Phylogenomics and molecular evolution of foot-and-mouth disease virus

Molecules and Cells

Volumn 31, Issue 5, 2011, Pages 413-421

  Yoon, Sook Hee ^a   Park, Woncheoul ^a   King, Donald P ^b   Kim, Heebal ^a  

^a Seoul National University   (South Korea)

^b INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

Author keywords

Foot and mouth disease virus; Molecular evolution; Phylogenomics

Indexed keywords

POLYPROTEIN;

ARTICLE; BAYES THEOREM; CLADISTICS; FOOT AND MOUTH DISEASE VIRUS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENOMICS; SEROTYPE; UNINDEXED SEQUENCE; VIRUS ISOLATION;

ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; FOOT-AND-MOUTH DISEASE; FOOT-AND-MOUTH DISEASE VIRUS; GENOMICS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

FOOT-AND-MOUTH DISEASE VIRUS;

EID: 79960698117     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-011-0249-6     Document Type: Article

References (25)

1. Barteling S.J. (2002). Development and performance of inactivated vaccines against foot and mouth disease. Rev. Sci. Tech. 21, 577-588. (Pubitemid 36080125)
2. Balamurugan V., Kumar, R.M., and Suryanarayana, V.V. (2004) Past and present vaccine development strategies for the control of foot-and-mouth disease. Acta Virol. 48, 201-214. (Pubitemid 47434291)
3. Carrillo, C., Tulman, E.R., Delhon, G., Lu, Z., Carreno, A., Vagnozzi, A., Kutish, G.F., and Rock, D.L. (2005). Comparative genomics of foot-and-mouth disease virus. J. Virol. 79, 6487-6504. (Pubitemid 40617252)
4. Cooke, J.N., and Westover, K.M. (2008). Serotype-specific differences in antigenic regions of foot-and-mouth disease virus (FMDV): a comprehensive statistical analysis. Infect. Genet. Evol. 8, 855-863.
5. Cottam, E.M., Haydon, D.T., Paton, D.J., Gloster, J., Wilesmith, J.W., Ferris, N.P., Hutchings, G.H., and King, D.P. (2006). Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. J. Virol. 80, 11274-11282. (Pubitemid 44706567)
6. Domingo, E., Baranowski, E., Escarmis, C., and Sobrino, F. (2002). Foot and-mouth disease virus. Comp. Immunol. Microbiol. Infect. Dis. 25, 297-308.
7. Drake, J.W., and Holland, J.J. (1999). Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. USA 96, 13910-13913.
8. Drummond, A.J., and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214.
9. Drummond, A.J., Ho, S.Y.W., Phillips, M.J., and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi: 10.1371/ journal.pbio.0040088).
10. Hall, T.A. (1999). BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acid Symp. Ser. 41, 95-98.
11. Huelsenbeck, J.P., and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (Pubitemid 32851390)
12. Lewis-Rogers, N., McClellan, D.A., and Crandall, K.A. (2008). The evolution of foot-and-mouth disease virus: impacts of recombination and selection. Infect. Genet. Evol. 8, 786-798.
13. Mohapatra, J.K., Priyadarshini, P., Pandey, L., Subramaniam, S., Sanyal, A., Hemadri, D., and Pattnaik, B. (2009). Analysis of the leader proteinase (L(pro)) region of type A foot-and-mouth disease virus with due emphasis on phylogeny and evolution of the emerging VP3(59)-deletion lineage from India. Virus Res. 141, 34-46.
14. Nielsen, R., and Yang, Z. (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148, 929-936. (Pubitemid 28169008)
15. Pereira, H.G. (1977). Subtyping of foot-and-mouth disease virus. Dev. Biol. Stand. 35, 167-174. (Pubitemid 9054138)
16. Posada, D., and Crandall, K.A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818. (Pubitemid 28552116)
17. Ronquist, F., and Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. (Pubitemid 37038874)
18. Schumann, K.R., Knowles, N.J., Davies, P.R., Midgley, R.J., Valarcher, J.F., Raoufi, A.Q., McKenna, T.S., Hurtle, W., Burans, J.P., Martin, B.M., et al. (2008). Genetic characterization and molecular epidemiology of foot-and-mouth disease viruses isolated from Afghanistan in 2003-2005. Virus Genes 36, 401-413.
19. Sobrino, F., Saiz, M., Jimenez-Clavero, M.A., Nunez, J.I., Rosas, M.F., Baranowski, E., and Ley, V. (2001). Foot-and-mouth disease virus: a long known virus, but a current threat. Vet. Res. 32, 1-30. (Pubitemid 32155703)
20. Suchard, M.A., Weiss, R.E., and Sinsheimer, J.S. (2001). Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18, 1001-1013. (Pubitemid 32520473)
21. Suyama, M., Torrents, D., and Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acid Res. 34, W609-W612. (Pubitemid 44529842)
22. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997). The Clustal-windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res. 22, 4673-4680.
23. Tully, D.C., and Fares, M.A. (2006). Unravelling selection shifts among foot-and-mouth disease virus (FMDV) serotypes. Evol. Bioinform. 2, 237-251.
24. Tully, D.C., and Fares, M.A. (2008). The tale of a modern animal plague: tracing the evolutionary history and determining the time-scale for foot and mouth disease virus. Virology 382, 250-256.
25. Yang, Z. (1997). PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556. (Pubitemid 27480216)