Abstract:Non-pandemic variants of the Human Immunodeficiency Virus Type 1 (HIV-1) subtype B accounts for a significant fraction of HIV infections in several Caribbean islands, Northeastern South American countries and the Northern Brazilian states of Roraima and Amazonas. In this paper, we used a comprehensive dataset of HIV-1 subtype B pol sequences sampled in Amazonas and Roraima between 2007 and 2017 to reconstruct the phylogeographic and demographic dynamics of the major HIV-1 subtype B non-pandemic Brazilian linea… Show more
“…It is interesting to note that the B CAR (2.5-2.6) and B PAN (2.9-3.4) Amazonian clades reached similar highest median R e values. Furthermore, the highest median R e estimated here using a birth-death approach was comparable to the previous ones estimated for the B CAR−BR−I clade (3.8) using a coalescent-based approach (Arantes et al, 2019), but lower than those estimated for major B PAN Brazilian lineages spreading in the Southeastern region (5.0-7.9) (Mir et al, 2015). These findings support that differences in the spreading dynamics of subtype B lineages may reflect discrepancies in the connectivity of underlying transmission networks across different Brazilian states/regions, rather than intrinsic differences in viral transmissibility.…”
Section: Discussionsupporting
confidence: 79%
“…This finding is consistent with our BDSKY analyses that support a continuous expansion (R e > 1) of major B CAR and B PAN Amazonian clades over all the studied period. The BSKG model indicates a recent stabilization of some Amazonian B PAN clades since the late 2000s, and a previous study conducted by our group also indicated a recent epidemic stabilization of the clade B CAR−BR−I since the late 2000s (Arantes et al, 2019). Although the median estimated R e of the B CAR and B PAN Amazonian clades was somewhat lower between 2010 and 2018 (1.6-2.3) than during the previous decades (2.5-3.4), we found no solid evidence of epidemic stabilization or reduction in the BDSKY analyses.…”
Section: Discussionsupporting
confidence: 65%
“…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%
“…Our analysis confirmed that variants B CAR and B PAN were introduced multiple times in the Amazonas state, although the estimated number of B PAN introductions was 16 times higher than that of B CAR . The founder event that originated the clade B CAR–BR–I occurred in the late 1970s ( Divino et al, 2016 ; Arantes et al, 2019 ) and gave rise to 89% of B CAR and 19% of total subtype B infections in Amazonas. In sharp contrast, most B PAN sequences from Amazonas branched into multiple state-specific clusters of medium/small size (57%) or appeared as unclustered infections (19%).…”
Section: Discussionmentioning
confidence: 99%
“…Previous studies identified four major B PAN (B PAN–BR–I to B PAN–BR–IV ) and four major B CAR (B CAR–BR–I to B CAR–BR–IV ) clusters circulating in Brazil ( Mir et al, 2015 ; Divino et al, 2016 ). The lineage B CAR–BR–I aggregates the majority (51%) of non-pandemic subtype B sequences from Brazil ( Divino et al, 2016 ) and its most recent common ancestor (MRCA) could be traced back to Amazonas in the late 1970s, from a viral migration probably originated in the French Guiana ( Divino et al, 2016 ; Arantes et al, 2019 ). The cluster composition and the evolutionary history of the B PAN clade in the Amazonas state are currently unknown.…”
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.
“…It is interesting to note that the B CAR (2.5-2.6) and B PAN (2.9-3.4) Amazonian clades reached similar highest median R e values. Furthermore, the highest median R e estimated here using a birth-death approach was comparable to the previous ones estimated for the B CAR−BR−I clade (3.8) using a coalescent-based approach (Arantes et al, 2019), but lower than those estimated for major B PAN Brazilian lineages spreading in the Southeastern region (5.0-7.9) (Mir et al, 2015). These findings support that differences in the spreading dynamics of subtype B lineages may reflect discrepancies in the connectivity of underlying transmission networks across different Brazilian states/regions, rather than intrinsic differences in viral transmissibility.…”
Section: Discussionsupporting
confidence: 79%
“…This finding is consistent with our BDSKY analyses that support a continuous expansion (R e > 1) of major B CAR and B PAN Amazonian clades over all the studied period. The BSKG model indicates a recent stabilization of some Amazonian B PAN clades since the late 2000s, and a previous study conducted by our group also indicated a recent epidemic stabilization of the clade B CAR−BR−I since the late 2000s (Arantes et al, 2019). Although the median estimated R e of the B CAR and B PAN Amazonian clades was somewhat lower between 2010 and 2018 (1.6-2.3) than during the previous decades (2.5-3.4), we found no solid evidence of epidemic stabilization or reduction in the BDSKY analyses.…”
Section: Discussionsupporting
confidence: 65%
“…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%
“…Our analysis confirmed that variants B CAR and B PAN were introduced multiple times in the Amazonas state, although the estimated number of B PAN introductions was 16 times higher than that of B CAR . The founder event that originated the clade B CAR–BR–I occurred in the late 1970s ( Divino et al, 2016 ; Arantes et al, 2019 ) and gave rise to 89% of B CAR and 19% of total subtype B infections in Amazonas. In sharp contrast, most B PAN sequences from Amazonas branched into multiple state-specific clusters of medium/small size (57%) or appeared as unclustered infections (19%).…”
Section: Discussionmentioning
confidence: 99%
“…Previous studies identified four major B PAN (B PAN–BR–I to B PAN–BR–IV ) and four major B CAR (B CAR–BR–I to B CAR–BR–IV ) clusters circulating in Brazil ( Mir et al, 2015 ; Divino et al, 2016 ). The lineage B CAR–BR–I aggregates the majority (51%) of non-pandemic subtype B sequences from Brazil ( Divino et al, 2016 ) and its most recent common ancestor (MRCA) could be traced back to Amazonas in the late 1970s, from a viral migration probably originated in the French Guiana ( Divino et al, 2016 ; Arantes et al, 2019 ). The cluster composition and the evolutionary history of the B PAN clade in the Amazonas state are currently unknown.…”
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.
(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 3,704 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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