Background HIV-1 subtype B and subtype F are widespread in the AIDS epidemic of Brazil. 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 WYE-132 recombinant BF HIV-1 in the region. Introduction HIV-1 is usually 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]. The intersubtype recombinants are the result of recombination among the subtypes of HIV-1. Furthermore, these intersubtype recombinants can also recombine with HIV-1 of the same or different subtypes or with other recombinants to generate more complex recombinants. They emerge in almost every region of the world where more than one HIV-1 subtype is present. Currently, 48 circulating recombinant forms (CRFs) and a large number of C13orf1 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. It is reported that there are more than 545,000 AIDS cases in Brazil [3]. The epidemic is particularly severe in the southeastern part of the country, where large urban centers such as Rio de Janeiro and Sao Paulo are situated. At the end WYE-132 of 2008, the southeastern says (Espirito Santo, Minas Gerais, Rio de Janeiro and Sao Paulo) reported at least 323,000 diagnosed AIDS cases (59.3% of all cases in the country) with approximately 19.2 AIDS cases per 100,000 people [3]. The epidemic in the southeastern region of the country is complicated by multiple subtypes and recombinants of HIV-1 circulating in the population. For instance in the city of Sao Paulo, the major subtypes are subtype B (79%C88%) and subtype F WYE-132 (4%C11%) [4], [5]. Such a dense transmission network, with a high HIV-1 incidence rate and multiple subtypes present in the region, provides a perfect breeding ground for new HIV-1 recombinants. Indeed, HIV-1 recombinants between subtype B and subtype F have already been frequently identified because the launch of subtype F in Brazil [6], [7], [8], [9], [10], [11], [12]. Research show that up to 9% from the HIV-1 isolated in Sao Paulo possess a mosaic B/F genome [4], [5]; specifically, the CRF29_BF and CRF28_BF recombinants had been determined in your community in 1999 [13], [14]. CRF29_BF and CRF28_BF had been determined in sufferers on the Counselling and Tests Centers in Santos, which really is a port city located 80 km through the populous city of Sao Paulo [14]. CRF29_BF had been also determined in sufferers from Sao Rio and Paulo de Janeiro [6], [13]. These CRFs are specific from CRF12_BF genetically, that was initial discovered and discovered to become broadly circulating in Argentina [15] eventually, [16], [17]. A lot of the CRF28_BF and CRF29_BF genome belongs to subtype B and it is closely linked to the subtype B HIV-1 circulating in Brazil (Body 1A) [14]. The subtype F regions are from the Brazilian subtype F1 phylogenetically. CRF29_BF and CRF28_BF talk about equivalent recombination breakpoints in the and genes at nucleotide (nt) positions 1,322 and 2,571 (HXB2 numbering). CRF29_BF comes with an extra subtype F area spanning from nt 3,682 to 5,462, creating extra breakpoints in the and genes. Due to the normal recombination breakpoints the fact that recombinants share, it’s possible that a common ancestor of the BF recombinants emerged early in the epidemic and has evolved through subsequent recombination events. Physique 1 Mapping the recombination breakpoints of CRF. Although several studies have been carried out to characterize the epidemiology and phylogenetics of subtype B and subtype F HIV-1, and BF URFs in Brazil [4], [5], [6], [7], [8], [9], [10], [11], [13], [18], little is known about the evolutionary and demographic histories, and the epidemic potential of the CRF28_BF and CRF29_BF. Here, we reconstructed the evolutionary history of the.