Coreceptor Tropism in Human Immunodeficiency Virus Type 1 Subtype D: High Prevalence of CXCR4 Tropism and Heterogeneous Composition of Viral Populations

Abstract

In human immunodeficiency virus type 1 (HIV-1) subtype B, CXCR4 coreceptor use ranges from ϳ20% in early infection to ϳ50% in advanced disease. Coreceptor use by non-subtype B HIV is less well characterized. We studied coreceptor tropism of subtype A and D HIV-1 collected from 68 pregnant, antiretroviral drug-naive Ugandan women (HIVNET 012 trial). None of 33 subtype A or 10 A/D-recombinant viruses used the CXCR4 coreceptor. In contrast, nine (36%) of 25 subtype D viruses used both CXCR4 and CCR5 coreceptors. Clonal analyses of the nine subtype D samples with dual or mixed tropism revealed heterogeneous viral populations comprised of X4-, R5-, and dual-tropic HIV-1 variants. In five of the six samples with dual-tropic strains, V3 loop sequences of dual-tropic clones were identical to those of cocirculating R5-tropic clones, indicating the presence of CXCR4 tropism determinants outside of the V3 loop. These dual-tropic variants with R5-tropic-like V3 loops, which we designated "dual-R," use CCR5 much more efficiently than CXCR4, in contrast to dual-tropic clones with X4-tropic-like V3 loops ("dual-X"). These observations have implications for pathogenesis and treatment of subtype D-infected individuals, for the association between V3 sequence and coreceptor tropism phenotype, and for understanding potential mechanisms of evolution from exclusive CCR5 use to efficient CXCR4 use by subtype D HIV-1.Human immunodeficiency virus type 1 (HIV-1) infection requires interactions between the viral envelope (Env) surface glycoprotein (gp120), the cellular receptor (CD4), and a coreceptor (e.g., CCR5 and/or CXCR4) (36). CCR5, the most commonly used coreceptor, is present on primary T cells and macrophages. In contrast, CXCR4 is expressed on many cell types, including thymocytes, primary T cells, and macrophages (13). CXCR4-using viruses can induce formation of syncytia when cultured on the CXCR4-bearing MT2 cell line (syncytiuminducing, SI viruses) (3,8,21,33,48). SI or CXCR4-using viruses are typically found in individuals with advanced disease (2,9,16,18,19). However, it is not clear whether CXCR4 use precedes and causes more rapid disease progression or is merely the consequence of a change in target cell availability. The recent development of HIV-1 entry inhibitors that target CCR5 has heightened interest in coreceptor usage (44).Several surveys of coreceptor tropism were reported recently. Brumme et al. (6) studied almost 1,000 antiretroviral drug naive HIV-1-infected patients. CXCR4-using virus was detected in 18% of those individuals, more than 99% of which were also able to use CCR5 and were thus categorized as dualor mixed-tropic (DM). CXCR4 use was associated with decreased survival in univariate, but not multivariate, analyses. There was a statistically nonsignificant trend toward increased CXCR4 use in non-subtype B viruses (7 of 13 [54%] for nonsubtype B versus 143 of 675 [21%] for subtype B; C. J. Brumme and P. R. Harrigan, unpublished data). Moyle et al. (37) evaluated predictive factors for coreceptor use am...

HIV-1 dual/mixed tropic isolates show different genetic and phenotypic characteristics and response to maraviroc in vitro

“…This is consistent with previous studies showing the involvement of the V1, V2, and C4 domain in mechanisms underlying co-receptor usage (Huang et al, 2007;Kupfer et al, 2007;Thielen et al, 2010).…”

“…In addition, they are rarely observed in either drug naïve (<1%) or treatment-experienced patients (<5%) with preserved immunefunction (Brumme et al, 2005;Melby et al, 2006;Moyle et al, 2005;Wilkin et al, 2007;Simon et al, 2010). Conversely, a quite high proportion of patients harbouring dual/mixed-tropic viruses has been observed both in drug-naïve (prevalence ranging 12-15%) and in treatment-experienced patients (prevalence ranging 20-50%) (Church et al, 2008;Huang et al, 2007;Lihana et al, 2009;Moreno et al, 2009;Shepherd et al, 2008).…”

“…Preliminary findings recently highlighted the existence of different types of D/M viruses: those that are much more efficient in using the CCR5 co-receptor (R5 + /X4), those that use more efficiently the CXCR4 (R5/X4 + ), and those that can use with the same efficiency both co-receptors (R5/X4) (Loftin et al, 2010;Huang et al, 2007;Symons et al, 2011;Toma et al, 2010). These studies have been conducted using recombinant viruses, while nothing is known about the tropism characteristics of primary HIV-1 isolates, and their pathogenetic potential.…”

Evaluation of Eight Different Bioinformatics Tools To Predict Viral Tropism in Different Human Immunodeficiency Virus Type 1 Subtypes

“…Up to 19% of these individuals carried X4/X4R5 dual-tropic viruses, with no significant differences with a control group of patients infected with clade B viruses. In other studies that included a larger number of samples from clades C and D, it was noted that clade C might less frequently harbor X4 viruses, even in late disease stages (8,16,20,24,31), while conversely, clade D could be X4 tropic more frequently (10,14). The small number of samples with these variants in our study precluded the examination of this aspect more appropriately.…”

“…Genotypic predictors of HIV-1 tropism have been developed to circumvent these disadvantages; however, the high genetic variability of HIV-1 may represent a serious obstacle to ensure their reliability. In addition to these diagnostic obstacles, it is important to better understand HIV pathogenesis and explain why some HIV-1 clades seem to be more frequently X4 tropic than others, as recently claimed for subtypes A, D, and CRF14_BG (1,10,14,17,22), since patients infected with these variants might progress faster to AIDS and will benefit less from CCR5 antagonists.…”