HIV-1 Co-Receptor Usage Based on V3 Loop Sequence Analysis: Preferential Suppression of CXCR4 Virus Post HAART?

Abstract

Disease progression during human immunodeficiency virus type 1 (HIV-1) infection has been associated with a switch of viral coreceptor usage from CCR5 to CXCR4. The current study investigates the effect of anti retroviral therapy (ART) on the viral tropism in a group of patients based on the V3 loop sequence, in ART naïve patients prior to and 24 weeks after ART. Genomic DNA was extracted from the PBMCs of these patients, and the C2-V5 region of the HIV-1 env genes were cloned and sequenced. The coreceptor usage was predicated based on V3 loop amino acid sequences using Geno2pheno and PSSM programs. Our results indicate that following ART, the plasma viral loads of both CXCR4 and CCR5 viruses were significantly decreased. We observed a relatively higher ratio of R5 than X4 virus after 24 weeks of ART and both the positive charges and the net charges of the V3 regions were decreased significantly (p < 0.05) after ART. We conclude that ART significantly, reduced both X4 and R5 viruses with a preferential suppression of X4 virus. These data will help improve prognostic outcomes and help clinicians determine the course of treatment in patients who exhibit virologic failure while taking a CCR5 antagonist.

• HIV Co-receptor
• V3 loop
• CXCR4
• CCR5

ACKNOWLEDGMENTS

This study was supported in part by the National 11th Five-Year Major Projects of China (2008ZX10001-006, 2008ZX10001-001), and the National Natural Science Foundation of China (30872226).

Declaration of interest:This statement indicates no financial conflicts of interest and contribution of all authors. The authors alone are responsible for the content and writing of the paper. YJ drafted the manuscript and statistical analyses. PW participated at the Cloning and sequencing of C2–V5 region of HIV-1 env. HWZ assisted with manuscript and data anlysis. TZ and YZ assisted with patients’ care and data acquisition. HZZ conceived the study and participated in the data analysis. HW supervised and coordinated the study.