HIV-1 with predicted CXCR4 genotype identified in clade C from India.
OBJECTIVE
HIV-1 uses co-receptors CCR5 and CXCR4 in addition to CD4 for viral entry into cells. CCR5 is used in the early stages of HIV-1 infection, but viruses that utilize CXCR4 for viral entry emerge in the later stages. This is not common among clade C strains, with previous data from India showing the absence of the emergence of CXCR4-using strains. Sequence analysis has demonstrated that the V3 loop plays a very important role in determining the syncytium-inducing (SI) phenotype. The V3 region of the SI variants were observed to have positively charged amino acids at positions 11 and/or 25 and also a overall higher charge. This study looked at co-receptor usage among HIV-1 strains in India from individuals who were antiretroviral therapy (ART) naïve and those not responding to ART.


METHODS
Amplification and sequencing of the HIV-1 env gp120 V3 region was done on 40 ART-naïve individuals, who were selected for the study based on their CD4 counts, and eight patients who had not responded to ART. The sequences were submitted to Geno2Pheno and Web PSSM. The pol gene sequences of these strains were submitted to the REGA HIV-1 subtyping tool.


RESULTS
Forty-seven strains were identified as clade C and one strain as clade A1. Geno2Pheno identified three CXCR4-using strains, and the Web PSSM clade C matrix identified two.


CONCLUSIONS
We report, for the first time, CXCR4-using strains among HIV-1 clade C strains circulating in India.
Department of Clinical Virology, Christian Medical College, Vellore, India.
Abraham Joseph
AJ
Kandathil
Rajesh
R
Kannangai
Oriapadickal Cherian
OC
Abraham
Susanne Alexander
SA
Pulimood
Mark A
MA
Jensen
Gopalan
G
Sridharan
D000595:Amino Acid Sequence; D024882:Drug Resistance, Viral / Q000235:genetics; D015751:Genes, pol; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000097:blood; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007194:India; D008969:Molecular Sequence Data; D010802:Phylogeny; D019718:Receptors, CXCR4 / Q000235:genetics*
D015699:HIV Envelope Protein gp120; D019718:Receptors, CXCR4