Virus Genes

, Volume 45, Issue 2, pp 201–206 | Cite as

Near full-length genomic characterization of a HIV type 1 BC recombinant strain from Manipur, India

  • Roni Sarkar
  • Kamalesh Sarkar
  • N. Brajachand Singh
  • Y. Manihar Singh
  • Sekhar ChakrabartiEmail author


Genetic complexity of HIV-1 is brought about by recombination between HIV-1 subtypes which leads to the development of epidemiologically significant founder strains. In the present study, the near full-length genome sequence of an HIV-1 isolate from an injecting drug user of Manipur (India) was determined, which evidenced the presence of a novel HIV-1 BC recombinant strain. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. The recombination break points were detected using bootscan and simplot analyses. This isolate exhibited a mosaic structure consisting of subtype C backbone with subtype B insertions at the upstream of pol gene (3026–3259) and the downstream of env gene which spanned till the nef gene (8183–8961). Phylogenetic relationships determined with neighbor-joining trees, revealed that the subtype C sequences clustered with sequences from Indian subtype C HIV-1 strains, and the subtype B sequences clustered with HIV-1 subtype B strains from Thailand. This finding may create a complex scenario of HIV-1 epidemic among the injecting drug users of Manipur in near future.


Injecting drug users (IDUs) Polymerase chain reaction (PCR) Human immunodeficiency virus (HIV-1) Near full-length genome (NFLG) 



We sincerely acknowledge the cooperation of Manipur State AIDS Control and Prevention, India, in this study. We also thank the Department of Biotechnology, Govt. of India and Indian Council of Medical Research for financial support.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Roni Sarkar
    • 1
  • Kamalesh Sarkar
    • 1
  • N. Brajachand Singh
    • 2
  • Y. Manihar Singh
    • 2
  • Sekhar Chakrabarti
    • 1
    Email author
  1. 1.HIV/AIDS Laboratory, Division of VirologyNational Institute of Cholera and Enteric DiseasesKolkataIndia
  2. 2.RIMSImphalIndia

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