Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India.

AIDS Research and Therapy
Ujjwal NeogiAnita Shet

Abstract

Understanding co-receptor tropism of HIV-1 strains circulating in India will provide key analytical leverage for assessing the potential usefulness of newer antiretroviral drugs such as chemokine co-receptor antagonists among Indian HIV-infected populations. The objective of this study was to determine using in silico methods, HIV-1 tropism among a large number of Indian isolates both from primary clinical isolates as well as from database-derived sequences. R5-tropism was seen in 96.8% of a total of 1045 HIV-1 subtype C Indian sequences. Co-receptor prediction of 15 primary clinical isolates detected two X4-tropic strains using the C-PSSM matrix. R5-tropic HIV-1 subtype C V3 sequences were conserved to a greater extent than X4-tropic strains. X4-tropic strains were obtained from subjects who had a significantly longer time since HIV diagnosis (96.5 months) compared to R5-tropic strains (20.5 months). High prevalence of R5 tropism and greater homogeneity of the V3 sequence among HIV-1 subtype C strains in India suggests the potential benefit of CCR5 antagonists as a therapeutic option in India.

References

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Citations

Apr 27, 2013·AIDS Research and Human Retroviruses·Anthony Kebira NyamacheSamoel A Khamadi
Oct 20, 2011·The Journal of Antimicrobial Chemotherapy·Elena DelgadoLucía Pérez-Álvarez
Sep 17, 2013·ChemMedChem·Chie HashimotoHirokazu Tamamura
Jun 10, 2017·International Journal of STD & AIDS·Beatris M MartinSonia M Raboni
Nov 6, 2013·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Soham GuptaAnita Shet
Nov 24, 2011·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Ujjwal NeogiAnita Shet
May 30, 2020·AIDS Research and Human Retroviruses·Tennison Onoriode DigbanLarry Chikwelu Obi

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Methods Mentioned

BETA
PCR
Genotyping

Software Mentioned

REGA
ClustalW
PSSM
WebLogo
WebPSSM
CPSSM
ds
Kernel
Geno2pheno
Geographic

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