fields_of_study":["HIV Research and Treatment","HIV/AIDS Research and Interventions","HIV, Drug Use, Sexual Risk","0301 basic medicine","03 medical and health sciences","0303 health sciences","Africa South of the Sahara","Databases, Genetic","Genotype","HIV Infections","HIV-1","Humans","Phylogeny","Phylogeography","Population Surveillance","Prevalence","Risk Factors","Vulnerable Populations"],"mesh_terms":["Genotype","Humans","Phylogeny","Population Surveillance","Risk Factors","HIV-1","HIV Infections","Prevalence","Africa South of the Sahara","Databases, Genetic","Vulnerable Populations","Phylogeography"],"keywords":["Transmission (telecommunications)","Geography","Phylogenetic tree","Human immunodeficiency virus (HIV)","Demography","Incidence (geometry)","Location","Environmental health","Biology","Medicine","Virology","Genetics","Computer science","HIV-1","Sub-Saharan Africa","phylogenetics","Transmission Dynamics","Mixed Epidemics","Genotype","HIV Infections","Review","Microbiology","Vulnerable Populations","Risk Factors","Databases, Genetic","Prevalence","Humans","Africa South of the Sahara","Phylogeny","QR1-502","Phylogeography","Population Surveillance"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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