The HIV Epidemic in the Amazon Basin Is Driven by Prototypic and Recombinant HIV-1 Subtypes B and F

Abstract

This paper describes genetic subtypes of HIV-1 found in blood samples from 31 HIV-1-infected people who visited the Counseling and Testing AIDS Center of Instituto de Medicina Tropical in Manaus, Brazil. Manaus, the main city in Brazil's Amazon Basin, is also the closest urban connection for more than 100,000 Indians living in the rain forests of this region. Although to date there is no evidence of increased incidence of HIV-1 infection among the indigenous population, our understanding of both the prevalence and nature of the epidemic in the region as a whole is limited. From the 31 samples analyzed by C2V3 sequencing, we found almost equal proportions of HIV-1 strains belonging to subtype B (n = 16; 51.6%) and subtype F (n = 15; 48.4%), a finding that differs from results from previous studies conducted in urban areas of southeastern Brazil. We also observed the presence of the GWGR amino-acid sequence in the critical tetra-peptide crown of the env V3 loop in the HIV-1 subtype B samples analyzed. Among these samples, we also found 14 mosaic genomes (45.16%) in which different combinations of subtypes B, C, and F were identified between the p24 gag, pro, and env regions. Our data support the hypothesis that the Amazonian HIV-1 infections linked to the urban epidemic in southeastern Brazil. The genetic diversity and the prevalence of mosaic genomes among the isolates in our study confirm an integral role of recombination in the complex Brazilian epidemic.

HIV-1 Strains Identified in Brazilian Blood Donors: Significant Prevalence of B/F1 Recombinants

“…Subtype B was The results in this study are consistent with previous studies that show a high prevalence of subtype B in other population groups within Brazil. 3,6,8,12,15,16 In contrast, the frequencies of subtypes C and F1 were lower than some of the previous reports. [3][4][5][6] For subtype C, this may be due in part to the unequal geographic distribution of subtype C in the country with a higher prevalence in the south and decreasing prevalence moving into north and central Brazil.…”

“…[2][3][4] B/F1 recombinants are common where subtypes B and F1 cocirculate. 3,[5][6][7][8] Similarly, B/C recombinants are emerging in the south and southeastern regions of the country. 9 Although subtype B is the predominant strain found throughout Brazil, the epidemic is changing.…”

“…[2][3][4] Subtype F1 is declining with B/F1 recombinants now more common than nonrecombinant F1. 3,[5][6][7][8] The dynamic nature of the HIV epidemic in Brazil led us to evaluate HIV-1 subtypes present in HIV-infected blood donations. Blood donors represent a wider cross section of the population than selected high risk groups and thus may provide a broader overview of the HIV-1 strains circulating in Brazil.…”

Molecular screening shows extensive HIV-1 genetic diversity in Central West Brazil

“…There are regional differences in the pattern of HIV-1 subtypes. In the South the epidemic is driven by HIV-1 subtype C (pol region) (Soares et al, 2003), whereas equal proportions of HIV-1 subtypes B and F (env region) were found in the northern Amazon basin (Vicente et al, 2000). In the Northeast and Central West regions HIV-1 subtype B predominates and cases of subtype F and C and B/F recombinants involving the env, gag and pol regions occur (Cerqueira et al, 2004;Couto-Fernandez et al, 1999;Gadelha et al, 2003;Pereira et al, 2004;Pereira et al, 2006;Stefani et al, 2000).…”

Oh Brother, Where Art Thou? A Bayes Factor Test for Recombination with Uncertain Heritage

“…Some putative recombinants may be important vectors in HIV-1 epidemics (Liitsola et al, 1998;Vicente et al, 2000). The effects of recombination may also play an important role in vaccine development (Smith et al, 1998) and the evolution of drug resistance (Kellam and Larder, 1995;Yusa et al, 1997).…”