Characterization of Primary Isolates of HIV Type 1 CRF28_BF, CRF29_BF, and Unique BF Recombinants Circulating in São Paulo, Brazil

Abstract

We report for the first time the genetic and biological characterization of 10 HIV-1 primary isolates representing CRF28_BF and CRF29_BF together with additional unique BF recombinant forms (URFs) obtained by PBMC cocultivation. Recombination is an important factor promoting the increase in the genetic diversity of HIV-1. Notably, more than 20% of HIV-1 sequences worldwide were recombinants. Several recombinant viruses were reported in Brazil, and six circulating recombinant forms (CRFs) have been identified (CRF28_BF, CRF29_BF, CRF31_BC, CRF39_BF, CRF40_BF, and CRF46_BF). CRF28_BF and CRF29_BF were found to infect almost 30% of the patients in Sã o Paulo State. The near full-length genomes of these 10 primary isolates were amplified by nested PCR in three overlapping segments, purified, and sequenced. Three samples were related to CRF28_BF, three to CRF29_BF, and four were unique recombinant forms (URFs), as determined by their breakpoint profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolates was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four lymphotropic (X4) viruses, and three macrophage-tropic (R5) viruses with different V3-loop motifs, which challenges the notion that GWGR-carrying viruses are macrophage-tropic only. In sum, we report a much-anticipated well-characterized panel of viruses representing CRF28_BF, CRF29_BF, and URFs from Sã o Paulo State, Brazil.

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

“…This is in line with that recombinant forms of HIV-1 have been estimated to account for 18–20 per cent of infections worldwide ( Buonaguro, Tornesello, and Buonaguro 2007 ; Hemelaar et al 2011 , 2019 ). It was beyond the scope of this study to perform a detailed characterization of the individual mosaics and their ancestry (except for CRF01_AE); nonetheless, we note that our observed subtype distributions confirm a high prevalence of subtypes BC and BF in Africa and Latin America, respectively ( Carr et al 2001 ; Melo, Jamal, and Zanotto 2012 ). Also, we found subtype AB in Uganda, Thailand, and Greece, but our sample collection does not cover Eastern Europe where an AB recombinant was first described in 1998 to circulate among injecting drug users in Eastern Europe ( Liitsola et al 1998 ), and further reports on distribution and transmission of AB recombinants remain scarce ( Neogi et al 2017 ).…”