Abstract
BackgroundHIV-1 subtype B and subtype F are prevalent in the AIDS epidemic of Brazil. Recombinations between these subtypes have generated at least four BF circulating recombinant forms (CRFs). CRF28_BF and CRF29_BF are among the first two BF recombinants being identified in Brazil and they contributed significantly to the epidemic. However, the evolution and demographic histories of the CRFs are unclear.Methodology/Principal FindingsA collection of gag and pol sequences sampled within Brazil was screened for CRF28_BF-like and CRF29_BF-like recombination patterns. A Bayesian coalescent framework was employed to delineate the phylogenetic, divergence time and population dynamics of the virus having CRF28_BF-like and CRF29_BF-like genotype. These recombinants were phylogenetically related to each other and formed a well-supported monophyletic clade dated to 1988–1989. The effective number of infections by these recombinants grew exponentially over a five-year period after their emergence, but then decreased toward the present following a logistic model of population growth. The demographic pattern of both recombinants closely resembles those previously reported for CRF31_BC.ConclusionsWe revealed that HIV-1 recombinants of the CRF28_BF/CRF29_BF clade are still circulating in the Brazilian population. These recombinants did not exhibit a strong founder effect and showed a decreasing prevalence in the AIDS epidemic of Brazil. Our data suggested that multiple URFs may also play a role in shaping the epidemic of recombinant BF HIV-1 in the region.
Highlights
HIV-1 is classified into Group M, O, N and P
Our data suggested that multiple unique recombinant forms (URFs) may play a role in shaping the epidemic of recombinant BF HIV-1 in the region
Of the 433 subtype B pol sequences in the dataset, we found four sequences retrieved from the HIV Sequence Database that had recombination breakpoints similar to those of CRF28/29_BF (Figure 1B)
Summary
HIV-1 is classified into Group M, O, N and P. Group M HIV-1 dominates the AIDS pandemic with at least nine subtypes and multiple intersubtype recombinants currently identified [1]. 48 circulating recombinant forms (CRFs) and a large number of unique recombinant forms (URFs) have been identified. These CRFs and URFs accounted for almost 18% of new infections in 2004 [2] and they continue to play an increasingly important role in shaping the AIDS pandemic. HIV-1 subtype B and subtype F are prevalent in the AIDS epidemic of Brazil Recombinations between these subtypes have generated at least four BF circulating recombinant forms (CRFs). The evolution and demographic histories of the CRFs are unclear
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