Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Genomic analysis of a Chinese isolate of Getah-like virus and its phylogenetic relationship with other Alphaviruses

  • 420 Accesses

  • 19 Citations


An alphavirus, M-1 strain, was isolated from a pool of culicine mosquitoes collected in Hainan island of China during an arbovirus survey in 1964. In the present study, we determined the complete nucleotide sequence of the M-1 strain using RT-PCR and RACE techniques. The M-1 genome is 11,690 nucleotides (nt) in length and contains two open reading frames (ORFs) encoding four nonstructural proteins and five structural proteins, respectively. Searches using Blast and comparison analyses suggested that M-1 is closely linked to Sagiyama virus (SAGV, AB032553) with 98% identity and Getah viruse (GETV, AY702913) with 97.8% identity in the full-length nucleotide sequence. However, compared with SAGV, there is 1 deletion (3 nucleotides in length) in the Capsid region, a deletion in the 3′ untranslated region (10 nucleotides in length) and 2 insertions in the 3′ untranslated region involving a total of 5 nucleotides. Interestingly, from the 5′ UTR to the end of coding region, M-1 share the highest identity with GETV, even though the identity of 3′ UTR drops dramatically to 76.2%. Furthermore, phylogenetic analysis based on the complete genomic sequences and sequences for structural or non-structural proteins of M-1 and 15 alphaviruses showed that M-1 grouped with GETV first and then grouped together with SAGV. Based on the comparison analysis and phylogenetic analysis, we conclude that M-1 strain can be considered as a strain that is a Chinese isolate of Getah-like virus.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2


  1. 1.

    C.H. Calisher, N. Karabatsos, in The Arboviruses: Epidemiology and Ecology, ed by T.P. Monath (CRC Press, Inc., Baca Raton, FL, 1988), p. 19

  2. 2.

    J.H. Strauss, E.G. Strauss, Microbiol. Rev. 58, 491 (1994)

  3. 3.

    L.P. Nagata, W.G. Hu, M. Parker, D. Chau, G.A. Rayner, F.L. Schmaltz, J.P. Wong, J. Gen. Virol. 87 (Pt 8): 2353 (2006)

  4. 4.

    W.K. Reisen, T.P. Monath, in The Arboviruses: Epidemiology and Ecology, vol. V, ed by T.P. Monath (CRC Press, Boca Raton, FL, 1988), p. 89

  5. 5.

    D.E. Griffin, in The Togaviridae and Flaviviridae, ed by S. Schlesinger M.J. Schlesinger (Plenum Publishing Corp, New York, 1986), p. 209

  6. 6.

    C.J. Peters, J.M. Dalrymple, in Virology, ed by B.N. Fields, D.M. Knipe (Raven Press, New York, 1990), p. 713

  7. 7.

    D.A. Phillips, J.R. Murray, J.G. Asakov, M.A. Wiemers, Med. J. 152, 463 (1990)

  8. 8.

    M.B. Rennels: Neurol. Clin. 2, 241 (1984)

  9. 9.

    X.D. Li, F.X. Qiu, H. Yang, Y.N. Rao, Charles H. Calisher., Southeast Asian J. Trop. Med. Public Heath 4(23), 730 (1992)

  10. 10.

    S. Kumar, K. Tamura, M. Nei, Brief. Bioinform. 5, 150 (2004)

  11. 11.

    Y. Shirako, Y. Yamaguchi, J. Gen. Virol. 81, 1353 (2000)

  12. 12.

    S.G. Faragher, L. Dalgarno, J. Mol. Biol. 190, 141 (1986)

  13. 13.

    G. Wallner, C.W. Mandl, C. Kunz, F.X. Heinz, Virology 213, 169 (1995)

  14. 14.

    C.H. Calisher, R.E. Shope, W. Brandt, J. Casals, N. Karabatsos, F.A. Murphy, R.B. Tesh, M.E. Wiebe, Intervirology 14, 229 (1980)

  15. 15.

    N. Karabatsos, Am. J. Trop. Med. Hyg. 24, 527 (1975)

  16. 16.

    R.B. Tesh, Annu. Rev. Med. 33, 31 (1982)

  17. 17.

    A.C. Chanas, Z. Hubalek, B.K. Johnson, D.I. Simpson, Arch. Virol. 59(3), 231 (1979)

  18. 18.

    N.K. Blackburn, T.G. Besselaar, G. Gibson, Res. Virol. 146(1), 69 (1995)

  19. 19.

    R.S. Lanciotti, M.L. Ludwig, E.B. Rwaguma, J.J. Lutwama, T.M. Kram, N. Karabatsos, B.C. Cropp, B.R. Miller, Virology 252(1), 258 (1998)

  20. 20.

    A.M. Powers, A.C. Brault, R.B. Tesh, S.C. Weaver, J. Gen. Virol. 81(Pt 2), 471 (2000)

  21. 21.

    C.H. Calisher, N. Karabatsos, J.S. Lazuick, T.P. Monath, K.L. Wolff, Am. J. Trop. Med. Hyg. 38, 447 (1988)

  22. 22.

    C.S. Hahn, S. Lustig, E.G. Strauss, J.H. Strauss, Proc. Natl. Acad. Sci. U.S.A. 85(16), 5997 (1988)

  23. 23.

    J.R. Bell, R.M. Kinney, D.W. Trent, E.G. Strauss, J.H. Strauss, Proc. Natl. Acad. Sci. U.S.A. 81(15), 4702 (1984)

  24. 24.

    R.S. Levinson, J.H. Strauss, E.G. Strauss, Virology 175, 110 (1990)

  25. 25.

    S.C. Weaver, in Molecular Basis of Virus evolution, ed by A.J. Gibbs, C.H. Calisher, F. Garcia-Arenal (Cambridge University Press, Cambridge, England, 1995), p. 501

  26. 26.

    S.C. Weaver, W. Kang, Y. Shirako, T. Rumenapf, E.G. Strauss, J.H. Strauss, J. Virol. 71, 613 (1997)

  27. 27.

    A.M. Powers, A.C. Brault, Y. Shirako, E.G. Strauss, W. Kang, J.H. Strauss, S.C. Weaver, J. Virol. 75(21), 10118 (2001)

  28. 28.

    M.H.V. Van Regenmortel, in Virus Taxonomy. Classification and Nomenclature of Viruses, ed. by M.H.V. van Regenmortel, C.M. Fauquet, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon, J. Maniloff, M.A. Mayo, D.J. McGeogh, C.R. Pringle, R.B. Wickner. Seventh Report of the International Committee on Taxonomy of Viruses (Academic Press Inc., San Diego, CA, 2000)

Download references


We thank Blumenkrantz Deena, Wythe Sarah and Hongwei Wang for critical review of the manuscript.

Author information

Correspondence to Li-Fang Jiang.

Additional information

Jin-Sheng Wen and Wen-Zhong Zhao equally contributed to this work.

The nucleotide sequence data reported in this article have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number: EF011023.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wen, J., Zhao, W., Liu, J. et al. Genomic analysis of a Chinese isolate of Getah-like virus and its phylogenetic relationship with other Alphaviruses. Virus Genes 35, 597–603 (2007).

Download citation


  • Getah virus
  • Sagiyama virus
  • Alphavirus
  • Phylogenetic analysis