Reconstructing the Dissemination Dynamics of the Major HIV-1 Subtype B Non-Pandemic Lineage Circulating in Brazil

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 lineage, designated as BCAR-BR-I. Our analyses revealed that its origin could be traced to one of many viral introductions from French Guiana and Guyana into Northern Brazil, which probably occurred in the state of Amazonas around the late 1970s. The BCAR-BR-I clade was rapidly disseminated from Amazonas to Roraima, and the epidemic grew exponentially in these Northern Brazilian states during the 1980s and 1990s, coinciding with a period of economic and fast population growth in the region. The spreading rate of the BCAR-BR-I clade, however, seems to have slowed down since the early 2000s, despite the continued expansion of the HIV-1 epidemic in this region in the last decade.

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

“…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.…”

“…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.…”

“…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.…”

“…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%).…”

“…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.…”