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Updated: Jul 20, 2026
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
Genetic characteristics of the V3 region associated with CXCR4 usage in HIV-1 subtype C isolates
Mia Coetzer1, Tonie Cilliers, Li-Hua Ping
1AIDS Virus Research Unit, National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, Gauteng 2131, South Africa.
Insights
HIV-1 subtype C viruses less frequently use CXCR4 coreceptor. Genetic analysis of the V3 region revealed that specific changes in the GPGQ crown motif, particularly substitutions, enable CXCR4 usage, unlike subtype B viruses.
Area of Science:
- Virology
- Immunology
- Genetics
Background:
- HIV-1 subtype C viruses exhibit less frequent CXCR4 coreceptor usage compared to other subtypes.
- Understanding the genetic basis for coreceptor tropism is crucial for predicting viral evolution and disease progression.
Purpose of the Study:
- To investigate the genetic determinants within the V3 region of HIV-1 subtype C isolates that mediate CXCR4 coreceptor usage.
- To compare these determinants with those found in HIV-1 subtype B.
Main Methods:
- Analysis of 32 HIV-1 subtype C isolates with known coreceptor phenotypes (R5, R5X4, X4).
- Utilized a subtype C-specific V3 heteroduplex tracking assay (HTA) for sample complexity assessment.
- Performed nucleotide sequencing of the V3 region to identify genetic variations associated with CCR5 and CXCR4 usage.
Main Results:
- Distinct genetic differences were identified between CCR5 (R5) and CXCR4 (X4)-using HIV-1 subtype C viruses.
- HTA mobility ratios generally distinguished between R5 (>0.9) and X4 (<0.9) isolates.
- Sequence analysis revealed that CXCR4-using subtype C viruses often had increased positive amino acid charge, insertions, and loss of glycosylation sites in the V3 loop.
- A conserved GPGQ motif at the V3 loop tip in R5 subtype C viruses contrasted with substitutions (commonly R) in 75% of X4-using viruses, unlike the conserved GPGR motif in subtype B.
Conclusions:
- Changes within the V3 crown motif represent a potential pathway for HIV-1 subtype C to utilize CXCR4.
- The conserved GPGQ motif in R5 subtype C viruses may limit the development of CXCR4-using (X4) variants.
- These findings highlight subtype-specific mechanisms governing HIV-1 coreceptor tropism.
Abstract:
CXCR4 coreceptor usage appears to occur less frequently among HIV-1 subtype C viruses. The aim of this study was to investigate the genetic determinants within the V3 region of subtype C isolates able to use CXCR4. Thirty-two subtype C isolates with known phenotypes (16 R5, 8 R5X4 and 8 X4 isolates) were assessed. A subtype C-specific V3 heteroduplex tracking assay (HTA) was used to determine sample complexity, and nucleotide sequencing analysis was used to compare characteristics associated with CCR5 and CXCR4-using isolates. There were sufficient genetic differences to discriminate between R5 viruses and those able to use CXCR4. In general, R5 isolates had an HTA mobility ratio >0.9 whereas CXCR4-using isolates were usually <0.9. Multiple bands were more frequently seen among the dualtropic isolates. Sequence analysis of the V3 region showed that CXCR4-using viruses were often associated with an increased positive amino acid charge, insertions and loss of a glycosylation site, similar to HIV-1 subtype B. In contrast, where subtype B consensus V3 has a GPGR crown motif irrespective of coreceptor usage, all 16 subtype C R5 viruses had a conserved GPGQ sequence at the tip of the loop, while 12 of the 16 (75%) CXCR4-using viruses had substitutions in this motif, most commonly arginine (R). These findings were confirmed using a larger published data set. We therefore suggest that changes within the crown motif of subtype C viruses might be an additional pathway to utilise CXCR4 and thus GPGQ may limit the potential for the development of X4 viruses.
