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

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 B_CAR, which can mostly be found in the Caribbean region, and B_PAN, 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 B_PAN and B_CAR 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 B_CAR infections resulted from a single successful founder event that took place in the Amazonas state around the late 1970s, most B_PAN 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 (B_BR-I), and two others resulting from new introductions detected here. The reconstruction of the demographic history of the most prevalent B_PAN (n = 4) and B_CAR (n = 1) clades identified in Amazonas revealed that all clades displayed a continuous expansion [effective reproductive number (R _e) > 1] until most recent times. During the period of co-circulation from the late 1990s onward, the R_e of Amazonian B_PAN and B_CAR clusters behaved quite alike, fluctuating between 2.0 and 3.0. These findings support that the B_CAR and B_PAN 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, B_CAR and B_PAN variants continue to expand and show no signs of the epidemic stabilization observed in other parts of the country.

Keywords: Amazonas; Brazil; HIV-1; phylodynamics; subtype B.

FIGURE 1

ML phylogeographic analysis of major cluster B_CAR–BR–I disseminated in Brazil. A total of 296 B_CAR–BR–I Brazilian sequences sampled in Amazonas (n = 267) and other states (n = 29) were analyzed. The number in parenthesis indicates the inferred marginal probability that the clade ancestor was located in the Amazonas state. The location of taxonomic units at internal nodes across the ML tree was reconstructed and represented according to the color scheme shown in the map. Outside Amazonas state, other Brazilian units were aggregated according to the country region. AM, Amazonas; N, North; SE, Southeast. The tree was rooted using HIV-1 subtype D reference sequences (not shown). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site. Major migrations of viral clade B_CAR–BR–I are represented in the map.

FIGURE 2

ML phylogeographic analysis of major B_PAN–BR–I cluster disseminated in Brazil. A total of 844 B_PAN–BR–I Brazilian sequences sampled in Amazonas (n = 360) and other states from the Northern and Southeastern regions (n = 484) were analyzed together. We selected sequences from Northern and Southeastern states because were the regions more strongly connected with the Amazonas state. Major Amazonian clades B_{PAN–BR–I–AM–I} and B_{PAN–BR–I–AM–II} are indicated by colored shaded boxes along with cluster aLRT support (number at basal branch) and the inferred marginal probability that cluster ancestor was located in Amazonas state (in parentheses). The location of taxonomic units at internal nodes across the ML tree was reconstructed and represented according to the color scheme shown in the map. Sequences were grouped in three discrete locations: Amazonas state (AM), Northern region (N), and Southeastern region (SE). The tree was rooted using HIV-1 subtype D reference sequences (not shown). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site. Major migrations of viral clades B_{PAN–BR–I–AM–I} and B_{PAN–BR–I–AM–II} are represented in the map.

FIGURE 3

ML phylogeographic analysis of HIV-1 B_PAN Amazonian sequences that branched outside major Brazilian clades. A total of 530 B_PAN sequences sampled in Amazonas were aligned with: (A) Closely related B_PAN sequences sampled in other Brazilian states (n = 687) plus reference B_PAN sequences from the United States and France (n = 498), and (B) closely related B_PAN sequences sampled worldwide (n = 1,683). Major Amazonian clades B_PAN–AM–I and B_{PAN–AM–II} are indicated by colored shaded boxes along with cluster aLRT support (number at basal branch) and the inferred marginal probability that cluster ancestor was located in Amazonas state (in parenthesis). The location of taxonomic units at internal nodes across the ML tree was reconstructed and represented according to the color scheme shown in the map. Sequences were grouped in seven (A) and three (B) discrete locations: Amazonas state (AM), Central-Western region (CW), Northern region (N); Northeastern region (NE), Southeastern region (SE), Southern region (S), United States/France (US/FR), other Brazilian states (BR), and non-Brazilian (Non-BR). Tree was rooted using HIV-1 subtype D reference sequences (not shown). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site. Major migrations of viral clades (C) B_PAN–AM–I and (D) B_{PAN– AM–II} are represented in the maps.

FIGURE 4

Demographic history of subtype B cluster in Brazil’s Amazonas state. Each plot (A–E) details the demographic history of one subtype B large cluster (n ≥ 30) in Amazonas from the pandemic (B_PAN) and non-pandemic (B_CAR) forms. The graphs exhibit their effective number of HIV-1 infections under the Bayesian Skygrid (BSKG) model in blue (N_e, y-left-axis), and their effective reproductive number under the Birth-death Skyline (BDSKY) model in orange (N_e, y-right-axis). For both parameters are indicated their median (solid lines) and 95% HPD intervals (pale areas) estimates. A dashed vertical line indicates the TMRCA of the clades, accompanied by its median value. The last graph (F) compares the R_e obtained for the five clusters in the last period of analysis (2010–2018). For each cluster, its median R_e (solid line) and 95% HPD interval (pale area) inferred values are represented.