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Journal of Virology, November 2001, p. 10479-10487, Vol. 75, No. 21
Department of Microbiology, University of
Washington, Seattle, Washington 981951;
Department of Virology, Chittaranjan Cancer Research
Institute,2 and Department of Virology,
School of Tropical Medicine,3 Calcutta,
India; and Department of Epidemiology5
and Department of Infectious Diseases and
Microbiology,4 Graduate School of Public Health,
University of Pittsburgh, Pittsburgh, Pennsylvania 15213
Received 5 February 2001/Accepted 2 August 2001
India is experiencing a rapid spread of human immunodeficiency
virus type 1 (HIV-1), primarily through heterosexual
transmission of subtype C viruses. To delineate the molecular features
of HIV-1 circulating in India, we sequenced the V3-V4 region of viral
env from 21 individuals attending an HIV clinic in
Calcutta, the most populous city in the eastern part of the country,
and analyzed these and the other Indian sequences in the HIV database.
Twenty individuals were infected with viruses having a subtype C
env, and one had viruses with a subtype A
env. Analyses of 192 subtype C sequences that included
one sequence for each subject from this study and from the HIV database
revealed that almost all sequences from India, along with a small
number from other countries, form a phylogenetically distinct lineage
within subtype C, which we designate CIN. Overall,
CIN lineage sequences were more closely related to
each other (level of diversity, 10.2%) than to subtype C
sequences from Botswana, Burundi, South Africa, Tanzania, and Zimbabwe (range, 15.3 to 20.7%). Of the three positions identified as
signature amino acid substitution sites for CIN sequences
(K340E, K350A, and G429E), 56% of the CIN sequences
contained all three amino acids while 87% of the sequences contained
at least two of these substitutions. Among the non-CIN
sequences, all three amino acids were present in 2%, while 22%
contained two or more of these amino acids. These results suggest
that much of the current Indian epidemic is descended from a single
introduction into the country. Identification of conserved signature
amino acid positions could assist epidemiologic tracking and has
implications for the development of a vaccine against subtype C HIV-1
in India.
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.21.10479-10487.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Human Immunodeficiency Virus Type 1 Env
Sequences from Calcutta in Eastern India: Identification of
Features That Distinguish Subtype C Sequences in India from Other
Subtype C Sequences

*
Corresponding author. Mailing address: Department of
Infectious Diseases and Microbiology, 426 Parran Hall, 130 DeSoto St., Pittsburgh, PA 15261. Phone: (412) 624-7998. Fax: (412) 624-4953. E-mail: pgupta1+{at}pitt.edu.
Present address: Center for Genomic Sciences, Allegheny Singer
Research Institute, Pittsburgh, PA 15212.
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