Rapid fixation of a distinctive sequence motif in the 3′ noncoding region of the clade of West Nile virus invading North America

Gene

Volumn 399, Issue 2, 2007, Pages 152-161

  Hughes, Austin L ^a   Piontkivska, Helen ^b   Foppa, Ivo ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

^b KENT STATE UNIVERSITY   (United States)

Author keywords

Evolution of virulence; Flavivirus; Natural selection; RNA helicase; West Nile virus

Indexed keywords

NONSTRUCTURAL PROTEIN 3; RNA HELICASE; VIRUS PROTEIN; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; FLAVIVIRUS; GENETIC POLYMORPHISM; HUNGARY; ISRAEL; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN MOTIF; RNA STRUCTURE; UNINDEXED SEQUENCE; UNITED STATES; VIRUS GENOME; VIRUS ISOLATION; VIRUS VIRULENCE; WEST NILE FLAVIVIRUS;

3' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; NORTH AMERICA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, VIRAL; SELECTION (GENETICS); VARIATION (GENETICS); WEST NILE VIRUS;

FLAVIVIRUS; WEST NILE VIRUS;

EID: 34547693225     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2007.05.007     Document Type: Article

References (49)

1. Bakonyi T., Ivanics E., Erdélyi K., Ursu K., Ferenczi E., Weissenböck H., and Nowotny N. Lineage 1 and 2 strains of encephalitic West Nile virus, Central Europe. Emerg. Infect. Dis. 12 (2006) 618-623
2. Bertolotti L., Kitron U., and Goldberg T.L. Diversity and evolution of West Nile virus in Illinois and the United States, 2002-2005. Virology 360 (2006) 143-149
3. Brault A.C., Langevin S.A., Bowen R.A., Panella N.A., Biggerstaff B.J., Miller B.R., and Nicholas K. Differential virulence of West Nile strains for American Crows. Emerg. Infect. Dis. 10 (2004) 2161-2168
4. Brinton M.A. The molecular biology of West Nile virus: a new invader of the Western Hemisphere. Annu. Rev. Microbiol. 56 (2002) 371-402
5. Chen C.J., Kuo M.D., Chen L.J., Hsu S.L., Wang Y.M., and Lin J.H. RNA-protein interactions: involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA. J. Virol. 71 (1997) 3466-3473
6. Davis C.T., Beasley D.W., Guzman H., Raj P., D'Anton M., Novak R.J., Unnasch T.R., Tesh R.B., and Barrett A.D. Genetic variation among temporally and geographically distinct West Nile virus isolates, United States, 2001, 2002. Emerg. Infect. Dis. 9 (2003) 1423-1429
7. Davis C.T., Beasley D.W., Guzman H., Siirin M., Parsons R.E., Tesh R.B., and Barrett A.D. Emergence of attenuated West Nile virus variants in Texas, 2003. Virology 330 (2004) 342-350
8. Davis C.T., Ebel G.D., Lanciotti R.S., Brault A.C., Guzman H., Siirin M., Lambert A., Parsons R.E., Beasley D.W., Novak R.J., Elizondo-Quiroga D., Green E.N., Young D.S., Stark L.M., Drebot M.A., Artsob H., Tesh R.B., Kramer L.D., and Barrett A.D. Phylogenetic analysis of North American West Nile virus isolates, 2001-2004: evidence for the emergence of a dominant genotype. Virology 342 (2005) 252-265
9. Ebel G.D., Carricaburu J., Young D., Bernard K.A., and Kramer L.D. Genetic and phenotypic variation of West Nile Virus in New York, 2000-2003. Am. J. Trop. Med. Hyg. 71 (2004) 493-500
10. Eyre-Walker A. Changing effective population size and the McDonald-Kreitman test. Genetics 162 (2002) 2017-2024
11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
12. Gritsun T.S., and Gould E.A. Direct repeats in the 3′ untranslated regions of mosquito-borne flaviviruses: possible implications for virus transmission. J. Gen. Virol. 87 (2006) 3297-3305
13. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
14. Hughes A.L. MHC polymorphism and the design of captive breeding programs. Conserv. Biol. 5 (1991) 249-251
15. Hughes A.L. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169 (2005) 533-538
16. Hughes A.L. Micro-scale signature of purifying selection in Marburg virus genomes. Gene 392 (2007) 266-272
17. Hughes A.L., and Hughes M.A. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol. Ecol. 16 (2007) 1369-1376
18. Hughes A.L., and Nei M. Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection. Nature 335 (1988) 167-170
19. Hughes A.L., Packer B., Welch R., Bergen A.W., Chanock S.J., and Yeager M. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15754-15757
20. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
22. Kinney R.M., Huang C.Y.H., Whiteman M.C., Bowen R.A., Langevin S.A., Miller B.R., and Brault A.C. Avian virulence and thermostable replication of the North American strain of West Nile virus. J. Gen. Virol. 87 (2006) 3611-3622
23. Komar N., and Clark G.G. West Nile virus activity in Latin America and the Caribbean. Rev. Panam. Salud Publica 19 (2006) 112-117
24. Komar N., Langevin S., Hinten S., Nemeth N., Edwards E., Hettler D., Davis B., Bowen R., and Bunning M. Experimental infection of North American birds with the New York 1999 strain of West Nile virus. Emerg. Infect. Dis. 9 (2003) 311-322
25. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinf. 5 (2004) 150-163
26. Lanciotti R.S. Origin of the West Nile virus responsible for an outbreak of encephalitis in the Northeastern United States. Science 286 (1999) 2333-2337
27. Lanciotti R.S., Ebel G.D., Deubel V., Kerst A.J., Murri S., Meyer R., Bowen M., McKinney N., Morrill W.E., Crabtree M.B., Kramer L.D., and Roehrig J.T. Complete genome sequences and phylogenetic analysis of West Nile virus strains isolated from the United States, Europe, and the Middle East. Virology 298 (2002) 96-105
28. Lockhart P.J., Steel M.A., Hendy M.D., and Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11 (1994) 605-612
29. McClean R. West Nile virus in North American birds. Ornithol. Monogr. 60 (2006) 44-64
30. Markoff L. 5′- and 3′-noncoding regions in flavivirus RNA. Adv. Virus Res. 59 (2003) 177-228
31. Matthews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
32. McDonald J.H., and Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351 (1991) 114-116
33. Nash D., Mostashari F., Fine A., Miller J., O'Leary D., Murray K., Huang A., Rosenberg A., Greenberg A., Sherman M., Wong S., and Layton M. The outbreak of West Nile virus infection in the New York City area in 1999. New Engl. J. Med. 344 (2001) 1807-1814
34. Nei M., and Kumar S. Molecular Evolution and Phylogenetics (2000), Oxford University Press, New York
35. Ohta T. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 4548-4551
36. Proutski V., Gaunt M.W., Gould E.A., and Holmes E.C. Secondary structure of the 3′-untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development. J. Gen. Virol. 78 (1997) 1543-1549
37. Rodriguez F., Oliver J.F., Marí A., and Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485-501
38. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
39. Scherret J.H., Poidinger M., MacKenzie J.S., Broom A.K., Deubel V., Lipkin W.I., Briese T., Gould E.A., and Hall R.A. The relationships between West Nile and Kunjin viruses. Emerg. Infect. Dis. 7 (2001) 697-705
40. Smithburn K.C., Hughes T.P., Burke A.W., and Paul J.H. A neurotropic virus isolated from the blood of a native Ugandan. Am. J. Trop. Med. 20 (1940) 471-492
41. Strimmer K., and von Haeseler A. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13 (1996) 964-969
42. *and other methods) (1999), Sinauer, Sunderland MA
43. Tajima S., Nukui Y., Ito M., Takasaki T., and Kurane I. Nineteen nucleotides in the variable region of 3′ non-translated region are dispensible for the replication of dengue type 1 virus in vitro. Virus Res. 116 (2006) 38-44
44. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Diggins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
45. Wicker J.A., Whiteman M.C., Beasley D.W.C., Davis C.T., Zhang S., Schneider B.S., Higgs S., Kinney R.M., and Barrett A.D.T. A single amino acid substitution in the central portion of the West Nile virus NS4B protein confers a highly attenuated phenotype in mice. Virology 349 (2006) 245-253
46. Wu J., Bera A.K., Kuhn R.J., and Smith J.L. Structure of the flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. J. Virol. 79 (2005) 10268-10277
47. Yaremych S.A., Warner R.E., Mankin P.C., Brawn J.D., Raim A., and Novak R. West Nile virus and high death rate in American crows. Emerg. Infect. Dis. 10 (2004) 709-711
48. Yu L., and Markoff L. The topology of bulges in the long stem of the flavivirus 3′ stem-loop is a major determinant of RNA replication competence. J. Virol. 79 (2005) 2309-2324
49. Zhang J., Rosenberg H.F., and Nei M. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 3708-3713