Recombination in West Nile Virus: Minimal contribution to genomic diversity

Virology Journal

Volumn 6, Issue , 2009, Pages

  Pickett, Brett E ^a   Lefkowitz, Elliot J ^a  

^a University of Alabama at Birmingham   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; NONSTRUCTURAL PROTEIN 5; NS5 PROTEIN, FLAVIVIRUS; VIRUS PROTEIN;

ALGORITHM; ARTICLE; GENE SEQUENCE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ANALYSIS; TAXONOMY; VIRUS GENOME; VIRUS ISOLATION; VIRUS RECOMBINATION; WEST NILE FLAVIVIRUS; AFRICA; BIOLOGY; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETICS; SEQUENCE HOMOLOGY;

WEST NILE VIRUS;

AFRICA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENOME, VIRAL; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VIRAL NONSTRUCTURAL PROTEINS; WEST NILE VIRUS;

EID: 70350344982     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-6-165     Document Type: Article

References (39)

1. Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains. EM Botha W Markotter M Wolfaardt JT Paweska R Swanepoel G Palacios LH Nel M Venter, Emerg Infect Dis 2008 14 222 230 10.3201/eid1401.070457 18258114
2. In vitro resistance selection and in vivo efficacy of morpholino oligomers against West Nile virus. TS Deas CJ Bennett SA Jones M Tilgner P Ren MJ Behr DA Stein PL Iversen LD Kramer KA Bernard PY Shi, Antimicrob Agents Chemother 2007 51 2470 2482 10.1128/AAC.00069-07 17485503
3. Mosquitoes put the brake on arbovirus evolution: experimental evolution reveals slower mutation accumulation in mosquito than vertebrate cells. N Vasilakis ER Deardorff JL Kenney SL Rossi KA Hanley SC Weaver, PLoS Pathog 2009 5 1000467 10.1371/journal.ppat.1000467 e19503824
4. Complete genome analysis and virulence characteristics of the Louisiana West Nile virus strain LSU-AR01. AV Iyer MJ Boudreaux N Wakamatsu AF Roy A Baghian VN Chouljenko KG Kousoulas, Virus Genes 2009 38 204 214 10.1007/s11262-008-0321-2 19130199
5. Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient. J Aaskov K Buzacott E Field K Lowry A Berlioz-Arthaud EC Holmes, J Gen Virol 2007 88 3334 3340 10.1099/vir.0.83122-0 18024903
6. Widespread intra-serotype recombination in natural populations of dengue virus. M Worobey A Rambaut EC Holmes, Proc Natl Acad Sci USA 1999 96 7352 7357 10.1073/pnas.96.13.7352 10377418
7. Evidence of recombination in intrapatient populations of hepatitis C virus. V Sentandreu N Jimenez-Hernandez M Torres-Puente MA Bracho A Valero MJ Gosalbes E Ortega A Moya F Gonzalez-Candelas, PLoS ONE 2008 3 3239 10.1371/journal.pone.0003239 18800167
8. Phylogenetic evidence for recombination in dengue virus. EC Holmes M Worobey A Rambaut, Mol Biol Evol 1999 16 405 409 10331266
9. Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China. SP Chen M Yu T Jiang YQ Deng CF Qin JF Han ED Qin, Arch Virol 2008 153 1175 1179 10.1007/s00705-008-0090-1 18446424
10. The extent of homologous recombination in members of the genus Flavivirus. SS Twiddy EC Holmes, J Gen Virol 2003 84 429 440 10.1099/vir.0.18660-0 12560576
11. Evolutionary aspects of recombination in RNA viruses. M Worobey EC Holmes, J Gen Virol 1999 80 Pt 10 2535 2543 10573145
12. On the nature of poliovirus genetic recombinants. PD Cooper A Steiner-Pryor PD Scotti D Delong, J Gen Virol 1974 23 41 49 10.1099/0022-1317- 23-1-41 4364875
13. Purification, characterization, and comparison of poliovirus RNA polymerase from native and recombinant sources. KL Neufeld OC Richards E Ehrenfeld, J Biol Chem 1991 266 24212 24219 1660894
14. Packaging, replication and recombination of the segmented genome of bacteriophage Phi6 and its relatives. L Mindich, Virus Res 2004 101 83 92 10.1016/j.virusres.2003.12.008 15010219
15. Evolution of alphaviruses in the eastern equine encephalomyelitis complex. SC Weaver A Hagenbaugh LA Bellew L Gousset V Mallampalli JJ Holland TW Scott, J Virol 1994 68 158 169 8254725
16. Mouse neuroinvasive phenotype of West Nile virus strains varies depending upon virus genotype. DW Beasley L Li MT Suderman AD Barrett, Virology 2002 296 17 23 10.1006/viro.2002.1372 12036314
17. Gene expression in mice infected with West Nile virus strains of different neurovirulence. M Venter TG Myers MA Wilson TJ Kindt JT Paweska FJ Burt PA Leman R Swanepoel, Virology 2005 342 119 140 10.1016/j.virol.2005.07.013 16125213
18. Lineage 1 and 2 strains of encephalitic West Nile virus, central Europe. T Bakonyi E Ivanics K Erdelyi K Ursu E Ferenczi H Weissenbock N Nowotny, Emerg Infect Dis 2006 12 618 623 16704810
19. Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. H Malet MP Egloff B Selisko RE Butcher PJ Wright M Roberts A Gruez G Sulzenbacher C Vonrhein G Bricogne, et al. J Biol Chem 2007 282 10678 10689 10.1074/jbc.M607273200 17287213 (Pubitemid 47093413)
20. Discrepancy of hepatitis C virus genotypes as determined by phylogenetic analysis of partial NS5 and core sequences. Z Yun C Lara B Johansson I Lorenzana de Rivera A Sonnerborg, J Med Virol 1996 49 155 160 10.1002/(SICI)1096- 9071(199607)49:3<155::AID-JMV1>3.0.CO;2-3 8818959
21. Evidence of recombination in quasispecies populations of a Hepatitis C Virus patient undergoing anti-viral therapy. MP Moreno D Casane L Lopez J Cristina, Virol J 2006 3 87 10.1186/1743-422X-3-87 17062150
22. Phylogeny of the genus Flavivirus. G Kuno GJ Chang KR Tsuchiya N Karabatsos CB Cropp, J Virol 1998 72 73 83 9420202
23. Evolutionary influences in arboviral disease. SC Weaver, Curr Top Microbiol Immunol 2006 299 285 314 full-text 16568903
24. Evolutionary relationship between Old World West Nile virus strains. RN Charrel AC Brault P Gallian JJ Lemasson B Murgue S Murri B Pastorino H Zeller R de Chesse P de Micco X de Lamballerie, Virology 2003 315 381 388 10.1016/S0042-6822(03)00536-1 14585341
25. West Nile virus neuroinvasive disease. LE Davis R DeBiasi DE Goade KY Haaland JA Harrington JB Harnar SA Pergam MK King BK DeMasters KL Tyler, Ann Neurol 2006 60 286 300 10.1002/ana.20959 16983682
26. West Nile virus in the vertebrate world. KM van der Meulen MB Pensaert HJ Nauwynck, Arch Virol 2005 150 637 657 10.1007/s00705-004-0463-z 15662484
27. Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. B Selisko H Dutartre JC Guillemot C Debarnot D Benarroch A Khromykh P Despres MP Egloff B Canard, Virology 2006 351 145 158 10.1016/j.virol.2006.03.026 16631221
28. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
29. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383
30. RDP 2: recombination detection and analysis from sequence alignments. DP Martin C Williamson D Posada, Bioinformatics 2005 21 260 262 10.1093/bioinformatics/bth490 15377507
31. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. D Posada KA Crandall, Proc Natl Acad Sci USA 2001 98 13757 13762 10.1073/pnas.241370698 11717435
32. RDP: detection of recombination amongst aligned sequences. D Martin E Rybicki, Bioinformatics 2000 16 562 563 10.1093/bioinformatics/16.6.562 10980155
33. Analyzing the mosaic structure of genes. JM Smith, J Mol Evol 1992 34 126 129 1556748
34. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. MJ Gibbs JS Armstrong AJ Gibbs, Bioinformatics 2000 16 573 582 10.1093/bioinformatics/16.7.573 11038328
35. An exact nonparametric method for inferring mosaic structure in sequence triplets. MF Boni D Posada MW Feldman, Genetics 2007 176 1035 1047 10.1534/genetics.106.068874 17409078
36. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. GF Weiller, Mol Biol Evol 1998 15 326 335 9501499
37. Possible emergence of new geminiviruses by frequent recombination. M Padidam S Sawyer CM Fauquet, Virology 1999 265 218 225 10.1006/viro.1999.0056 10600594
38. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. DP Martin D Posada KA Crandall C Williamson, AIDS Res Hum Retroviruses 2005 21 98 102 10.1089/aid.2005.21.98 15665649
39. Application of phylogenetic networks in evolutionary studies. DH Huson D Bryant, Mol Biol Evol 2006 23 254 267 10.1093/molbev/msj030 16221896