Phylogenetic and evolutionary analyses of St. Louis encephalitis virus genomes

Molecular Phylogenetics and Evolution

Volumn 47, Issue 2, 2008, Pages 717-728

  Baillie, Gregory J ^a   Kolokotronis, Sergios Orestis ^a   Waltari, Eric ^a   Maffei, Joseph G ^b   Kramer, Laura D ^b   Perkins, Susan L ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b WADSWORTH CENTER   (United States)

Author keywords

Divergence times; Flavivirus; N linked glycosylation; Phylogeny; Positive selection; Recombination; St. Louis encephalitis virus

Indexed keywords

VIRUS ENVELOPE PROTEIN;

ARTICLE; BAYES THEOREM; DNA SEQUENCE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GLYCOSYLATION; METABOLISM; MOLECULAR EVOLUTION; OPEN READING FRAME; PHYLOGENY; ST LOUIS FLAVIVIRUS; STATISTICAL MODEL; TIME; VIRUS GENOME;

BAYES THEOREM; ENCEPHALITIS VIRUS, ST. LOUIS; EVOLUTION, MOLECULAR; GENOME, VIRAL; GLYCOSYLATION; LIKELIHOOD FUNCTIONS; OPEN READING FRAMES; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; TIME FACTORS; VARIATION (GENETICS); VIRAL ENVELOPE PROTEINS;

FLAVIVIRIDAE; FLAVIVIRUS; JAPANESE ENCEPHALITIS VIRUS; ST. LOUIS ENCEPHALITIS VIRUS;

EID: 42749095856     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.02.015     Document Type: Article

References (60)

1. Adams S.C., Broom A.K., Sammels L.M., Hartnett A.C., Howard M.J., Coelen R.J., Mackenzie J.S., and Hall R.A. Glycosylation and antigenic variation among Kunjin virus isolates. Virology 206 (1995) 49-56
2. Altekar G., Dwarkadas S., Huelsenbeck J., and Ronquist F. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20 (2004) 407-415
3. Beasley D., Whiteman M., Zhang S., Huang C., Schneider B., Smith D., Gromowski G., Higgs S., Kinney R., and Barrett A. Envelope protein glycosylation status influences mouse neuroinvasion phenotype of genetic lineage 1 West Nile virus strains. J. Virol. 79 (2005) 8339-8347
4. Billoir F., de Chesse R., Tolou H., de Micco P., Gould E., and de Lamballerie X. Phylogeny of the genus flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector. J. Gen. Virol. 81 (2000) 781-790
5. Bowen G., Monath T., Kemp G., Kerschner J., and Kirk L. Geographic variation among St. Louis encephalitis virus strains in the viremic responses of avian hosts. Am. J. Trop. Med. Hyg. 29 (1980) 1411-1419
6. Brault A.C., Huang C.Y., Langevin S.A., Kinney R.M., Bowen R.A., Ramey W.N., Panella N.A., Holmes E.C., Powers A.M., and Miller B.R. A single positively selected West Nile viral mutation confers increased virogenesis in American crows. Nat. genet. 39 (2007) 1162-1166
7. Bryant J.E., Holmes E.C., and Barrett A.D. Out of Africa: a molecular perspective on the introduction of yellow fever virus into the Americas. PLoS Pathog. 3 (2007) e75
8. Chambers T., Hahn C., Galler R., and Rice C. Flavivirus genome organization, expression, and replication. Annu. Rev. Microbiol. 44 (1990) 649-688
9. Chambers T., Halevy M., Nestorowicz A., Rice C., and Lustig S. West Nile virus envelope proteins: nucleotide sequence analysis of strains differing in mouse neuroinvasiveness. J. Gen. Virol. 79 (1998) 2375-2380
10. Day J. Predicting St. Louis encephalitis virus epidemics: lessons from recent, and not so recent, outbreaks. Annu. Rev. Entomol. 46 (2001) 111-138
11. Don R.H., Cox P.T., Wainwright B.J., Baker K., and Mattick J.S. 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 19 (1991) 4008
12. Drummond, A., Rambaut, A., 2006. BEAST. University of Oxford, Oxford, UK. Available from: .
13. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
14. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
15. Halevy M., Akov Y., Ben-Nathan D., Kobiler D., Lachmi B., and Lustig S. Loss of active neuroinvasiveness in attenuated strains of West Nile virus: pathogenicity in immunocompetent and SCID mice. Arch. Virol. 137 (1994) 355-370
16. Hanada K., Suzuki Y., and Gojobori T. A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol. Biol. Evol. 21 (2004) 1074-1080
17. Hanna S., Pierson T., Sanchez M., Ahmed A., Murtadha M., and Doms R. N-linked glycosylation of west nile virus envelope proteins influences particle assembly and infectivity. J. Virol. 79 (2005) 13262-13274
18. Holmes E. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J. Virol. 77 (2003) 11296-11298
19. Jenkins G.M., Rambaut A., Pybus O.G., and Holmes E.C. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54 (2002) 156-165
20. Jones J., Krag S., and Betenbaugh M. Controlling N-linked glycan site occupancy. Biochim. Biophys. Acta 1726 (2005) 121-137
21. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
22. Kishino H., and Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29 (1989) 170-179
23. Kosakovsky-Pond S.L., and Frost S.D. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21 (2005) 2531-2533
24. Kosakovsky-Pond S.L., and Frost S.D. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22 (2005) 1208-1222
25. Kosakovsky-Pond S.L., Frost S.D., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
26. Kosakovsky-Pond S.L., Posada D., Gravenor M.B., Woelk C.H., and Frost S.D. GARD: a genetic algorithm for recombination detection. Bioinformatics 22 (2006) 3096-3098
27. Kramer L., and Chandler L. Phylogenetic analysis of the envelope gene of St. Louis encephalitis virus. Arch. Virol. 146 (2001) 2341-2355
28. Kuno G., and Chang G. Biological transmission of arboviruses: reexamination of and new insights into components, mechanisms, and unique traits as well as their evolutionary trends. Clin. Microbiol. Rev. 18 (2005) 608-637
29. Lanave C., Preparata G., Saccone C., and Serio G. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20 (1984) 86-93
30. Lee E., Weir R.C., and Dalgarno L. Changes in the dengue virus major envelope protein on passaging and their localization on the three-dimensional structure of the protein. Virology 232 (1997) 281-290
31. Li J., Bhuvanakantham R., Howe J., and Ng M. The glycosylation site in the envelope protein of West Nile virus (Sarafend) plays an important role in replication and maturation processes. J. Gen. Virol. 87 (2006) 613-622
32. Lindenbach B., and Rice C. Flaviviridae: the viruses and their replication. In: Knipe D., and Howley P. (Eds). Fields Virology (2001), Lippincott-Raven Publishers, Philadelphia 991-1041
33. Lorenz I.C., Kartenbeck J., Mezzacasa A., Allison S.L., Heinz F.X., and Helenius A. Intracellular assembly and secretion of recombinant subviral particles from tick-borne encephalitis virus. J. Virol. 77 (2003) 4370-4382
34. Martin D., and Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16 (2000) 562-563
35. Martin D., Williamson C., and Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21 (2005) 260-262
36. Martin D.P., Posada D., Crandall K.A., and Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retroviruses 21 (2005) 98-102
37. Monath T., Cropp C., Bowen G., Kemp G., Mitchell C., and Gardner J. Variation in virulence for mice and rhesus monkeys among St. Louis encephalitis virus strains of different origin. Am. J. Trop. Med. Hyg. 29 (1980) 948-962
38. Newton M.A., and Raftery A.E. Approximate Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. Ser. B 56 (1994) 3-48
39. Padidam M., Sawyer S., and Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 265 (1999) 218-225
40. Posada D. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol. Biol. Evol. 19 (2002) 708-717
41. Posada D., and Crandall K. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
42. Posada D., and Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 98 (2001) 13757-13762
43. Posada D., Crandall K.A., and Holmes E.C. Recombination in evolutionary genomics. Annu. Rev. Genet. 36 (2002) 75-97
44. Rambaut A., and Drummond A. Tracer v1.3 (2005), University of Oxford, Oxford, UK
45. Reisen W. Epidemiology of St. Louis encephalitis virus. Adv. Virus Res. 61 (2003) 139-183
46. Rodriguez F., Oliver J.L., Marin A., and Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485-501
47. Ronquist F., and Huelsenbeck J. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
48. Scherret J., Mackenzie J., Khromykh A., and Hall R. Biological significance of glycosylation of the envelope protein of Kunjin virus. Ann. NY Acad. Sci. 951 (2001) 361-363
49. Shirato K., Miyoshi H., Goto A., Ako Y., Ueki T., Kariwa H., and Takashima I. Viral envelope protein glycosylation is a molecular determinant of the neuroinvasiveness of the New York strain of West Nile virus. J. Gen. Virol. 85 (2004) 3637-3645
50. Smith J.M. Analyzing the mosaic structure of genes. J. Mol. Evol. 34 (1992) 126-129
51. Suchard M.A., Weiss R.E., and Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18 (2001) 1001-1013
52. * and Other Methods) (2003), Sinauer Associates, Sunderland, MA
53. Trent D., Kinney R., Johnson B., Vorndam A., Grant J., Deubel V., Rice C., and Hahn C. Partial nucleotide sequence of St. Louis encephalitis virus RNA: structural proteins, NS1, ns2a, and ns2b. Virology 156 (1987) 293-304
54. Trent D., Monath T., Bowen G., Vorndam A., Cropp C., and Kemp G. Variation among strains of St. Louis encephalitis virus: basis for a genetic, pathogenetic, and epidemiologic classification. Ann. NY Acad. Sci. 354 (1980) 219-237
55. Twiddy S., and Holmes E. The extent of homologous recombination in members of the genus Flavivirus. J. Gen. Virol. 84 (2003) 429-440
56. Twiddy S., Woelk C., and Holmes E. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J. Gen. Virol. 83 (2002) 1679-1689
57. Vigerust D.J., and Shepherd V.L. Virus glycosylation: role in virulence and immune interactions. Trends Microbiol. 15 (2007) 211-218
58. Vorndam V., Mathews J., Barrett A., Roehrig J., and Trent D. Molecular and biological characterization of a non-glycosylated isolate of St. Louis encephalitis virus. J. Gen. Virol. 74 (1993) 2653-2660
59. Woelk C., and Holmes E. Reduced positive selection in vector-borne RNA viruses. Mol. Biol. Evol. 19 (2002) 2333-2336
60. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-314