# Covariation of Amino Acid Substitutions in the HIV-1 Envelope Glycoprotein gp120 and the Antisense Protein ASP Associated with Coreceptor Usage

## TL;DR

This study finds that amino acid changes in an HIV-1 protein called ASP are linked to changes in the V3 loop of the virus's envelope, which determines how the virus enters cells.

## Contribution

The study introduces a new computational method to predict HIV-1 coreceptor usage and identifies ASP amino acid signatures coevolving with the V3 loop.

## Key findings

- A statistical method predicted HIV-1 coreceptor tropism with 94.4% accuracy using V3 loop sequences.
- Five ASP amino acid positions were found to correlate with viral tropism.
- ASP substitutions are significantly linked to substitutions in six V3 loop positions.

## Abstract

The tropism of the Human Immunodeficiency Virus type 1 (HIV-1) is determined by the use of either or both chemokine coreceptors CCR5 (R5) and CXCR4 (X4) for entry into the target cell. The ability of HIV-1 to bind R5 or X4 is determined primarily by the third variable loop (V3) of the viral envelope glycoprotein gp120. HIV-1 strains of pandemic group M contain an antisense gene termed asp, which overlaps env outside the region encoding the V3 loop. We previously showed that the ASP protein localizes on the envelope of infectious HIV-1 virions, suggesting that it may play a role in viral entry. In this study, we first developed a statistical method to predict coreceptor tropism based on Fisher’s linear discriminant analysis. We obtained three linear discriminant functions able to predict coreceptor tropism with high accuracy (94.4%) when applied to a training dataset of V3 sequences of known tropism. Using these functions, we predicted the tropism in a dataset of HIV-1 strains containing a full-length asp gene. In the amino acid sequence of ASP proteins expressed from these asp genes, we identified five positions with substitutions significantly associated with viral tropism. Interestingly, we found that these substitutions correlate significantly with substitutions at six amino acid positions of the V3 loop domain associated with tropism. Altogether, our computational analyses identify ASP amino acid signatures coevolving with V3 and potentially affecting HIV-1 tropism, which can be validated through in vitro and in vivo experiments.