Objective: To investigate the new single nucleotide polymorphism (SNP) sites of HIV-1 coreceptor CCR5 gene and conduct genotyping of CCR5-894C deletion allele in Chinese populations.
Methods: The full length fragment of CCR5 gene coding region was amplified by PCR amplification and sequenced in 45 healthy subjects from Han ethnic group. The sequencing data was analyzed by using DNAstar software for identification of new SNP sites. Furthermore, the genotyping of CCR5-894C deletion variant was performed by PCR-RFLP assay in 627 indigenous Chinese individuals including HIV-1 carriers, HIV-1 high risk population of STDs or IDUs as well as normal contrast.
Results: Totally six SNPs and one cytosine base deletion at the 894 nucleotide of CCR5 gene coding region were found in forty five Chinese Han subjects. Four SNPs, i.e. 184A-->G, 503G-->T, 668G-->A, 999G-->T, cause alteration of corresponding amino acids in CCR5 protein and two SNPs are nonsense mutations. The 894C deletion mutation results in a frame shift mutation of CCR5 gene. Among the six SNPs identified, the three sites 184A-->G, 503G-->T, 999G-->T were firstly reported only in Chinese people. The allelic frequencies of mutant 184G, 503T and 999T alleles were 1.1%, 21.1% and 10.0% in Han healthy subjects, respectively. PCR-RFLP assay showed the frequencies of CCR5-894C deletion alleles are 1.11%, 0.53% and 0% for Chinese Han, Tibetan and Mongolian healthy individuals, respectively. There was not significant different of the frequencies of CCR5-894C deletion allele among HIV-1 high risk populations, HIV-1 carries and healthy subjects.
Conclusion: The subjects from Chinese Han group has its own distinctive SNP sites in the HIV-1 coreceptor CCR5 gene, three new SNPs (184A-->G, 503G-->T, 999G-->T) were firstly identified. Taking together, the significance and implication of these distinctive SNP sites and the 894C deletion mutation in the pathogenesis of HIV/AIDS disease need to be further studied.