Analysis of HIV Type 1 BF Recombinant Sequences from South America Dates the Origin of CRF12_BF to a Recombination Event in the 1970s

Abstract

HIV-1 epidemics in South America are believed to have originated in part from the subtype B epidemic initiated in the Caribbean/North America region. However, circulation of BF recombinants in similar proportions was extensively reported. Information currently shows that many BF recombinants share a recombination structure similar to that found in the CRF12_BF. In the present study, analyzing a set of 405 HIV sequences, we identified the most likely origin of the BF epidemic in an early event of recombination. We found that the subtype B epidemics in South America analyzed in the present study were initiated by a founder event that occurred in the early 1970s, a few years after the introduction of these strains in the Americas. Regarding the F/BF recombinant epidemics, by analyzing a subtype F genomic segment within the viral gene gag present in the majority of the BF recombinants, we found evidence of a geographic divergence very soon after the introduction of subtype F strains in South America. Moreover, through analysis of a subtype B segment present in all the CRF12_BF-like recombination structure, we estimated the circulation of the subtype B strain that gave rise to that recombinant structure around the same time period estimated for the introduction of subtype F strains. The HIV epidemics in South America were initiated in part through a founder event driven by subtype B strains coming from the previously established epidemic in the north of the continent. A second introduction driven by subtype F strains is likely to have encountered the incipient subtype B epidemic that soon after their arrival recombined with them, originating the BF epidemic in the region. These results may explain why in South America the majority of F sequences are found as BF recombinants.

Caracterización de los subtipos de VIH-1 presentes en Córdoba (Argentina) desde casi el inicio de la infección, utilizando los genes POL y ENV.

“…In the six data sets of the pure pol and env genes (Figs. 4 and 5), these two sequences clustered together in the trees, reinforcing the monophyletic origin proposed by Dilernia et al 30 . However, more than one recombination event between subtypes B and F1 must have occurred, since several strains could be considered as URF_B/F1.…”

“…Regarding the epidemic of subtypes C, B, F1 and recombinants B/F1 in South America 28,29,30,31 , most studies stated the need of analyzing sequences of "pure" subtypes to determine if introductions in different countries occurred once or multiple times from different geographic origins. Following these recommendations, we divided the sequences of the pol and env genes into "pure" data sets.…”

“…There are different estimations of the date of the most recent common ancestor (MRCA) for this subtype in the region: Aulicino et al 33 suggested that it could be traced back until 1976 and Dilernia et al 30 30 estimated that the MRCA of Argentinean subtype B can be traced to 1972 (10 years before the first AIDS case was diagnosed in this country) and probably this subtype recombined with F1 in the late 70's. The recombinant CRF12_B/F1 would have a monophyletic origin which occurred in 1982.…”

A clustering phenomenon among HCV‐1a strains among patients coinfected with HIV from Buenos Aires, Argentina

“…Interestingly, several studies [Aulicino et al, 2007;Bello et al, 2010;Dilernia et al, 2011] have reported recently that the origin of the HIV-BF subtype in South America dates from the beginning of the 1970s, overlapping with the HPD 95% found for the HCV-1a Argentinean sequences included into the cluster M. Nevertheless, the 95% HPD intervals found for the tMRCA of the HCV-1a cluster, final conclusions remain elusive. This limitation deserves further investigation with a longer time span of sampling that allows reaching short confidence intervals for dates, and higher precision.…”

“…Reverse transcription was performed with MMLV reverse transcriptase (Promega, Madison, WI) and random hexamers (Promega). The HCV-E2, HCV-NS5A and HIV-pol nested-PCR protocols were performed as described previously [Bolcic et al, 2008a;Dilernia et al, 2011] thus obtaining HCV-E2, HCV-NS5A, and HIV-pol amplicons with lengths of 321 bp (positions 2211-2531), 405 bp (positions 6918-7322), and 1,060 bp (positions 2253-3315) nucleotides, respectively. The products amplified were electrophoresed on 1.5% agarose gel and visualized by ethidium bromide staining.…”