Molecular and structural characterization of HIV-1 subtype B Brazilian isolates with GWGR tetramer at the tip of the V3-loop

Abstract

One of most intriguing features of the HIV-1 subtype B epidemic in Brazil is the high frequency of isolates exhibiting tryptophan (W) in the tetramer (GWGR) at the tip of the V3 loop. We observed that the frequencies of glutamic and aspartic acids at site 25 of the V3 loop are quite distinct in GWGR isolates compared with viruses with other tetramers. The basic amino acids at sites 11 and 25 of V3 are strongly linked with CCR5-to-CXCR4 coreceptor shift. We therefore predicted phenotype usage and found that GWGR isolates are exclusively CCR5-using. Further evidence of this came from intrahost sequences, where basic amino acid substitutions at sites 11 and 25 emerged only in isolates presenting a tryptophan-to-glycine replacement at the tetramer of the V3. In addition, modeled 3D-structures of the V3 loop of GWGR and GGGR in intrahost viruses differ essentially in the binding region of the coreceptor.

HIV-1 tropism and CD4 T lymphocyte recovery in a prospective cohort of patients initiating HAART in Ribeirão Preto, Brazil

“…2C). An important prevalence of X4 variants in GWGR viruses was observed using both the geno2pheno [clonal20%] (44%) and the geno2pheno [clinical20%] (67%) algorithms, contrary to previous studies, which suggested that GWGR viruses are rarely X4 (da Silva 2006, Leal et al 2008). This difference could be due to the algorithm used, as most studies use the 11/25 rule as a prediction criterion.…”

“…Interestingly, three V3 tip sequences of non-GWGR tryptophan-harbouring viruses, classified here as "other motifs", were predicted as X4. These viruses had a G→R polymorphism in the V3 loop tip at position 17 ( 15 GWRR 18 ), two had basic amino acids at codons 11 or 25 and one had a G→R substitution at position 28, a highly conserved codon (Leal et al 2008, Franca et al 2011. GWRR seems to be a very rare motif previously documented in the state of Rio de Janeiro, Brazil and Paraguay and its biological relevance is yet to be understood (Cabello et al 1995, Tanuri et al 1999 The small number of samples in this study limits the strength of these observations and it is conceivable that these outcomes may be different if a larger cohort was sampled and a longer follow-up period was employed.…”

Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic

“…The typical subtype B signature was identified as B-GPGR, whereas viruses harbouring the alternative W (tryptophan) signature were assigned as B"-GWGR. Assuming that the epidemiological, serological and clinical differences observed between the B and B" signatures in previous studies are accurate (Hendry et al 1996, Santoro-Lopes et al 2000, Casseb et al 2002, Brito et al 2006, Leal et al 2008, Pinto et al 2008), sequences presenting related motifs that retained the P or W at second position of the tetrapeptide (XPXX and XWXX) were also considered as B-GPGR or B"-GWGR, respectively, because these most likely evolved from an ancestral sequence containing one of these motifs (Diaz et al 2008). Sequences depicting an amino acid other than W or P at position 16 of the V3 loop were evaluated separately.…”

“…The pandemic form of subtype B, which is prevalent in European, American and Asian countries, is typically characterised as having a GPGR motif (B-GPGR) at the tip of the V3 loop. However, several molecular studies have shown that various genetically and antigenically distinct V3 motifs, which are diversified particularly at the second position of the tetramer, co-circulate in the HIV-1B epidemic (Shimizu et al 1992, Morgado et al 1994, Candotti et al 1999, Kim et al 1999, Leal et al 2008, Franca et al 2011). In particular, some strains have been found to harbour an alternative signature in which the second residue of the tetrapeptide, proline, is substituted with tryptophan (B"-GWGR) (Potts et al 1993, Casseb et al 1998, 2002, Morgado et al 1998, Santoro-Lopes et al 2000, Brito et al 2006, Araujo et al 2010, Franca et al 2011).…”

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

“…52 We would argue that our finding was relevant, since it provided empirical evidence against the belief that variants carrying the GWGR tetramer would exclusively use the CCR5 coreceptor. 53 Crucially, these findings provide further biological evidence that this motif (GWGR) alone does not determine the coreceptor usage. 54 Moreover, CXCR4-tropic viruses were more common than CCR5-tropic viruses (7 and 3, respectively), regardless of the recombination profile and patient clinical status.…”