HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network

Gräf, Tiago; Bello, Gonzalo; Andrade, Paula; Arantes, Ighor; Pereira, João Marcos; Silva, Alexandre Bonfim Pinheiro da; Veiga, Rafael Valente; Mariani, Diana; Boullosa, Lídia Theodoro; Arruda, Monica Barcelos; Couto-Fernandez, José Carlos; Dennis, Ann M.; Rasmussen, David A.; Tanuri, Amílcar

doi:10.1038/s41598-021-94542-5

Cited by 16 publications

(16 citation statements)

References 34 publications

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“…Previous studies demonstrate that the expanding HIV-1 subtype B epidemic in the Northern Brazilian state of Amazonas was driven by both pandemic (B PAN ) and non-pandemic (B CAR ) viral variants ( Cabello et al, 2015 ; Divino et al, 2016 ; Arantes et al, 2019 ; Crispim et al, 2019 ; Chaves et al, 2021 ; Gräf et al, 2021 ), thus creating a great opportunity to compare the epidemic dynamics of both subtype B forms spreading in the same population. This study revealed that the B PAN and B CAR epidemics in Amazonas have been shaped by different evolutionary histories, but displayed very similar transmissibility and expansion dynamics at most recent times.…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we used a total of 1,272 HIV-1 subtype B pol sequences (nucleotides 2,253–3,275 of reference strain HXB2) from Amazonas state sampled between 2009 and 2018 that were either available at the Los Alamos HIV Database 1 by March 2021 or were recently published ( Chaves et al, 2021 ; Gräf et al, 2021 ) and made available in GenBank 2 . Only one sequence per subject was selected.…”

Section: Methodsmentioning

confidence: 99%

“…Amazonian subtype B sequences classified as “others B CAR lineages” were aligned with sequences representative of the B CAR diversity in the Caribbean region ( n = 228) that were also described previously ( Cabello et al, 2014 ; Mendoza et al, 2014 ). Finally, Amazonian subtype B sequences classified as “others B PAN lineages” were aligned with: (i) one subset of closely related B PAN sequences from Brazil ( n = 687) selected from a large dataset of Brazilian sequences ( n = 88,441) described previously ( Gräf et al, 2021 ) and (ii) one subset of closely related B PAN sequences from different countries ( n = 1,700) selected from a large dataset of worldwide sampled sequences ( n = 71,160) recovered from Los Alamos HIV Database. We used the basic local alignment search tool (BLAST) 3 to select the 10 subtype B reference sequences (Brazilian and worldwide) with the highest similarity score (>95%) to each Amazonian subtype B sequence.…”

Section: Methodsmentioning

confidence: 99%

“…The HIV-1 subtype B epidemic in Brazil is mainly driven by the B PAN clade, with a few notable exceptions, like the Northern state of Amazonas, which is characterized by the co-circulation of the B PAN (75%) and B CAR (25%) variants at a high prevalence ( Divino et al, 2016 ; Crispim et al, 2019 ; Gräf et al, 2021 ). Among regional HIV-1 epidemics in Brazil, the one in the state of Amazonas stands out as the second largest AIDS detection rate (34.8 cases per 100,000 inhabitants) in the country, well above the mean national rate (17.8 cases per 100,000 inhabitants) ( Ministério da Saúde, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Dissemination Dynamics of HIV-1 Subtype B Pandemic and Non-pandemic Lineages Circulating in Amazonas, Brazil

et al. 2022

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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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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Dissemination Dynamics of HIV-1 Subtype B Pandemic and Non-pandemic Lineages Circulating in Amazonas, Brazil

et al. 2022

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“…the presence of CRF31_BC and CRF02_ AG in pregnant women suggests a recent introduction and dissemination of these recombinant forms, originating respectively from African countries and southern Brazilian states [10]. Phylogenetic analysis of HIV-1 genotyping sequences proved to be eff ective in studying the molecular epidemiology of HIV-1 in Brazil [11,12].…”

Section: Discussionmentioning

confidence: 99%

Low Prevalence of Transmitted HIV-1 Antiretroviral Resistance in Pregnant Women from Rio de Janeiro, Brazil

Couto-Fernandez¹,

Jesus²

2022

J Biomed Res Environ Sci

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Background: HIV screening during antenatal care is being expanded in Brazil for early diagnosis of HIV-1 infection during pregnancy and prevention of vertical transmission. HIV genotyping in pregnant women is crucial to reduce the risk of vertical transmission in those carrying resistant strains and may also be used for Transmitted Drug Resistance (TDR) surveillance purpose. We evaluated prevalence and patterns of HIV-1 TDR and HIV subtype distribution in recently diagnosed ARV naïve pregnant women from Rio de Janeiro, Brazil. Methods: 299 blood samples of recently diagnosed HIV-1-infected pregnant women from four reference antenatal care public health units in Rio de Janeiro were consecutively collected and analyzed from 2005 to 2015.ViroseqTM (Abbott) and TrugeneTM HIV-1 Genotyping Systems (Siemens) were used for genotyping and the Standford Algorithm for Interpretation of HIV-1 Resistance for TDR and subtype identification. Results: The most prevalent HIV-1 subtype was the subtype B (77%), followed by subtype F (15%), BF recombinant forms (4%), subtype C (2%) and the recombinant forms: CRF02_AG, CRF31_BC and DF identified in one subject each. Overall, the TDR mutations was 11.7%, 2.7% associated to the Nucleoside Reverse Transcriptase Inhibitors (NRTIs) of the samples, 2.7% to Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) and 1% to Protease Inhibitors (PIs). Mutations associated with NRTI resistance were TAMs, F77L, M184V; associated with NNRTI resistance were K103N, Y188H and L100I and. mutations associated to PIs were D30N, M46I, and V82L. Conclusions: HIV-1 subtype B was the most prevalent subtype observed in our study. For the first time infections with the circulating recombinant forms CRF02_AG and CRF31_BC were described in a pregnant woman, suggesting the spread of African derived virus in Brazil and the introduction in Rio de Janeiro of the CRF31_BC coming from South Brazil. Our results strongly suggest the need of establishing a regular surveillance system for transmitted HIV-1 drug resistance in pregnant women in Brazil and its integration in antenatal care management policies for HIV-1 infected women should be considered.

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Patterns of pregnancy loss among women living with and without HIV in Brazil, 2008–2018

Yang

Cambou²,

Segura³

et al. 2022

AJOG Global Reports

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HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network

Cited by 16 publications

References 34 publications

Dissemination Dynamics of HIV-1 Subtype B Pandemic and Non-pandemic Lineages Circulating in Amazonas, Brazil

Dissemination Dynamics of HIV-1 Subtype B Pandemic and Non-pandemic Lineages Circulating in Amazonas, Brazil

Low Prevalence of Transmitted HIV-1 Antiretroviral Resistance in Pregnant Women from Rio de Janeiro, Brazil

Patterns of pregnancy loss among women living with and without HIV in Brazil, 2008–2018

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