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

Ujjwal Neogi; Sreenivasa B. Prarthana; George D'Souza; Ayesha DeCosta; Vijesh S. Kuttiatt; Udaykumar Ranga; Anita Shet

doi:10.1186/1742-6405-7-24

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

Ujjwal Neogi, Sreenivasa B. Prarthana, George D'Souza, Ayesha DeCosta, Vijesh S. Kuttiatt, Udaykumar Ranga, Anita Shet

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Background: 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.Results: 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).Conclusions: 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.

Original language	English (US)
Article number	24
Journal	AIDS research and therapy
Volume	7
DOIs	https://doi.org/10.1186/1742-6405-7-24
State	Published - Jul 21 2010
Externally published	Yes

ASJC Scopus subject areas

Molecular Medicine
Virology
Pharmacology (medical)

Access to Document

10.1186/1742-6405-7-24

Cite this

@article{3dad650da8f445a28533d73dbb27e113,

title = "Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India",

abstract = "Background: 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.Results: 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).Conclusions: 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.",

author = "Ujjwal Neogi and Prarthana, {Sreenivasa B.} and George D'Souza and Ayesha DeCosta and Kuttiatt, {Vijesh S.} and Udaykumar Ranga and Anita Shet",

note = "Funding Information: We thank the staff of the Infectious Disease Clinic, St. John{\textquoteright}s Hospital, Bangalore, for assistance with patient recruitment. We are thankful to Mr. Soham Gupta and Ms. Pravat Nalini for their critical review of this manuscript. This study was partially funded by European Union Framework Program 7. Part of this work was presented at AIDS 2010, XVIII International AIDS Conference, Austria, Vienna, 18-23 July 2010.",

year = "2010",

month = jul,

day = "21",

doi = "10.1186/1742-6405-7-24",

language = "English (US)",

volume = "7",

journal = "AIDS research and therapy",

issn = "1742-6405",

publisher = "BioMed Central",

}

TY - JOUR

T1 - Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences

T2 - Therapeutic implications for India

AU - Neogi, Ujjwal

AU - Prarthana, Sreenivasa B.

AU - D'Souza, George

AU - DeCosta, Ayesha

AU - Kuttiatt, Vijesh S.

AU - Ranga, Udaykumar

AU - Shet, Anita

N1 - Funding Information: We thank the staff of the Infectious Disease Clinic, St. John’s Hospital, Bangalore, for assistance with patient recruitment. We are thankful to Mr. Soham Gupta and Ms. Pravat Nalini for their critical review of this manuscript. This study was partially funded by European Union Framework Program 7. Part of this work was presented at AIDS 2010, XVIII International AIDS Conference, Austria, Vienna, 18-23 July 2010.

PY - 2010/7/21

Y1 - 2010/7/21

N2 - Background: 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.Results: 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).Conclusions: 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.

AB - Background: 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.Results: 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).Conclusions: 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.

UR - http://www.scopus.com/inward/record.url?scp=77954686960&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77954686960&partnerID=8YFLogxK

U2 - 10.1186/1742-6405-7-24

DO - 10.1186/1742-6405-7-24

M3 - Article

C2 - 20646329

AN - SCOPUS:77954686960

SN - 1742-6405

VL - 7

JO - AIDS research and therapy

JF - AIDS research and therapy

M1 - 24

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this