This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Siddappa, N. B. Articles by Ranga, U. Search for Related Content PubMed PubMed Citation Articles by Siddappa, N. B. Articles by Ranga, U.

 Previous Article  |  Next Article 

Journal of Clinical Microbiology, June 2004, p. 2742-2751, Vol. 42, No. 6
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.6.2742-2751.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India

Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research,¹ Department of Neuropathology,³ Department of Neurology,¹⁰ Department of Neurovirology,² National Institute of Mental Health and NeurosciencesMicrotest Innovations Pvt. Ltd.,⁴ Seva Free Clinic, Bangalore, Karnataka,⁶ Department of Infectious Diseases, Medical College Hospital, Thiruvananthapuram, Kerala,⁷ Department of Virology, Chittaranjan National Cancer Institute, Kolkata, West Bengal,⁸ Government General Chest Hospital, Erragadda, Osmania Medical College, Hyderabad, Andhra PradeshIndia,⁹ Center for Genomic Sciences, Allegheny-Singer Research Institute,⁵ Thomas E. Starzl Transplantation Institute, Department of Surgery,¹¹ Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania,¹²

Received 25 September 2003/ Returned for modification 29 October 2003/ Accepted 21 February 2004

Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-B sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.