Related Experiment Video
Updated: Apr 6, 2026
Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
Coreceptor usage of plasma and cerebrospinal fluid-derived HIV-1 subtype C variants
Suhina Sirkisson1, Nelisiwe Zikhali1, Christina Chang2,3
1HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
Background:
HIV-1 subtype C (HIV-1C) may use multiple coreceptors to enter cells. However, the differences in coreceptor usage between HIV-1C Env variants from peripheral blood and those from the central nervous system (CNS) are still not completely understood. This study characterised the coreceptor usage of viral populations that circulate in the central nervous system (CNS) and plasma compartments to enhance understanding of HIV-1C pathogenesis and inform the appropriate use of entry inhibitors.
Methods:
We characterised the in vitro coreceptor usage of HIV-1C envelope protein (Env) variants circulating in peripheral blood and the cerebrospinal fluid (CSF) of twelve participants living with HIV and cryptococcal meningitis coinfection. We evaluated the coreceptor usage using Geno2pheno, Phenoseq and Web-PSSM coreceptor prediction tools, and confirmed coreceptor usage in U87 cell lines. We also analysed HIV-1 Env V3 loop characteristics for associations with CCR5 or CXCR4 usage.
Results:
Our findings indicated that CSF-derived clones primarily used CCR5, while plasma-derived clones varied usage between CCR5, CXCR4 and CCR3 in vitro. HIV-1 Envs with a long V3 loop (37 amino acids), absence of potential N-linked glycosylation sites (PNGS), and a high net charge (> 5 +) were associated with CXCR4 usage. Whereas shorter or standard-length V3 loops (34-35 amino acids), presence of PNGS, lower net charge (range + 2 to + 5) and a GPGQ crown motif were associated with CCR5 usage.
Conclusion:
Our findings reveal compartment-specific heterogeneity in HIV-1 subtype C coreceptor usage during advanced infection. CSF-derived variants were primarily limited to CCR5 usage, while plasma-derived variants exhibited broader usage of CXCR4 and alternative coreceptors. Phenotypic validation, together with distinct V3 loop signatures, provides evidence of viral adaptation to divergent tissue environments and highlights limitations of genotypic tropism prediction alone. These findings advance the understanding of HIV-1C pathogenesis and have implications for evaluating coreceptor usage in the context of entry inhibitor-based interventions particularly in regions where HIV-1C is endemic and diagnostic resources are limited.
