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

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.