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.
Highlights
The HIV-1 subtype B pandemic started when the ancestral virus arrived and first established itself in the Caribbean region during the mid-1960s (Gilbert et al, 2007)
The HIV-1 subtype B epidemic in Brazil is mainly driven by the both pandemic (BPAN) clade, with a few notable exceptions, like the Northern state of Amazonas, which is characterized by the cocirculation of the BPAN (75%) and BCAR (25%) variants at a high prevalence (Divino et al, 2016; Crispim et al, 2019; Gräf et al, 2021)
The sub-lineage assignment reveals that most BCAR Amazonian sequences belong to the major Brazilian clade BCAR−BR−I (89%), while the remaining sequences were classified within clades BCAR−BR−II (1%), BCAR−BR−III (1%), or branched outside known Brazilian clades (8%) (Table 1)
Summary
The HIV-1 subtype B pandemic started when the ancestral virus arrived and first established itself in the Caribbean region during the mid-1960s (Gilbert et al, 2007). The subsequent subtype B spread generated a set of local clades, designated as BCAR, that remained mostly confined to the Caribbean region (Gilbert et al, 2007; Cabello et al, 2014). One of those viruses, migrated from the Caribbean to the United States around the late 1960s and established a pandemic clade, called BPAN, that was disseminated worldwide (Worobey et al, 2016). 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). Despite important advances in HIV diagnosis and treatment, the Amazonas HIV/AIDS epidemic is not stabilized and has displayed a rising AIDS incidence over the last 10 years (Ministério da Saúde, 2020)
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