South-to-Southeast Expansion of HIV-1 Subtype C in Brazil

Abstract

HIV-1 group M subtype C (HIV-1C) is the predominant genetic variant in southern Brazil but has been sparsely detected in other regions of the country. Our study aimed to identify HIV-1C transmission links across Brazil using phylogenetic reconstruction and to infer trends in geographical patterns and dissemination beyond the southern region. We retrieved 3693 HIV-1C (partial pol) sequences from NCBI and LANL databases and applied maximum likelihood phylogenetic reconstruction to infer transmission clusters, using clade confidence (SH-aLRT) and intracluster genetic distance as critical parameters. Our results suggest that the Southern states of Brazil have played a key role in fueling the HIV-1C epidemic in São Paulo, particularly through transmissions from Paraná and Santa Catarina. In contrast, despite having one of the highest HIV-1C prevalence rates of Brazil, Rio Grande do Sul exhibited a highly concentrated epidemic with limited epidemiological linkages to other states. São Paulo seems to be a crucial hub for HIV-1C dissemination, connecting the epidemic in the southern states with other regions. Central states may act as secondary hubs, facilitating connections between the southeastern and northeastern regions. This study enhances the understanding of the geographical dynamics and expansion patterns of HIV-1C in Brazil, emphasizing the significance of regional epidemiological connections.

Keywords: Brazil; HIV‐1; epidemic; molecular phylogenetics; subtype C; transmission clusters.

Figure 1

Quantitative and geographic distribution of transmission clusters identified in the HIV‐1 subtype C phylogenetic reconstruction encompassing sequences isolated in Africa and Brazil (1998–2017). (A) Maximum likelihood phylogenetic reconstruction of 3693 HIV‐1 subtype C pol sequences. Clustered sequences are highlighted and colored by region of sampling in Brazil (clustering criteria: node support ≥ 85 and maximum genetic distance = 0.03). (B) Number of clusters and total individuals included in Brazilian transmission clusters. Phylogenetic clusters are categorized as intrastate (dark gray) or interstate (light gray). (C) Geographic distribution of Brazilian transmission clusters. Size of the red circles are proportional to the amount of subtype C sequences in each state.

Figure 2

Sankey Diagram representing the spatial distribution of HIV‐1 subtype C sequences included in transmission clusters, Brazil. Brazilian states: AP (Amapá), AM (Amazonas), BA (Bahia), CE (Ceará), ES (Espírito Santo), GO (Goiás), MA (Maranhão), MS (Mato Grosso do Sul), MG (Minas Gerais), PA (Pará), PR (Paraná), PE (Pernambuco), RJ (Rio de Janeiro), RS (Rio Grande do Sul), RO (Rondônia), SC (Santa Catarina), SP (São Paulo).

Figure 3

Temporal distribution of transmission clusters and viral growth of HIV‐1 subtype C in São Paulo, Paraná, Santa Catarina and Rio Grande do Sul. (A) Temporal distribution of intrastate transmission clusters. (B) Correlation between the number of sequences within transmission clusters and the year of sampling for transmission clusters (Intrastate cluster sequences only). (C) Effective population size of HIV‐1C for four states in Brazil (total number of sequences, clustered and non‐clustered).