Molecular characterization of M1146, an American isolate of Ljungan virus (LV) reveals the presence of a new LV genotype

Journal of General Virology

Volumn 84, Issue 4, 2003, Pages 837-844

  Johansson, E Susanne ^a   Niklasson, Bo ^b   Tesh, Robert B ^c   Shafren, Darren R ^d   Travassos da Rosa, Amelia P A ^c   Lindberg, A Michael ^a  

^a LINNAEUS UNIVERSITY   (Sweden)

^b Apodemus AB   (Sweden)

^c University of Texas Medical Branch School of Medicine   (United States)

^d UNIVERSITY OF NEWCASTLE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; VIRUS PROTEIN;

ANIMAL CELL; ANIMAL TRAPPING; ANTIGENICITY; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ORGANIZATION; GENOTYPE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHYLOGENY; PICORNAVIRUS; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SHORT SURVEY; SPECIES; STATISTICAL SIGNIFICANCE; SWEDEN; UNITED STATES; VIRUS CHARACTERIZATION; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN; VOLE;

ANIMALS; ARVICOLINAE; BASE SEQUENCE; CAPSID PROTEINS; CLONING, MOLECULAR; GENOTYPE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OREGON; PHYLOGENY; PICORNAVIRIDAE; SEQUENCE ALIGNMENT; SWEDEN; VIRAL NONSTRUCTURAL PROTEINS;

ANIMALIA; CLETHRIONOMYS GLAREOLUS; DNA VIRUSES; LJUNGAN VIRUS; MICROTUS MONTANUS; MIRIDAE; MURIDAE; PICORNAVIRIDAE; RNA VIRUSES;

EID: 0037385514     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.18792-0     Document Type: Short Survey

References (49)

1. Abrahams, J. P., van den Berg, M., van Batenburg, E. & Pleij, C. (1990). Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res 18, 3035-3044.
2. Auvinen, P. & Hyypiä, T. (1990). Echoviruses include genetically distinct serotypes. J Gen Virol 71, 2133-2139.
3. Beard, C. W. & Mason, P. W. (2000). Genetic determinants of altered virulence of Taiwanese foot-and-mouth disease virus. J Virol 74, 987-991.
4. Cohen, S. H., Naviaux, R. K., vanden Brink, K. M. & Jordan, G. W. (1988). Comparison of the nucleotide sequences of diabetogenic and nondiabetogenic encephalomyocarditis virus. Virology 166, 603-607.
5. Doherty, M., Todd, D., McFerran, N. & Hoey, E. M. (1999). Sequence analysis of a porcine enterovirus serotype 1 isolate: relationships with other picornaviruses. J Gen Virol 80, 1929-1941.
6. Donnelly, M. L. L., Gani, D., Flint, M., Monaghan, S. & Ryan, M. D. (1997). The cleavage activities of aphthovirus and cardiovirus 2A proteins. J Gen Virol 78, 13-21.
7. Donnelly, M. L. L., Hughes, L. E., Luke, G., Mendoza, H., ten Dam, E., Gani, D. & Ryan, M. D. (2001a). The 'cleavage' activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring '2A-like' sequences. J Gen Virol 82, 1027-1041.
8. Donnelly, M. L. L., Luke, G., Mehrotra, A., Li, X., Hughes, L. E., Gani, D. & Ryan, M. D. (2001b). Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translation effect: a putative ribosomal 'skip'. J Gen Virol 82, 1013-1025.
9. Ghazi, F., Hughes, P. J., Hyypiä, T. & Stanway, G. (1998). Molecular analysis of human parechovirus type 2 (formerly echovirus 23). J Gen Virol 79, 2641-2650.
10. Gorbalenya, A. E. & Koonin, E. V. (1993). Comparative analysis of the amino acid sequences of the key enzymes of the replication and expression of positive-strand RNA viruses. Sov Sci Rev D Physicochem Biol 11, 1-84.
11. Govan, V. A., Leat, N., Allsopp, M. & Davison, S. (2000). Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses. Virology 277, 457-463.
12. Hahn, H. & Palmenberg, A. C. (2001). Deletion mapping of the encephalomyocarditis virus primary cleavage site. J Virol 75, 7215-7218.
13. Hinton, T. M. & Crabb, B. S. (2001). The novel picornavirus Equine rhinitis B virus contains a strong type II internal ribosomal entry site which functions similarly to that of Encephalomyocarditis virus. J Gen Virol 82, 2257-2269.
14. Hughes, P. J. & Stanway, G. (2000). The 2A proteins of three diverse picornaviruses are related to each other and to the H-rev107 family of proteins involved in the control of cell proliferation. J Gen Virol 81, 201-207.
15. Hyypiä, T., Horsnell, C., Maaronen, M., Kahn, M., Kalkkinen, N., Auvinen, P., Kinnunen, L. & Stanway, G. (1992). A distinct picornavirus group identified by sequence analysis. Proc Natl Acad Sci U S A 89, 8847-8851.
16. Isawa, H., Asano, S., Sahara, K., Iizuka, T. & Bando, H. (1998). Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses. Arch Virol 143, 127-143.
17. Johansson, S., Niklasson, B., Maizel, J., Gorbalenya, A. E. & Lindberg, A. M. (2002). Molecular analysis of three Ljungan virus isolates reveals a new, close-to-root lineage of the Picornaviridae with a cluster of two unrelated 2A proteins. J Virol 76, 8920-8930.
18. Johnson, H. N. (1965). Diseases derived from wildlife. Calif Health 23, 35-39.
19. Johnson, K. N. & Christian, P. D. (1998). The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family. J Gen Virol 79, 191-203.
20. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275-282.
21. Kaku, Y., Sarai, A. & Murakami, Y. (2001). Genetic reclassification of porcine enteroviruses. J Gen Virol 82, 417-424.
22. King, A. M. Q., Brown, F., Christian, P. & 8 other authors (2000). Picornaviridae. In Virus Taxonomy. Seventh Report of the International Committee for the Taxonomy of Viruses, pp. 657-678. Edited by M. H. V. Van Regenmortel, C. M. Fauquet, D. H. L. Bishop, C. H. Calisher, E. B. Carsten, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner. New York: Academic Press.
23. Kozak, M. (1986). Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283-292.
24. Lindberg, A. M. & Johansson, S. (2002). Phylogenetic analysis of Ljungan virus and A-2 plaque virus, new members of the Picornaviridae. Virus Res 85, 61-70.
25. Main, A. J., Shope, R. E. & Wallis, R. C. (1976). Characterization of Whitney's Clethrionomys gapperi virus isolates from Massachusetts. J Wildl Dis 12, 154-164.
26. Marvil, P., Knowles, N. J., Mockett, A. P., Britton, P., Brown, T. D. & Cavanagh, D. (1999). Avian encephalomyelitis virus is a picornavirus and is most closely related to hepatitis A virus. J Gen Virol 80, 653-662.
27. Mateu, M. G. (1995). Antibody recognition of picornaviruses and escape from neutralization: a structural view. Virus Res 38, 1-24.
28. Nicholas, K. B., Jr, N. H. B. & Deerfield, D. W. (1997). GENEDOC: analysis and visualization of genetic variation. EMBNET News 4, 1-4.
29. Niklasson, B., Hörnfeldt, B. & Lundman, B. (1998). Could myocarditis, insulin-dependent diabetes mellitus, and Guillain-Barré syndrome be caused by one or more infectious agents carried by rodents? Emerg Infect Dis 4, 187-193.
30. Niklasson, B., Kinnunen, L., Hörnfeldt, B., Hörling, J., Benemar, C., Hedlund, K. O., Matskova, L., Hyypiä, T. & Winberg, G. (1999). A new picornavirus isolated from bank voles (Clethrionomys glareolus). Virology 255, 86-93.
31. Page, R. D. M. (1996). TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357-358.
32. Palmenberg, A. C., Parks, G. D., Hall, D. J., Ingraham, R. H., Seng, T. W. & Pallai, P. V. (1992). Proteolytic processing of the cardioviral P2 region: primary 2A/2B cleavage in clone-derived precursors. Virology 190, 754-762.
33. Pevear, D. C., Borkowski, J., Calenoff, M., Oh, C. K., Ostrowski, B. & Lipton, H. L. (1988). Insights into Theiler's virus neurovirulence based on a genomic comparison of the neurovirulent GDVII and less virulent BeAn strains. Virology 165, 1-12.
34. Pöyry, T., Kinnunen, L., Hyypiä, T., Brown, B., Horsnell, C., Hovi, T. & Stanway, G. (1996). Genetic and phylogenetic clustering of enteroviruses. J Gen Virol 77, 1699-1717.
35. Pringle, C. R. (1999). Virus taxonomy at the XIth International Congress of Virology, Sydney, Australia, 1999. Arch Virol 144, 2065-2070.
36. Pringle, F. M., Gordon, K. H., Hanzlik, T. N., Kalmakoff, J., Scotti, P. D. & Ward, V. K. (1999). A novel capsid expression strategy for Thosea asigna virus (Tetraviridae). J Gen Virol 80, 1855-1863.
37. Racaniello, V. R. (2001). Picornaviridae: The viruses and their replication. In Fields Virology, 4th edn, pp. 685-722. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Matrin, B. Riozman & S. E. Straus. Philadelphia: Lippincott Williams & Wilkins.
38. Strimmer, K. & von Haeseler, A. (1996). Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13, 964-969.
39. Strimmer, K. & von Haeseler, A. (1997). Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 94, 6815-6819.
40. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
41. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTALwindows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
42. Whitney, E., Roz, A. P. & Rayner, G. A. (1970). Two viruses isolated from rodents (Clethrionomys gapperi and Microtus pennsylvanicus) trapped in St. Lawrence county, New York. J Wildl Dis 6, 48-55.
43. Wilson, J. E., Powell, M. J., Hoover, S. E. & Sarnow, P. (2000). Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20, 4990-4999.
44. Wu, C.-Y., Lo, C.-F., Huang, C.-J., Yu, H.-T. & Wang, C.-H. (2002). The complete genome sequence of Perina nuda picorna-like virus, an insect-infecting RNA virus with a genome organization similar to that of mammalian picornaviruses. Virology 294, 312-323.
45. Wutz, G., Auer, H., Nowotny, N., Grosse, B., Skern, T. & Kuechler, E. (1996). Equine rhinovirus serotypes 1 and 2: relationship to each other and to aphthoviruses and cardioviruses. J Gen Virol 77, 1719-1730.
46. Xia, X. (2000). DAMBE: data analysis in molecular biology and evolution, 4.0.30 edn. Department of Ecology and Biodiversity, University of Hong Kong, Hong Kong, Japan.
47. Yamashita, T., Sakae, K., Tsuzuki, H., Suzuki, Y., Ishikawa, N., Takeda, N., Miyamura, T. & Yamazaki, S. (1998). Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans. J Virol 72, 8408-8412.
48. Zell, R., Dauber, M., Krumbholz, A., Henke, A., Birch-Hirschfeld, E., Stelzner, A., Prager, D. & Wurm, R. (2001). Porcine teschoviruses comprise at least eleven distinct serotypes: molecular and evolutionary aspects. J Virol 75, 1620-1631.
49. Zuker, M., Mathews, D. H. & Turner, D. H. (1999). Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology, pp. 11-43. Edited by J. Barciszewski & B. F. C. Clark. Dordrecht: Kluwer.