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Updated: Jun 25, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 28, 2010

Global distribution of the CCR2-64I/CCR5-59653T HIV-1 disease-protective haplotype.

J J Martinson¹, L Hong, R Karanicolas

¹Department of Biological Anthropology, Oxford University, UK.

AIDS (London, England)

|April 26, 2000

Summary

The CCR2-64I and CCR5-59653T genetic variants are widespread globally, with higher frequencies in Africa and Asia. These variants are strongly linked and likely represent an ancient mutation predating modern human dispersal.

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Published on: August 31, 2014

Area of Science:

Immunogenetics
Human Population Genetics
Virology

Background:

Polymorphisms in CC-chemokine receptors CCR5 and CCR2 influence HIV-1 disease progression.
The CCR2-64I variant (Valine to Isoleucine at position 64) is linked to a CCR5 regulatory mutation (CCR5-59653T).
While not conferring resistance, CCR2-64I allele carriers show slower HIV-1 disease progression.

Purpose of the Study:

To determine the global distribution of CCR2-64I and CCR5-59653T genetic variants.
To define the degree of linkage disequilibrium between CCR2-64I and CCR5-59653T.

Main Methods:

Development of real-time PCR allele discrimination assays using molecular beacons.
Genotyping of 3923 individuals across 53 globally distributed populations.
Spectral genotyping assays for chemokine receptor mutations.

Main Results:

CCR2-64I and CCR5-59653T variants are present in nearly all studied populations.
Allele frequencies are highest (~35%) in Africa and Asia, decreasing in Northern Europe.
Strong linkage disequilibrium confirmed between CCR2-64I and CCR5-59653T (96.92% concordance).

Conclusions:

The CCR2-64I/CCR5-59653T haplotype exhibits a broader geographical distribution than CCR5-delta32.
This suggests the CCR2-64I/CCR5-59653T haplotype is a significantly older mutation.
Its origin likely predates the dispersal of modern humans.