Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages)

Abstract

The phenotypic classification of HIV-1 has been based on biological characteristics of viral isolates in culture, which include replication in MT-2 cells (syncytium inducing; SI versus non-syncytium inducing; NSI), replication kinetics in peripheral blood mononuclear cells (rapid–high versus slow–low growth), or host cell range (macrophage tropic versus T cell line tropic) [1,2]. Assessing the HIV-1 phenotype in vitro provides a link to pathogenesis in vivo. The V3 genotype, based on amino acid sequence of envelope (gp120SU), is related to the NSI/SI phenotype and provides a biomarker for disease progression [3,4]. In general, NSI variants are associated with acute infection and display low V3 net charges (≤ + 4), whereas SI variants emerge late in the disease and display high V3 net charges (≥ + 5) [5–7]. An improved system to classify the HIV-1 phenotype is based on chemokine receptor usage, particularly CXCR4 (X4) and CCR5 (R5), and tropism for different cell types in culture. This classification system distinguishes dual tropic viruses that infect both macrophages and T cell lines, as well as viruses that use both R5 and X4 among SI strains [8–12]. Although the use of X4 as a co-receptor and the infection of T cell lines is correlated with advanced disease [7], a relationship between V3 genotype and viral phenotype, as defined by co-receptor usage and tropism, is unclear. We developed a model for predicting viral phenotype (i.e. co-receptor usage and tropism) based on genotypic variables within the V3 domain of gp120SU. V3 sequences were evaluated for 43 subtype B HIV-1 isolates with known co-receptor usage (Table 1). Cell tropism was available for 17 of the 43 isolates [13–16; unpublished data]. The position and charge of V3 amino acids between Cys263 and Cys296 [4] in relation to the actual phenotype were defined for each virus. The actual phenotype was assigned a numerical value: 1 = R5 and macrophage tropic (M-R5); 2 = X4 alone or in combination with R5 and dual tropic (D-X4 or D-R5X4); or 3 = X4 and T cell line tropic (T-X4). Using multiple linear regression (SigmaStat; SPSS Inc., Chicago, IL, USA), a combination of four genotypic variables in V3 were identified as positive predictors of viral phenotype: (i) number of positively charged amino acid residues (K or R); (ii) number of negatively charged residues (D or E); (iii) net V3 charge [(K + R) − (D + E)]; and (iv) an isoleucine residue at position 292. An equation to predict viral phenotype based on these genetic variables was generated:EQUATION Table 1: Envelope data used to generate predictive model.