Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions

Abstract

The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.

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

“…Genomic DNA was extracted from whole blood samples (QIAamp ® DNA Blood Mini Kit/QIAGEN, Qiagen, Hilden, Germany). The double-stranded proviral HIV-1 DNA was amplified by nested-PCR employing Platinum Taq DNA polymerase (Invitrogen, Carlsbad, CA, United States) into four overlapping fragments [(#1 (408–2594), #2 (2253–4830), #3 (4653–7811), and #4 (6954–9625) relative position to HXB2 genome] using HIV-1 specific primers as described in Reis et al (2017). The amplified DNA fragments were purified (kit QIAquick ® PCR Purification Kit/QIAGEN, Qiagen, Hilden, Germany) and sequenced ( Big Dye Terminator Sequencing Kit v. 3.1 , Applied Biosystems, Foster City, CA, United States; ABI Prism 3100 Genetic Analyzer, Applied Biosystems, Foster City, CA, United States).…”

“…The cocirculation of distinct HIV-1 subtypes is known to increase the chances of coinfection and of the generation of BF1, F1CB, BC, and CF1 intersubtype recombinant viruses (Jetzt et al, 2000; Faria et al, 2014). In the last decade, 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).…”

“…Previous studies from our group in the HIV-1 pol region reported variable rates of intersubtype recombinant BF1, F1CB, BC, and CF1 viruses among over 800 patients living in six Brazilian States located in the Central Western, Northern, and Northeastern Brazilian regions (Cardoso et al, 2009, 2010, 2011; Cardoso and Stefani, 2009; Carvalho et al, 2011; Ferreira et al, 2011; Alcântara et al, 2012; da Silveira et al, 2012; da Costa et al, 2013; Moura et al, 2015a,b; Lima et al, 2016b). Recently near full and full-length genomes revealed a noteworthy diversity of BF1 recombinants among these patients and allowed the identification of the CRF90_BF1 and of several URFs BF1 (Reis et al, 2017). In this study, we summarize HIV-1 molecular data in pol among this large group of patients from six Brazilian states.…”

Potential overestimation of HIV-1 sub-subtype F1 circulation in Rio de Janeiro, Brazil

“…A subset of samples classified as sub-subtype F1 for all HIV-1 genomic regions analysed were further assayed by full-length amplification using four overlapping fragments amplified by nested PCR, as previously described in Reis et al (2017) .…”

Characterization of HIV-1 genetic diversity and antiretroviral resistance in the state of Maranhão, Northeast Brazil

“…In the North and Central-west region, there is a higher prevalence of subtypes B (74-90%) and F (6.7-14%) [10; 11]. Recently, in the Midwest, 2 new CRFs were identified, CRF 90_BF [12] and CRF_99BF [13].…”