{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:24:55Z","timestamp":1760149495301,"version":"build-2065373602"},"reference-count":52,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2023,7,29]],"date-time":"2023-07-29T00:00:00Z","timestamp":1690588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior\u2014Brasil (CAPES)","award":["001","APP0032\/2016","65083\/2015-8","G0A0621N"],"award-info":[{"award-number":["001","APP0032\/2016","65083\/2015-8","G0A0621N"]}]},{"DOI":"10.13039\/501100006181","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado da Bahia","doi-asserted-by":"publisher","award":["001","APP0032\/2016","65083\/2015-8","G0A0621N"],"award-info":[{"award-number":["001","APP0032\/2016","65083\/2015-8","G0A0621N"]}],"id":[{"id":"10.13039\/501100006181","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Brazilian National Council for Scientific and Technological Development","award":["001","APP0032\/2016","65083\/2015-8","G0A0621N"],"award-info":[{"award-number":["001","APP0032\/2016","65083\/2015-8","G0A0621N"]}]},{"name":"Fonds voor Wetenschappelijk Onderzoek Vlaanderen","award":["001","APP0032\/2016","65083\/2015-8","G0A0621N"],"award-info":[{"award-number":["001","APP0032\/2016","65083\/2015-8","G0A0621N"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d","award":["001","APP0032\/2016","65083\/2015-8","G0A0621N"],"award-info":[{"award-number":["001","APP0032\/2016","65083\/2015-8","G0A0621N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: To achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African, and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains.<\/jats:p>","DOI":"10.3390\/v15081650","type":"journal-article","created":{"date-parts":[[2023,7,31]],"date-time":"2023-07-31T01:28:46Z","timestamp":1690766926000},"page":"1650","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Detection of the Emerging, Highly Pathogenic HIV-1 Subtype D in Bahia, Northeast Brazil"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6102-6672","authenticated-orcid":false,"given":"Filipe Ferreira","family":"de Almeida Rego","sequence":"first","affiliation":[{"name":"Escola Bahiana de Medicina e Sa\u00fade P\u00fablica, Avenida Dom Jo\u00e3o VI, 275, Brotas, Salvador  40290-000, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9095-5860","authenticated-orcid":false,"given":"Laise","family":"de Moraes","sequence":"additional","affiliation":[{"name":"Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Rua Waldemar Falc\u00e3o, 121, Candeal, Salvador 40296-710, Bahia, Brazil"},{"name":"Programa de P\u00f3s-Gradua\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pra\u00e7a Ramos de Queir\u00f3s, s\/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5849-7326","authenticated-orcid":false,"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Instituto Rene Rachou, Funda\u00e7\u00e3o Oswaldo Cruz, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte 30190-002, Minas Gerais, Brazil"},{"name":"Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 21-00128 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 Adriano G\u00f3es","family":"Silva","sequence":"additional","affiliation":[{"name":"Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Rua Waldemar Falc\u00e3o, 121, Candeal, Salvador 40296-710, Bahia, Brazil"},{"name":"Programa de P\u00f3s-Gradua\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pra\u00e7a Ramos de Queir\u00f3s, s\/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil"},{"name":"Centro Estadual Especializado em Diagn\u00f3stico, Assist\u00eancia e Pesquisa, Secretaria de Sa\u00fade do Estado da Bahia, Salvador 40110-050, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0506-8568","authenticated-orcid":false,"given":"Felipe Guimar\u00e3es","family":"Torres","sequence":"additional","affiliation":[{"name":"Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Rua Waldemar Falc\u00e3o, 121, Candeal, Salvador 40296-710, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcio","family":"de Oliveira Silva","sequence":"additional","affiliation":[{"name":"Centro Estadual Especializado em Diagn\u00f3stico, Assist\u00eancia e Pesquisa, Secretaria de Sa\u00fade do Estado da Bahia, Salvador 40110-050, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"da Purifica\u00e7\u00e3o Pereira da Silva","sequence":"additional","affiliation":[{"name":"Centro Estadual Especializado em Diagn\u00f3stico, Assist\u00eancia e Pesquisa, Secretaria de Sa\u00fade do Estado da Bahia, Salvador 40110-050, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3234-8426","authenticated-orcid":false,"given":"Johan","family":"Van Weyenbergh","sequence":"additional","affiliation":[{"name":"Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0261-3495","authenticated-orcid":false,"given":"Luciane Amorim","family":"Santos","sequence":"additional","affiliation":[{"name":"Escola Bahiana de Medicina e Sa\u00fade P\u00fablica, Avenida Dom Jo\u00e3o VI, 275, Brotas, Salvador  40290-000, Bahia, Brazil"},{"name":"Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Rua Waldemar Falc\u00e3o, 121, Candeal, Salvador 40296-710, Bahia, Brazil"},{"name":"Programa de P\u00f3s-Gradua\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pra\u00e7a Ramos de Queir\u00f3s, s\/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricardo","family":"Khouri","sequence":"additional","affiliation":[{"name":"Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz, Rua Waldemar Falc\u00e3o, 121, Candeal, Salvador 40296-710, Bahia, Brazil"},{"name":"Programa de P\u00f3s-Gradua\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Pra\u00e7a Ramos de Queir\u00f3s, s\/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil"},{"name":"Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, 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