Identification of potential recombination breakpoints in human parechoviruses

Journal of Virology

Volumn 83, Issue 7, 2009, Pages 3379-3383

  Zoll, Jan ^a   Galama, Jochem M D ^a   Van Kuppeveld, Frank J M ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE SEQUENCE; GENETIC ALGORITHM; NONHUMAN; NUCLEOTIDE SEQUENCE; PARECHOVIRUS; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS RECOMBINATION; VIRUS STRAIN; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC RECOMBINATION; GENETICS; HUMAN; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

PARECHOVIRUS;

VIRUS RNA;

CLUSTER ANALYSIS; GENOME, VIRAL; HUMANS; MOLECULAR SEQUENCE DATA; PARECHOVIRUS; PHYLOGENY; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 63149186259     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.02529-08     Document Type: Article

References (32)

1. Abed, Y., and G. Boivin. 2005. Molecular characterization of a Canadian human parechovirus (HPeV)-3 isolate and its relationship to other HPeVs. J. Med. Virol. 77:566-570.
2. Agol, V. I. 1997. Recombination and other genomic rearrangements in picornaviruses. Semin. Virol. 8:1-9.
3. Al-Sunaidi, M., C. H. Williams, P. J. Hughes, D. P. Schnurr, and G. Stanway. 2007. Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains. J. Virol. 81:1013-1021.
4. Bedard, K. M., and B. L. Semler. 2004. Regulation of picornavirus expression. Microbes Infect. 6:702-713.
5. Benschop, K. S. M., J. Schinkel, M. E. Luken, P. J. M. van den Broek, M. F. C. Beersma, N. Menelik, H. W. M. van Eijk, H. L. Zaaijer, C. M. J. E. VandenBroucke-Grauls, M. G. H. M. Beld, and K. C. Wolthers. 2006. Fourth human parechovirus serotype. Emerg. Infect. Dis. 12:1572-1575.
6. Benschop, K. S. M., C. H. Williams, K. C. Wolthers, G. Stanway, and P. Simmonds. 2008. Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints. J. Gen. Virol. 89:1030-1035.
7. Chao, M. 2007. RNA recombination in hepatitis delta virus: implications regarding the abilities of mammalian RNA polymerases. Virus Res. 127:208-215.
8. de Souza Luna, L. K., S. Baumgarte, K. Grywna, M. Panning, J. F. Drexler, and C. Drosten. 2008. Identification of a contemporary human parechovirus type 1 by VIDISCA and characterisation of its full genome. Virol. J. 5:26.
9. de Vries, M., K. Pyre, R. Berkhout, W. Vermeulen-Oost, R. Dijkman, M. F. Jebbink, S. Bruisten, B. Berkhout, and L. van der Hoek. 2008. Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures. J. Clin. Microbiol. 46:759-762.
10. Felsenstein, J., and G. A. Churchill. 1996. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
11. Ghazi, F., P. J. Hughes, T. Hyypia, and G. Stanway. 1998. Molecular analysis of human parechovirus type 2 (formerly echovirus 23). J. Gen. Virol. 79: 2641-2650.
12. Gmyl, A. P., S. A. Korshenko, E. V. Belousov, E. V. Khitrina, and V. I. Agol. 2003. Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9:1221-1231.
13. Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:383-402.
14. Hughes, A. L. 2004. Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins. Infect. Genet. Evol. 4:143-152.
15. Hyypiä, T., C. Horsnell, M. Maaronen, M. Khan, N. Kalkkinen, P. Auvinen, L. Kinnunen, and G. Stanway. 1992. A distinct picornavirus group identified by sequence analysis. Proc. Natl. Acad. Sci. USA 89:8847-8851.
16. Ito, M., T. Yamashita, H. Tsuzuki, N. Takeda, and K. Sakae. 2004. Isolation and identification of a novel human parechovirus. J. Gen. Virol. 85:391-398.
17. Kosakovsky Pond, S. L., D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. W. Frost. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096-3098.
18. Kosakovsky Pond, S. L., D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. W. Frost. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23:1891-1901.
19. Kottaridi, C, E. Bolanaki, Z. Kyriakopoulou, E. Dedepsidis, A, Pratti, and P. Markoulatos. 2007. Possible recombination and gene adaptation exchanges among clinical echovirus strains: crossing the temporal and topological barriers. Diagn. Microbiol. Infect. Dis. 58:407-412.
20. Lindberg, A. M., P. Andersson, C. Savolainen, M. N. Mulders, and T. Hovi. 2003. Evolution of the genome of human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. J. Gen. Virol. 84:1223-1235.
21. Lole, K. S., R. C. Bollinger, R. S. Paranjape, D. Gadkari, S. S. Kulkarni, N. G. Novak, R. Ingersoll, H. W. Sheppard, and S. C. Ray. 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.
22. Lukashev, A. N., V. A. Lashkevich, O. E. Ivanova, G. A. Koroleva, A. E. Hinkkanen, and J. Ilonen. 2005. Recombination in circulating human enterovirus B: independent evolution of structural and non-structural genome regions. J. Gen. Virol. 86:3281-3290.
23. Lukashev, A. N. 2005. Role of recombination in evolution of enteroviruses. Rev. Med. Virol. 15:157-167.
24. Martínez-Salas, E., A. Pachedo, P. Serrano, and N. Fernandez. 2008. New insights into internal ribosome entry site elements relevant for viral gene expression. J. Gen. Virol. 89:611-626.
25. Mirand, A., C. Henquell, C. Archimbaud, H. Peigue-Lafeuille, and J. L. Bailly. 2007. Emergence of recent echoviras 30 lineages is marked by serial genetic recombination events. J. Gen. Virol. 88:166-176.
26. Oberste, M. S., S. Peñaranda, and M. A. Pallansch. 2004. RNA recombination plays a major role in genomic change during circulation of coxsackie B viruses. J. Virol. 78:2948-2955.
27. Simmonds, P., and J. Welch. 2006. Frequency and dynamics of recombination within different species of human enteroviruses. J. Virol. 80:483-493.
28. Simmonds, P. 2006. Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J. Virol. 80:11124-11140.
29. Wakatsuki, K., D. Kawamoto, H. Hiwaki, K. Watanabe, and H. Yoshida. 2008. Identification and characterization of two strains of human parechovirus 4 isolated from two clinical cases in Fukuoka City, Japan. J. Clin. Microbiol. 46:3144-3146.
30. Watanabe, K., M. Oie, M. Higuchi, M. Nishikawa, and M. Fujii. 2007. Isolation and characterization of novel human parechovirus from clinical samples. Emerg. Infect. Dis. 13:889-895.
31. Wolthers, K. C, K. S. Benschop, J. Schinkel, R. Molenkamp, R. M. Bergevoet, I. J. Spijkerman, H. C. Kraakman, and D. Pajkrt. 2008. Human parechoviruses as an important viral cause of sepsislike illness and meningitis in young children. Clin. Infect. Dis. 47:358-363.
32. Zoll, J., H. A, Heus, F. J. M. van Kuppeveld, and W. J. G. Melchers. 30 August 2008. The structure-function relationship of the enterovirus 3′ UTR. Virus Res. [Epub ahead of print.] doi:10.1016/j. virasres.2008.07.014.