Evolution of CXCR4-Using Human Immunodeficiency Virus Type 1 SF162 Is Associated with Two Unique Envelope Mutations

Abstract

CCR5-using human immunodeficiency virus type 1 (HIV-1) isolates typically gain CXCR4 use via multiple mutations in V3 and often V1/V2 regions of envelope, and patterns of mutations are distinct for each isolate. Here, we report that multiple CXCR4-using variants of a parental CCR5-using HIV-1 isolate, SF162, obtained by either target cell selection or CCR5 inhibition have a common mutation pattern characterized by the same two V3 mutations and that these mutations preexisted in some of the SF162 stocks. These results imply that SF162 has a single pathway for acquiring CXCR4 use and that prolonged culture is sufficient to select for R5X4 variants.Human immunodeficiency virus type 1 (HIV-1) isolated from infected individuals uses CCR5 and/or CXCR4 coreceptors for cell entry (27). Infection is transmitted by CCR5-using HIV-1 variants (R5) that often later evolve into variants using CXCR4 exclusively or together with CCR5 (X4 or R5X4), and this evolution is associated with accelerating progression to AIDS (5,6,12,39). R5 or X4 phenotype is determined by the amino acid sequence of HIV-1 gp120, particularly of V3 and V1/V2, and less frequently of other regions (4,7,8,10,11,17,21,23,30,(34)(35)(36). The cause and mechanisms of the evolution towards CXCR4 usage are not fully understood. Target cell selection and the abundance of natural ligands for CCR5 and CXCR4 are thought to be two important selection factors (24,25,29), which have been modeled in vitro by propagation of R5 variants in cell lines expressing CXCR4 only (13,18,30,32) or in the presence of CCR5 ligands (1,15,26,28,37). Evolution towards CXCR4 usage in vivo (38, 39) and in vitro seems to go along multiple pathways, and most R5X4 variants have diverse mutation patterns, although some common features (e.g., charged amino acids at positions 11 and 25 of the V3 loop) have been observed (20,22,32).Earlier, it was reported that CXCR4-using variants of the R5 HIV-1 SF162 isolate (9) selected by viral propagation on CXCR4-expressing T-cell lines acquired two consistent mutations in V3, I309R and A316V (13, 18). Here, we have independently selected for CXCR4-using variants by propagating SF162 in cells expressing CXCR4 but not CCR5 (see reference 32) or in peripheral blood mononuclear cells (PBMC) in the presence of escalating concentrations of RANTES. We found that the same two V3 mutations occurred in seven independently selected CXCR4-using variants of SF162 and that the I309R mutation precedes the A316V mutation under both modes of selection. Moreover, even without RANTES, serial passage of SF162 in PBMC also selected for the same two V3 mutations, albeit more slowly than in T-cell lines or in high RANTES concentrations. Interestingly, one of the SF162 stocks obtained by culture in PBMC of HIV-1 from the AIDS Research and Reference Reagent Program already contained a minor population (11%) harboring the I309R mutation and an even smaller population (Ͻ2%) with both the I309R and A316V mutations.In the first set of experiments virus was selected in the course o...

Primary HIV-1 Strains Use Nef To Downmodulate HLA-E Surface Expression

“…HLA-E eGFP (-) HLA class I mCherry (-) • HIV-1 NL4-3 staining levels more directly related to the highly expressed HLA-A and HLA-B molecules (32). Of note, in contrast to previous reports (48,55), infection with HIV-1 SF162 did not reduce HLA-I surface levels in our experiments, a finding that may be ascribed to potential mutations accumulated during propagation of the viral stock (56). Employing a mixed-effect linear regression model, we observed that downregulation of HLA-I surface expression was significantly associated with reduced HLA-E surface levels on HIV-1-infected CD4 ϩ T cells (for each ϩ1% of HLA-E change, the mean surface HLA-I change was ϩ0.72% [95% confidence interval, 0.44% to 0.99%; P ϭ 0.0001]) ( Fig.…”

Coreceptor Switch in R5-Tropic Simian/Human Immunodeficiency Virus-Infected Macaques

“…The same two V3 mutations are seen for multiple CXCR4-using variants selected either by target cell limitation or CCR5 inhibition, leading to the conclusion that SF162 has a single pathway for acquiring CXCR4 use (21). We show here that coreceptor switch of a SHIV molecular clone expressing the SF162 envelope in RM requires amino acid residue changes in the V3 loop that are different from those reported in tissue culture systems.…”

“…In vitro, two amino acid residue changes in the V3 domain of HIV-1 strain SF162 are sufficient to expand to CXCR4 usage (8,16,21). The same two V3 mutations are seen for multiple CXCR4-using variants selected either by target cell limitation or CCR5 inhibition, leading to the conclusion that SF162 has a single pathway for acquiring CXCR4 use (21).…”

Different Tempo and Anatomic Location of Dual-Tropic and X4 Virus Emergence in a Model of R5 Simian-Human Immunodeficiency Virus Infection

“…infected macaque (28), the switch or expansion to CXCR4 usage in both i.r. infected macaques was associated with V3 loop sequence mutations similar to those reported in humans but differed from those required to confer expanded CXCR4 usage to the parental SF162 envelope in tissue culture systems (13,26,32). In the case of DR16, the emergence of a positively charged amino acid at position 11 in V3 was shown to be associated with CXCR4 coreceptor phenotype and with increased clinical progression in HIV-1-infected individuals (12,20).…”