Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

Archives of Virology

Volumn 157, Issue 1, 2012, Pages 75-83

  Carney, Jennifer ^a   Daly, Janet M ^a,c   Nisalak, Ananda ^b   Solomon, Tom ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN;

ANIMAL; ANIMAL DISEASE; ARTICLE; CLASSIFICATION; GENETIC RECOMBINATION; GENETIC SELECTION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; JAPANESE ENCEPHALITIS; JAPANESE ENCEPHALITIS VIRUS; MOLECULAR GENETICS; MOSQUITO; PHYLOGENY; SWINE; SWINE DISEASE; THAILAND; VIROLOGY; VIRUS GENOME;

ANIMALS; CULICIDAE; ENCEPHALITIS VIRUS, JAPANESE; ENCEPHALITIS, JAPANESE; GENOME, VIRAL; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION, GENETIC; SWINE; SWINE DISEASES; THAILAND; VIRAL NONSTRUCTURAL PROTEINS;

JAPANESE ENCEPHALITIS VIRUS; SUIDAE;

EID: 84855308971     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-011-1143-4     Document Type: Article

References (37)

1. Aaskov J, Buzacott K, Field E, Lowry K, Berlioz-Arthaud A, Holmes EC (2007) Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient. J Gen Virol 88: 3334-3340.
2. Chambers TJ, Hahn CS, Galler R, Rice CM (1990) Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 44: 649-688.
3. Chen SP, Yu M, Jiang T, Deng YQ, Qin CF, Han JF, Qin ED (2008) Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China. Arch Virol 153: 1175-1179.
4. Chen WR, Rico-Hesse R, Tesh RB (1992) A new genotype of Japanese encephalitis virus from Indonesia. Am J Trop Med Hyg 47: 61-69.
5. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
6. Chuang CK, Chen WJ (2009) Experimental evidence that RNA recombination occurs in the Japanese encephalitis virus. Virology 394: 286-297.
7. Chung KM, Liszewski MK, Nybakken G, Davis AE, Townsend RR, Fremont DH, Atkinson JP, Diamond MS (2006) West Nile virus nonstructural protein NS1 inhibits complement activation by binding the regulatory protein factor H. Proc Natl Acad Sci USA 103: 19111-19116.
8. Chung KM, Thompson BS, Fremont DH, Diamond MS (2007) Antibody recognition of cell surface-associated NS1 triggers Fc-gamma receptor-mediated phagocytosis and clearance of West Nile Virus-infected cells. J Virol 81: 9551-9555.
9. de Silva A, Messer W (2004) Arguments for live flavivirus vaccines. Lancet 364: 500.
10. Evans JD, Seeger C (2007) Differential effects of mutations in NS4B on West Nile virus replication and inhibition of interferon signaling. J Virol 81: 11809-11816.
11. Gould EA, Moss SR, Turner SL (2004) Evolution and dispersal of encephalitic flaviviruses. Arch Virol (Suppl) 18: 65-84.
12. Hanna JN, Ritchie SA, Phillips DA, Lee JM, Hills SL, van den Hurk AF, Pyke AT, Johansen CA, Mackenzie JS (1999) Japanese encephalitis in north Queensland, Australia, 1998. Med J Aust 170: 533-536.
13. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
14. Konishi E, Pincus S, Fonseca BA, Shope RE, Paoletti E, Mason PW (1991) Comparison of protective immunity elicited by recombinant vaccinia viruses that synthesize E or NS1 of Japanese encephalitis virus. Virology 185: 401-410.
15. Kuwayama M, Ito M, Takao S, Shimazu Y, Fukuda S, Miyazaki K, Kurane I, Takasaki T (2005) Japanese encephalitis virus in meningitis patients, Japan. Emerg Infect Dis 11: 471-473.
16. Lai MM (1992) RNA recombination in animal and plant viruses. Microbiol Rev 56: 61-79.
17. Libraty DH, Young PR, Pickering D, Endy TP, Kalayanarooj S, Green S, Vaughn DW, Nisalak A, Ennis FA, Rothman AL (2002) High circulating levels of the dengue virus nonstructural protein NS1 early in dengue illness correlate with the development of dengue hemorrhagic fever. J Infect Dis 186: 1165-1168.
18. Lindenbach BD, Rice CM (1997) trans-Complementation of yellow fever virus NS1 reveals a role in early RNA replication. J Virol 71: 9608-9617.
19. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73: 152-160.
20. Macdonald J, Tonry J, Hall RA, Williams B, Palacios G, Ashok MS, Jabado O, Clark D, Tesh RB, Briese T, Lipkin WI (2005) NS1 protein secretion during the acute phase of West Nile virus infection. J Virol 79: 13924-13933.
21. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics (Oxford, England) 21: 260-262.
22. Munoz-Jordan JL, Sanchez-Burgos GG, Laurent-Rolle M, Garcia-Sastre A (2003) Inhibition of interferon signaling by dengue virus. Proc Natl Acad Sci USA 100: 14333-14338.
23. Munoz-Jordan JL, Laurent-Rolle M, Ashour J, Martinez-Sobrido L, Ashok M, Lipkin WI, Garcia-Sastre A (2005) Inhibition of alpha/beta interferon signaling by the NS4B protein of flaviviruses. J Virol 79: 8004-8013.
24. Nam JH, Chae SL, Won SY, Kim EJ, Yoon KS, Kim BI, Jeong YS, Cho HW (2001) Short report: genetic heterogeneity of Japanese encephalitis virus assessed via analysis of the full-length genome sequence of a Korean isolate. Am J Trop Med Hyg 65: 388-392.
25. Olsthoorn RC, Bol JF (2001) Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA 7: 1370-1377.
26. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics (Oxford, England) 14: 817-818.
27. Pyke AT, Williams DT, Nisbet DJ, van den Hurk AF, Taylor CT, Johansen CA, Macdonald J, Hall RA, Simmons RJ, Mason RJ, Lee JM, Ritchie SA, Smith GA, Mackenzie JS (2001) The appearance of a second genotype of Japanese encephalitis virus in the Australasian region. Am J Trop Med Hyg 65: 747-753.
28. Rambaut A (2006) FigTree. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh.
29. Shapka N, Nagy PD (2004) The AU-rich RNA recombination hot spot sequence of Brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination. J Virol 78: 2288-2300.
30. Solomon T, Ni H, Beasley DW, Ekkelenkamp M, Cardosa MJ, Barrett AD (2003) Origin and evolution of Japanese encephalitis virus in southeast Asia. J Virol 77: 3091-3098.
31. Solomon T, Winter PM (2004) Neurovirulence and host factors in flavivirus encephalitis-evidence from clinical epidemiology. Arch Virol 18(Suppl): 161-170.
32. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony (and other methods). Sinauer Associates, Sunderland.
33. Twiddy SS, Holmes EC (2003) The extent of homologous recombination in members of the genus Flavivirus. J Gen Virol 84: 429-440.
34. Uchil PD, Satchidanandam V (2001) Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent. Am J Trop Med Hyg 65: 242-251.
35. Wang LH, Fu SH, Wang HY, Liang XF, Cheng JX, Jing HM, Cai GL, Li XW, Ze WY, Lv XJ, Wang HQ, Zhang DL, Feng Y, Yin ZD, Sun XH, Shui TJ, Li MH, Li YX, Liang GD (2007) Japanese encephalitis outbreak, Yuncheng, China, 2006. Emerg Infect Dis 13: 1123-1125.
36. Wilson JR, de Sessions PF, Leon MA, Scholle F (2008) West Nile virus nonstructural protein 1 inhibits TLR3 signal transduction. J Virol 82: 8262-8271.
37. Worobey M, Rambaut A, Holmes EC (1999) Widespread intra-serotype recombination in natural populations of dengue virus. Proc Natl Acad Sci USA 96: 7352-7357.