Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

ABSTRACT
The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1
epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other
parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and
a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected
from individuals in 13 municipalities in the Brazilian southern region. HIV-1 env and pol genes were submitted to phylogenetic
analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and
logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however,
an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state,
subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth
rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer
time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men
who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region.