1887

Abstract

In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3′ non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5′ cap nucleotide, an I-poly(A) tract and the 3′ poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5′ NTR and repeated sequence elements (RSEs) within the 3′ NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o’nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as ‘polymerase slippage’, as has been reported for vesicular stomatitis virus.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-83-12-3075
2002-12-01
2019-12-12
Loading full text...

Full text loading...

/deliver/fulltext/jgv/83/12/0833075a.html?itemId=/content/journal/jgv/10.1099/0022-1317-83-12-3075&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. ( 1990; ). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.[CrossRef]
    [Google Scholar]
  2. Barr, J. N. & Wertz, G. W. ( 2001; ). Polymerase slippage at vesicular stomatitis virus gene junctions to generate polyA is regulated by the upstream 3′-AUAC-5′ tetranucleotide: implications for the mechanism of transcription termination. Journal of Virology 75, 6901-6913.[CrossRef]
    [Google Scholar]
  3. Barr, J. N., Whelan, S. P. J. & Wertz, G. W. ( 1997; ). Cis-acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation. Journal of Virology 71, 8718-8725.
    [Google Scholar]
  4. Blackburn, N. K., Besselaar, T. G. & Gibson, G. ( 1995; ). Antigenic relationship between Chikungunya virus strains and o’nyong-nyong virus using monoclonal antibodies. Research Virology 146, 69-73.[CrossRef]
    [Google Scholar]
  5. Calisher, C. H., Shope, R. E., Brandt, W., Casals, J., Karabatsos, N., Murphy, F. A., Tesh, R. B. & Wiebe, M. E. ( 1980; ). Proposed antigenic classification of registered arboviruses. I. Togaviridae, Alphavirus. Intervirology 14, 229-232.[CrossRef]
    [Google Scholar]
  6. Chanas, A. C., Hubalek, Z., Johnson, B. K. & Simpson, D. I. H. ( 1979; ). A comparative study of o’nyong-nyong virus with Chikungunya virus and plaque variants. Archives of Virology 59, 231-238.[CrossRef]
    [Google Scholar]
  7. Diallo, M., Thonnon, J., Traore-Lamizana, M. & Fontenille, D. ( 1999; ). Vectors of Chikungunya virus in Senegal: current data and transmission cycles. American Journal of Tropical Medicine and Hygiene 60, 281-286.
    [Google Scholar]
  8. Faragher, S. G., Meek, A. D. J., Rice, C. M. & Dalgarno, L. ( 1988; ). Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus. Virology 163, 509-526.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.[CrossRef]
    [Google Scholar]
  10. Felsenstein, J. (1993). phylip: phylogeny inference package, version 3.5c. University of Washington, Seattle, Washington, USA.
  11. Hammon, W. McD., Rudnick, A. & Sather, G. E. ( 1960; ). Viruses associated with epidemic hemorrhagic fevers of the Philippines and Thailand. Science 131, 1102-1103.[CrossRef]
    [Google Scholar]
  12. Hardy, W. R. & Strauss, J. H. ( 1989; ). Processing the nonstructural polyproteins of Sindbis virus: nonstructural proteinase is in the C-terminal half of nsP2 and functions both in cis and in trans. Journal of Virology 63, 4653-4664.
    [Google Scholar]
  13. Igarashi, A. ( 1978; ). Isolation of a Singh’s Aedes albopictus cell clone sensitive to dengue and Chikungunya viruses. Journal of General Virology 40, 531-544.[CrossRef]
    [Google Scholar]
  14. Kaariainen, L., Takkinen, K., Keranen, S. & Soderlund, H. ( 1987; ). Replication of the genome of alphaviruses. Journal of Cell Science 7(Suppl.), 231–250.
    [Google Scholar]
  15. Kamer, G. & Argos, P. ( 1984; ). Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Research 12, 7269-7282.[CrossRef]
    [Google Scholar]
  16. Kinney, R. M., Tsuchiya, K. R., Sneider, J. M. & Trent, D. W. ( 1992; ). Genetic evidence that epizootic Venezuelan equine encephalitis (VEE) viruses may have evolved from enzootic VEE subtype I-D virus. Virology 191, 569-580.[CrossRef]
    [Google Scholar]
  17. Lanciotti, R. S., Ludwig, M. L., Rwaguma, E. B., Lutwama, J. J., Kram, T. M., Karabatsos, N., Cropp, B. C. & Miller, B. R. ( 1998; ). Emergence of epidemic o’nyong-nyong fever in Uganda after a 35-year absence: genetic characterization of the virus. Virology 252, 258-268.[CrossRef]
    [Google Scholar]
  18. Lee, E., Stocks, C., Lobigs, P., Hislop, A., Straub, J., Marshall, I., Weir, R. & Dalgarno, L. ( 1997; ). Nucleotide sequence of the Barmah forest virus genome. Virology 227, 509-514.[CrossRef]
    [Google Scholar]
  19. Levinson, R. S., Strauss, J. H. & Strauss, E. G. ( 1990; ). Complete sequence of the genomic RNA of o’nyong-nyong virus and its use in the construction of alphavirus phylogenetic trees. Virology 175, 110-123.[CrossRef]
    [Google Scholar]
  20. Morita, K., Tanaka, M. & Igarashi, A. ( 1991; ). Rapid identification of dengue virus serotypes by using polymerase chain reaction. Journal of Clinical Microbiology 29, 2107-2110.
    [Google Scholar]
  21. Ou, J.-H., Strauss, E. G. & Strauss, J. H. ( 1981; ). Comparative studies of the 3′-terminal sequences of several alphavirus RNAs. Virology 109, 281-289.[CrossRef]
    [Google Scholar]
  22. Ou, J.-H., Trent, D. W. & Strauss, J. H. ( 1982a; ). The 3′-noncoding regions of alphavirus RNAs contain repeating sequences. Journal of Molecular Biology 156, 719-730.[CrossRef]
    [Google Scholar]
  23. Ou, J.-H., Rice, C. M., Dalgarno, L., Strauss, E. G. & Strauss, J. H. ( 1982b; ). Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA. Proceedings of the National Academy of Sciences, USA 79, 5235-5239.[CrossRef]
    [Google Scholar]
  24. Ou, J.-H., Strauss, E. G. & Strauss, J. H. ( 1983; ). The 5′-terminal sequences of the genomic RNAs of several alphaviruses. Journal of Molecular Biology 168, 1-15.[CrossRef]
    [Google Scholar]
  25. Page, R. D. M. ( 1996; ). Treeview: an application to display phylogenetic trees on personal computers. Cabios 12, 357-358.
    [Google Scholar]
  26. Pfeffer, M., Kinney, R. M. & Kaaden, O.-R. ( 1998; ). The alphavirus 3′-nontranslated region: size heterogeneity and arrangement of repeated sequence elements. Virology 240, 100-108.[CrossRef]
    [Google Scholar]
  27. Porterfield, J. H. ( 1980; ). Antigenic characteristics and classification of Togaviridae. In The Togaviruses , pp. 13-46. Edited by R. W. Schlesinger. New York:Academic Press.
  28. Powers, A. M., Brault, A. C., Tesh, R. B. & Weaver, S. C. ( 2000; ). Re-emergence of chikungunya and o’nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships. Journal of General Virology 81, 471-479.
    [Google Scholar]
  29. Ross, R. W. ( 1956; ). The Newala epidemic. III. The virus: isolation, pathogenic properties and relationship to the epidemic. Journal of Hygiene 54, 177-191.[CrossRef]
    [Google Scholar]
  30. Sarkar, J. K., Chatterjee, S. N. & Chakravarty, S. K. ( 1964; ). Haemorrhagic fever in Calcutta: some epidemiological observations. Indian Journal of Medical Research 52, 651-659.
    [Google Scholar]
  31. Strauss, E. G. & Strauss, J. H. ( 1986; ). Structure and replication of the alphavirus genome. In The Togaviridae and Flaviviridae , pp. 35-90. Edited by S. Schlesinger & M. J. Schlesinger. New York:Plenum Press.
  32. Strauss, J. H. & Strauss, E. G. ( 1988; ). Evolution of RNA viruses. Annual Review of Microbiology 42, 657-683.[CrossRef]
    [Google Scholar]
  33. Strauss, J. H. & Strauss, E. G. ( 1994; ). The alphaviruses: gene expression, replication and evolution. Microbiological Reviews 58, 491-562.
    [Google Scholar]
  34. Strauss, E. G., Rice, C. M. & Strauss, J. H. ( 1984; ). Complete nucleotide sequence of the genomic RNA of Sindbis virus. Virology 133, 92-110.[CrossRef]
    [Google Scholar]
  35. Thaikruea, L., Charearnsook, O., Reanphumkarnkit, S., Dissomboon, P., Phonjan, R., Ratchbud, S., Kounsang, Y. & Buranapiyawong, D. ( 1997; ). Chikungunya in Thailand: a re-emerging disease? Southeast Asian Journal of Tropical Medicine and Public Health 28, 359-364.
    [Google Scholar]
  36. Van Regenmortel, M. H. V., Fauquet, C. M., Bishop, D. H. L., Carstens, E. B., Estes, M. K., Lemon, S. M., Maniloff, J., Mayo, M. A., McGeoch, D. J., Pringle, C. R. & Wickner, R. B (editors) (2000). Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses. San Diego: Academic Press.
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-83-12-3075
Loading
/content/journal/jgv/10.1099/0022-1317-83-12-3075
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error