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de Almeida Rego FF, de Moraes L, Giovanetti M, Silva JAG, Torres FG, de Oliveira Silva M, da Purificação Pereira da Silva M, Van Weyenbergh J, Santos LA, Khouri R. Genomic Detection of the Emerging, Highly Pathogenic HIV-1 Subtype D in Bahia, Northeast Brazil. Viruses 2023; 15:1650. [PMID: 37631993 PMCID: PMC10458544 DOI: 10.3390/v15081650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
(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.
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Affiliation(s)
- Filipe Ferreira de Almeida Rego
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
| | - Laise de Moraes
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte 30190-002, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 21-00128 Rome, Italy
| | - José Adriano Góes Silva
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Felipe Guimarães Torres
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
| | - Marcio de Oliveira Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Maria da Purificação Pereira da Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Johan Van Weyenbergh
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
| | - Luciane Amorim Santos
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
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Arantes I, Gräf T, Andrade P, Oliveira Chaves Y, Guimarães ML, Bello G. Dissemination Dynamics of HIV-1 Subtype B Pandemic and Non-pandemic Lineages Circulating in Amazonas, Brazil. Front Microbiol 2022; 13:835443. [PMID: 35330760 PMCID: PMC8940292 DOI: 10.3389/fmicb.2022.835443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
The HIV-1 epidemic in the Amazonas state, as in most of Brazil, is dominated by subtype B. The state, nonetheless, is singular for its significant co-circulation of the variants BCAR, which can mostly be found in the Caribbean region, and BPAN, a clade that emerged in the United States and aggregates almost the totality of subtype B infections world-wide. The Amazonian HIV-1 epidemic provides a unique scenario to compare the epidemic potential of BPAN and BCAR clades spreading in the same population. To reconstruct the spatiotemporal dynamic and demographic history of both subtype B lineages circulating in Amazonas, we analyzed 1,272 HIV-1 pol sequences sampled in that state between 2009 and 2018. Our phylogeographic analyses revealed that while most BCAR infections resulted from a single successful founder event that took place in the Amazonas state around the late 1970s, most BPAN infections resulted from the expansion of multiple clusters seeded in the state since the late 1980s. Our data support the existence of at least four large clusters of the pandemic form in Amazonas, two of them nested in Brazil’s largest known subtype B cluster (BBR–I), and two others resulting from new introductions detected here. The reconstruction of the demographic history of the most prevalent BPAN (n = 4) and BCAR (n = 1) clades identified in Amazonas revealed that all clades displayed a continuous expansion [effective reproductive number (Re) > 1] until most recent times. During the period of co-circulation from the late 1990s onward, the Re of Amazonian BPAN and BCAR clusters behaved quite alike, fluctuating between 2.0 and 3.0. These findings support that the BCAR and BPAN variants circulating in the Brazilian state of Amazonas displayed different evolutionary histories, but similar epidemic trajectories and transmissibility over the last two decades, which is consistent with the notion that both subtype B variants display comparable epidemic potential. Our findings also revealed that despite significant advances in the treatment of HIV infections in the Amazonas state, BCAR and BPAN variants continue to expand and show no signs of the epidemic stabilization observed in other parts of the country.
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Affiliation(s)
- Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Paula Andrade
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Yury Oliveira Chaves
- Laboratório de Diagnóstico e Controle de Doenças Infecciosas na Amazônia, Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz (FIOCRUZ), Manaus, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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