A phylogenomic study of the genus Alphavirus employing whole genome comparison

Comparative and Functional Genomics

Volumn 6, Issue 4, 2005, Pages 217-227

  Luers, Aimée J ^a   Adams, Sandra D ^a   Smalley, John V ^b   Campanella, James J ^a  

^a MONTCLAIR STATE UNIVERSITY   (United States)

^b Bergen Community College   (United States)

Author keywords

Alphavirus; Phylogenetics; Phylogenomics; Semliki Forest Virus; Sindbis Virus; Togaviridae

Indexed keywords

COMPLEMENTARY DNA; VIRUS DNA;

ALPHA VIRUS; AMINO ACID SEQUENCE; ARTICLE; BARMAH FOREST VIRUS; CLADISTICS; COMPARATIVE STUDY; CORRELATION ANALYSIS; DNA SEQUENCE; GENETIC ANALYSIS; MIDDELBURG ALPHAVIRUS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; RUBELLA VIRUS; SALMON PANCREATIC DISEASE VIRUS; SEMLIKI FOREST ALPHAVIRUS; SEQUENCE ALIGNMENT; SLEEPING DISEASE VIRUS; SOUTHERN ELEPHANT SEAL VIRUS; STRAIN DIFFERENCE; VIRUS CAPSID; VIRUS GENOME; VIRUS STRAIN; WESTERN EQUINE ENCEPHALOMYELITIS ALPHAVIRUS;

EID: 20444391307     PISSN: 15316912     EISSN: None     Source Type: Journal    
DOI: 10.1002/cfg.478     Document Type: Article

References (28)

1. Boucher P, Castric J, Laurencin F. 1994. Observation of virus-like particles in rainbow-trout Onchornychus mykiss infected with sleeping disease virulent material. Bull Eur Assoc Fish Pathol 14: 215-216.
2. Boucher P, Laurencin F. 1996. Sleeping disease and pancreas disease: comparative histopathology and acquired cross-protection. J Fish Dis 19: 303-310.
3. Calisher C, Monath T, Muth D, et al. 1980. Characterization of Fort Morgan Virus, an alphavirus of the Western Equine Encephalitis Virus Complex in an unusual ecosystem. Am J Trop Med Hyg 29: 1428-1440.
4. Calisher C, Karabatsos N. 1988. Arbovirus Serogroups: Definition and Geographic Distribution. CRC Press: Boca Raton, FL.
5. Calisher CH, Karabatsos N, Lazuick J, Monath T, Wolff K. 1988. Reevaluation of the Western Equine Encephalitis antigenic complex of alphaviruses (Family Togaviridae) as determined by neutralization tests. Am J Trop Med Hyg 38: 447-452.
6. Campanella J, Bitincka L, Smalley J. 2003. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformat 4: 29.
7. Chen X, Kwong S, Li M. 2000. A compression algorithm for DNA sequences based on approximate matching. Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB), Tokyo, Japan; 107-118.
8. Christie K, Fryand K, Holtet L, Rowley H. 1998. Isolation of pancreas disease virus from farmed Atlantic salmon, Salmo salar L., in Norway. J Fish Dis 21: 391-394.
9. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
10. Felsenstein J. 1989. PHYLIP phylogeny inference package. Cladistics 5: 164-166.
11. Frey TK. 1994. Molecular biology of rubella virus. Adv Virus Res 44: 69-160.
12. Frolov I, Hoffman T, Pragai B, et al. 1996. Alphavirus-based expression vectors: strategies and applications. Proc Natl Acad Sci USA 93: 11 371-11 377.
13. Hahn C, Strauss E, Strauss J. 1988. Western equine encephalitis virus is a recombinant virus. Proc Natl Acad Sci USA 85: 5997-6001.
14. Levinson R, Strauss J, Strauss E. 1990. Determination of the complete nucleotide sequence of the genomic RNA of O'Nyong Nyong Virus and its use in the construction of phylogenetic trees. Virology 175: 110-123.
15. National Center for Biotechnology Information. 2004. www.ncbi.nlm.nih.gov
16. National Center for Biotechnology Information (BLAST). 2004. www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
17. Page RD. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
18. Powers A, Brault A, Shirako Y, et al. 2001. Evolutionary relationships and systematics of alphaviruses. J Virol 75: 10118-10131.
19. Saitou N, Nei M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
20. Schlesinger S, Dubensky T. 1999. Alphavirus vectors for gene expression and vaccines. Curr Opin Biotechnol 10: 434-439.
21. Strauss J, Strauss E. 1994. The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 58: 491-562.
22. Strauss J, Strauss E. 1997. Recombination in alphaviruses. Semin Virol 8: 85-94.
23. Thompson JD, Gibson TJ, Plewniak F, et al. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4872-4882.
24. Villoing S, Béarzotti M, Chilmonczyk S, Castric J, Brémont B. 2000. Rainbow Trout Sleeping Disease Virus is an atypical alphavirus. J Virol 74: 173-183.
25. Weaver S, Hagenbaugh A, Bellew L, et al. 1993. A comparison of the nucleotide sequences of Eastern and Western Equine Encephalomyelitis Viruses with those of other alphaviruses and related RNA viruses. Virology 197: 375-390.
26. Weaver S, Hagenbaugh A, Bellew L, et al. 1994. Evolution of alphaviruses in the Eastern Equine Encephalomyelitis complex. J Virol 68: 158-169.
27. Weaver S, Wenli K, Shirako Y, et al. 1997. Recombinational history and molecular evolution of Western Equine Encephalomyelitis complex alphaviruses. J Virol 71: 613-623.
28. Weston J, Villoing S, Brémont M, et al. 2002. Comparison of two aquatic alphaviruses, Salmon Pancreas Disease Virus and Sleeping Disease Virus, by using genome sequence analysis, monoclonal reactivity, and cross-infection. J Virol 76: 6155-6163.