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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 Chakrabarti
Article
  • 175 Downloads

Abstract

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.

Keywords

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

Notes

Acknowledgments

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.

References

  1. 1.
    J. Hemelaar, E. Gouws, P.D. Ghys, S. Osmanov, Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20, W13–W23 (2006)PubMedCrossRefGoogle Scholar
  2. 2.
    R.A. Katz, A.M. Skalka, Generation of diversity in retroviruses. Annu. Rev. Genet. 24, 409–445 (1990)PubMedCrossRefGoogle Scholar
  3. 3.
    H.M. Temin, Sex and recombination in retroviruses. Trends Genet. 7, 71–74 (1991)PubMedGoogle Scholar
  4. 4.
    D.P. Wooley, R.A. Smith, S. Czajak, R.C. Desrosiers, Direct demonstration of retroviral recombination in a rhesus monkey. J. Virol. 71, 9650–9653 (1997)PubMedGoogle Scholar
  5. 5.
    B.R. Gundlach, M.G. Lewis, S. Sopper, T. Schnell, J. Sodroski, C. Stahl-Hennig, K. Uberla, Evidence for recombination of live, attenuated immunodeficiency virus vaccine with challenge virus to a more virulent strain. J. Virol. 74, 3537–3542 (2000)PubMedCrossRefGoogle Scholar
  6. 6.
    Z. Gu, Q. Gao, E.A. Faust, M.A. Wainberg, Possible involvement of cell fusion and viral recombination in generation of human immunodeficiency virus variants that display dual resistance to AZT and 3TC. J. Gen. Virol. 76, 2601–2605 (1995)PubMedCrossRefGoogle Scholar
  7. 7.
    F.E. McClutchan, J.K. Carr, D. Murphy, S. Piyasirisilp, F. Gao, B. Hahn, X.F. Yu, C. Beyrer, D.L. Birx, Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. AIDS Res. Hum. Retroviruses 18, 1135–1140 (2002)PubMedCrossRefGoogle Scholar
  8. 8.
    Y.M. Chen, Y.C. Lan, S.F. Lai, J.Y. Yang, S.F. Tsai, S.H. Kuo, HIV-1 CRF07_BC infections, injecting drug users, Taiwan. Emerg. Infect. Dis. 12, 703–705 (2006)PubMedCrossRefGoogle Scholar
  9. 9.
    K.S. Lole, R.C. Bollinger, R.S. Paranjape, D. Gadkari, S.S. Kulkarni, N.G. Novak, R. Ingersoll, H.W. Sheppard, S.C. Ray, Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73, 152–160 (1999)PubMedGoogle Scholar
  10. 10.
    N.B. Siddappa, P.K. Dash, A. Mahadevan, N. Jayasuryan, F. Hu, B. Dice, R. Keefe, K.S. Satish, B. Satish, K. Sreekanthan, R. Chatterjee, K. Venu, P. Satishchandra, V. Ravi, S.K. Shankar, R. Shankarappa, U. Ranga, 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. J. Clin. Microbiol. 42, 2742–2751 (2004)PubMedCrossRefGoogle Scholar
  11. 11.
    A. Maitra, B. Singh, S. Banu, A. Deshpande, K. Robbins, M.L. Kalish, S. Broor, P. Seth, Subtypes of HIV type 1 circulating in India: partial envelope sequences. AIDS Res. Hum. Retroviruses 15, 941–944 (1999)PubMedCrossRefGoogle Scholar
  12. 12.
    S. Sarkar, P. Mookherjee, A. Roy, T.N. Naik, J.K. Singh, A.R. Sharma, Descriptive epidemiology of intravenous heroin users—a new risk group for transmission of HIV in India. J. Infect. 23(2), 201–207 (1991)PubMedCrossRefGoogle Scholar
  13. 13.
    S. Sarkar, N. Das, S. Panda, T.N. Naik, K. Sarkar, B.C. Singh, J.M. Ralte, S.M. Aier, S.P. Tripathy, Rapid spread of HIV among injecting drug users in northeastern states of India. Bull. Narc. 45(1), 91–105 (1993)PubMedGoogle Scholar
  14. 14.
    D.K. Mandal, S. Jana, S.K. Bhattacharya, S. Chakrabarti, HIV-1 subtypes circulating in eastern and northeastern regions of India. AIDS Res. Hum. Retroviruses 18, 1219–1227 (2002)PubMedCrossRefGoogle Scholar
  15. 15.
    P. Bhanja, S. Sengupta, N.Y. Singh, K. Sarkar, S.K. Bhattacharya, S. Chakrabarti, Determination of gag and env subtypes of HIV-1 detected among injecting drug users in Manipur, India: Evidence for intersubtype recombination. Virus Res. 114, 149–153 (2005)PubMedCrossRefGoogle Scholar
  16. 16.
    R. Sarkar, S. Sengupta, R. Mullick, N.B. Singh, K. Sarkar, S. Chakrabarti, Implementation of a multiregion hybridization assay to characterize HIV-1 strains detected among injecting drug users in Manipur, India. Intervirology 52(4), 175–178 (2009)PubMedCrossRefGoogle Scholar
  17. 17.
    Y. Nadai, L.M. Eyzaguirre, N.T. Constantine, A.M. Sill, F. Cleghorn, W.A. Blattner, J.K. Carr, Protocol for nearly full-length sequencing of HIV-1 RNA from plasma. PLoS One 3(1), e1420 (2008)PubMedCrossRefGoogle Scholar
  18. 18.
    N. Saitou, M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)PubMedGoogle Scholar
  19. 19.
    M.O. Salminen, J.K. Carr, D.S. Burke, F.E. McCutchan, Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 11, 1423–1425 (1995)PubMedCrossRefGoogle Scholar
  20. 20.
    S. Tovanabutra, C. Beyrer, S. Sakkhachornphop, The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002. AIDS Res. Hum. Retroviruses 20, 465–475 (2004)PubMedCrossRefGoogle Scholar
  21. 21.
    M.L. Kalish, A. Baldwin, S. Raktham, The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: implications for HIV vaccine trials. AIDS 9, 851–857 (1995)PubMedCrossRefGoogle Scholar
  22. 22.
    Y. Takebe, K. Motomura, M. Tatsumi, H.H. Lwin, M. Zaw, S. Kusagawa, High prevalence of diverse forms of HIV-1 intersubtype recombinants in central Myanmar: geographical hot spot of extensive recombination. AIDS 17, 2077–2087 (2003)PubMedCrossRefGoogle Scholar
  23. 23.
    S. Chakrabarti, S. Panda, A. Chatterjee, HIV-1 subtypes in injecting drug users and their noninjecting wives in Manipur, India. Indian J. Med. Res. 111, 189–194 (2000)PubMedGoogle Scholar
  24. 24.
    A. Carmen, G.V. Stimson, M. Hickman, Global overview of injecting drug use and HIV infection among injecting drug users. AIDS 18, 295–303 (2004)CrossRefGoogle Scholar

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
  1. 1.HIV/AIDS Laboratory, Division of VirologyNational Institute of Cholera and Enteric DiseasesKolkataIndia
  2. 2.RIMSImphalIndia

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