Anand, D Alex

Christy, H Jemmy

Pasupuleti, Renuka

English

PubMed

H Christy

D Anand

Renuka Pasupuleti

Springer - Publisher Connector

ORAL PRESENTATION Open Access
Molecular determinants analysis and co receptor
tropism prediction of V3 loop of HIV-1 “C” clade
sequences isolated from India using insilico
approach
H Jemmy Christy*, D Alex Anand, Renuka Pasupuleti
From First International Science Symposium on HIV and Infectious Diseases (HIV SCIENCE 2012)
Chennai, India. 20-22 January 2012
Background
The V3 loop of the env gene in HIV-C type is consid-
ered as a major viral determinant for coreceptor specifi-
city. The tip motif of v3 loop is known for antibody
neutralization, so sequence variation in this motif have
an impact on virus infectivity and disease progression.
So analysis of genetic diversity in the V3 loop Tip motif
help us to improve the CCR5 antagonist’s development
as well as vaccine target.
Methods
HIV-1 “C” type env sequences of Indian isolates were
retrieved from HIV sequence database. Coreceptor
Tropism prediction by different web-based interpreta-
tion system like (WebPSSM, Geno2pheno, (ds) Kernel,
WetCat) was performed. The diversity of V3 loop tip
motif, glycosylation motifs were analyzed using N-Gly-
cosite. Relative frequencies of each amino acid in v3
loop were determined using Web Logo.
Results
In this study, lower numbers of positive charges of v3
loop, in the range of 4 to 5, reveals the prevalence of R5
tropism. Thus majority of the V3 sequences of HIV-1
Indian isolates were predicted as R5-tropism and we
identified few mutational prevalence like for R5-pre-
dicted viruses -E25D, Y21F and for X4-predicted viruses
E25KRQ, I12, H34Y. Overall eight different tetrameric
tip motifs [GPGQ, GPGR, GPAQ, GPRR, GPGL, RPRQ,
EPGQ, and GSGQ] were identified.
Conclusion
High prevalence of R5 tropism, higher no of conserved
motif regions in the V3 sequence among HIV strains in
India reveals the need of potential CCR5 antagonists.
GPGQ and GPGR is highly conserved in all the
sequences and this pattern could be an ideal target for
AIDS therapy.
Published: 4 May 2012
doi:10.1186/1471-2334-12-S1-O18
Cite this article as: Christy et al.: Molecular determinants analysis and co
receptor tropism prediction of V3 loop of HIV-1 “C” clade sequences
isolated from India using insilico approach. BMC Infectious Diseases 2012
12(Suppl 1):O18.
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Submit your manuscript at 
www.biomedcentral.com/submit* Correspondence: jemmyjacob@gmail.com
Sathyabama University, Chennai, India
Christy et al. BMC Infectious Diseases 2012, 12(Suppl 1):O18
http://www.biomedcentral.com/1471-2334/12/S1/O18
© 2012 Christy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.


Molecular determinants analysis and co receptor tropism prediction of V3 loop of HIV-1 “C” clade sequences isolated from India using insilico approach

Christy H

Anand D

Pasupuleti Renuka

Directory of Open Access Journals

BMC Infectious Diseases

H Jemmy Christy

D Alex Anand

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Molecular determinants analysis and co receptor tropism prediction of V3 loop of HIV-1 “C” clade sequences isolated from India using insilico approach

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