Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms.

Mônica N G Reis,Mariane M A Stefani,Monick L Guimarães,Gonzalo Bello

doi:10.3389/fmicb.2019.00097

Mônica N G Reis, Mariane M A Stefani + Show 2 more

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https://doi.org/10.3389/fmicb.2019.00097

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Abstract

Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous pol region studies (2003–2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in pol were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B (n = 629), 6.4% subtype C (n = 53), 4.2% subtype F1 (n = 35), 13.4% intersubtype recombinants: 10.5% BF1 (n = 87), 2.3% BC (n = 19), 0.4% F1CB (n = 3), and 0.2% CF1 (n = 2). Two full and one partial BF1C genomes allowed the characterization of the CRF81_cpx that has 9 breakpoints dividing the genome into 10 subregions. Basic Local Alignment Search Tool searches (Los Alamos HIV Sequence Database) identified six other sequences with the same recombination profile in pol, five from Brazil, and one from Italy. The estimated median TMRCA of CRF81_cpx was 1999 (1992–2003). CRF60_BC-like sequences, originally described in Italy, were also found. Two full and one near full-length BF1 genomes led to the characterization of the new CRF99_BF1 that has six recombination breakpoints dividing the genome into seven subregions. Two new URFs BF1, with six recombination breakpoints and seven subregions were also characterized. The description of the first Brazilian BF1C CRF81_cpx and of the new CRF99_BF1 corroborate the important role of CRFs in the HIV/AIDS epidemic throughout Brazil. Our data also highlight the value of HIV-1 full-genome sequence studies in order to fully reveal the complexity of the epidemic in a huge country as Brazil.

Highlights

MATERIALS AND METHODSRecombination of HIV-1 group M subtypes is considered a driving force for its genetic diversity worldwide (Worobey and Holmes, 1999)
The phylogenetic analyses of the pol (PR/reverse transcriptase (RT)) region in 828 patients from six Brazilian States showed that 76% was subtype B (629 out of 828), 6.4% was subtype C (53 out of 828), and 4.2% was subtype F1 (35 out of 828)
Our study with near-full and full-length genome sequences of recombinant viruses describes two new HIV-1 circulating recombinant forms (CRFs): the BF1C CRF81_cpx and the CRF99_BF1 that were identified among over 800 patients living in six Brazilian states

Summary

Introduction

MATERIALS AND METHODSRecombination of HIV-1 group M subtypes is considered a driving force for its genetic diversity worldwide (Worobey and Holmes, 1999). HIV1 subtype B predominates in all geographic regions, except in Southern region where subtype C is a major variant (Soares et al, 2005; Gräf and Pinto, 2013; Delatorre et al, 2017). The distribution of F1 subtype has significant regional variances ranging from low prevalence, in most regions, to high frequency in Pernambuco state, Northeastern Brazil (Cavalcanti et al, 2012; Gaspareto et al, 2012; Silveira et al, 2012; Lima et al, 2016a). Different circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been described including BC recombinants especially in the Southern and BF1 recombinants in different Brazilian regions (Guimarães et al, 2008, 2010; Passaes et al, 2009; Ferreira et al, 2011; da Silveira et al, 2012; Pessôa et al, 2014b, 2016; Moura et al, 2015a,b; Gräf et al, 2016; Lima et al, 2016b; Reis et al, 2017)

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