References

Aragones, L., A. Bosch and R.M. Pinto, 2008. Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: Codon usage constraints limit capsid variability. J. Virol., 82: 1688-1700.
CrossRef  |  Direct Link  |  

Aragones, L., S. Guix, E. Ribes, A. Bosch and R.M. Pinto, 2010. Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid. PLoS Pathogens, Vol. 6, No. 3. 10.1371/journal.ppat.1000797

Bahir, I., M. Fromer, Y. Prat and M. Linial, 2009. Viral adaptation to host: A proteome-based analysis of codon usage and amino acid preferences. Mol. Syst. Biol., Vol. 5. 10.1038/msb.2009.71

Becher, P., M. Orlich, A.D. Shannon, G. Horner, M. Konig and H.J. Thiel, 1997. Phylogenetic analysis of pestiviruses from domestic and wild ruminants. J. Gen. Virol., 78: 1357-1366.
Direct Link  |  

Carbrey, E.A., W.C. Stewart, J.I. Kresse and M.L. Snyder, 1976. Natural infection of pigs with bovine viral diarrhea virus and its differential diagnosis from hog cholera. J. Am. Vet. Med. Assoc., 169: 1217-1219.
PubMed  |  

Coleman, J.R., D. Papamichail, S. Skiena, B. Futcher, E. Wimmer and S. Mueller, 2008. Virus attenuation by genome-scale changes in codon pair bias. Science, 320: 1784-1787.
CrossRef  |  

Cutter, A.D., J.D. Wasmuth and M.L. Blaxter, 2006. The evolution of biased codon and amino acid usage in nematode genomes. Mol. Biol. Evol., 23: 2303-2315.
CrossRef  |  

Drake, J.W., 1993. Rates of spontaneous mutation among RNA viruses. Proc. Natl. Acad. Sci. USA., 90: 4171-4175.
Direct Link  |  

Duret, L. and L.D. Hurst, 2001. The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution. Mol. Biol. Evol., 18: 757-762.
PubMed  |  Direct Link  |  

Gustafsson, C., S. Govindarajan and J. Minshull, 2004. Codon bias and heterologous protein expression. Trends Biotechnol., 22: 346-353.
CrossRef  |  PubMed  |  

Karlin, S., B.E. Blaisdell and G.A. Schachtel, 1990. Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: Data and hypotheses. J. Virol., 64: 4264-4273.
Direct Link  |  

Karlin, S., W. Doerfler and L.R. Cardon, 1994. Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?. J. Virol., 68: 2889-2897.
Direct Link  |  

Kawashima, Y., K. Pfafferott, J. Frater, P. Matthews, R. Payne and M. Addo et al., 2009. Adaptation of HIV-1 to human leukocyte antigen class I. Nature, 458: 641-645.
CrossRef  |  PubMed  |  

Knight, R.D., S.J. Freeland and L.F. Landweber, 2001. Rewiring the keyboard: Evolvability of the genetic code. Nat. Rev. Genet, 2: 49-58.
CrossRef  |  PubMed  |  

Laddomada, A., 2000. Incidence and control of CSF in wild boar in Europe. Vet. Microbiol., 73: 121-130.
CrossRef  |  PubMed  |  

Liess, B. and V. Moennig, 1990. Ruminant pestivirus infection in pigs. Rev. Sci. Tech., 9: 151-161.
PubMed  |  

Liu, Y.S., J.H. Zhou, H.T. Chen, L.N. Ma, Y.Z. Ding, M. Wang and J. Zhang, 2010. Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus. Infect. Genet. Evol., 10: 797-803.
CrossRef  |  

Liu, Y.S., J.H. Zhou, H.T. Chen, L.N. Ma, Z. Pejsak, Y.Z. Ding and J. Zhang, 2011. The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern. Infect. Genet. Evol., 11: 1168-1173.
CrossRef  |  

Loan, R.W. and M.M. Storm, 1968. Propagation and transmission of hog cholear virus in nonporcine hosts. Am. J. Vet. Res., 29: 807-811.
PubMed  |  

Nakamura, Y., T. Gojobori and T. Ikemura, 2000. Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Res., 28: 292-292.
CrossRef  |  

Nettleton, P.F., J.A. Gilray, P. Russo and E. Dlissi, 1998. Border disease of sheep and goats. Vet. Res., 29: 327-340.
PubMed  |  

Plotkin, J.B., H. Robins and A.J. Levine, 2004. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA., 101: 12588-12591.
CrossRef  |  Direct Link  |  

Roehe, P.M., M.J. Woodward and S. Edwards, 1992. Characterisation of p20 gene sequences from a border disease-like pestivirus isolated from pigs. Vet. Microbiol., 33: 231-238.
CrossRef  |  PubMed  |  

Sanchez, G., A. Bosch and R.M. Pinto, 2003. Genome variability and capsid structural constraints of hepatitis A virus. J. Virol., 77: 452-459.
CrossRef  |  Direct Link  |  

Santos, M.A., G. Moura, S.E. Massey and M.F. Tuite, 2004. Driving change: The evolution of alternative genetic codes. Trends Genet., 20: 95-102.
CrossRef  |  

Sharp, P.M., T.M.F. Tuohy and K.R. Mosurski, 1986. Codon usage in yeast cluster-analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res., 14: 5125-5143.
Direct Link  |  

Shimizu, M. and T. Kumagai, 1989. Experimental infection of pregnant goats with swine fever virus. Vet. Microbiol., 20: 207-214.
CrossRef  |  PubMed  |  

Sugiyama, T., M. Gursel, F. Takeshita, C. Coban and J. Conover et al., 2005. CpG RNA: Identification of novel single-stranded RNA that stimulates human CD14⁺CD11c⁺ monocytes. J. Immunol., 174: 2273-2279.
Direct Link  |  

Terpstra, C. and G. Wensvoort, 1998. Natural infections of pigs with bovine viral diarrhoea virus associated with signs resembling swine fever. Res. Vet. Sci., 45: 137-142.
PubMed  |  

Vilcek, S. and P.F. Nettleton, 2006. Pestiviruses in wild animals. Vet. Microbiol., 116: 1-12.
CrossRef  |  PubMed  |  

Wong, E.H., D.K. Smith, R. Rabadan, M. Peiris amd L.L. Poon, 2010. Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol. Biol., Vol: 10. 10.1186/1471-2148-10-253

Zhi, N., Z. Wan, X. Liu, S. Wong, D.J. Kim, N.S. Young and S. Kajigaya, 2010. Codon optimization of human parvovirus B19 capsid genes greatly increases their expression in nonpermissive cells. J. Virol., 84: 13059-13062.
CrossRef  |  Direct Link  |  

Zhou, J., W.J. Liu, S.W. Peng, X.Y. Sun and I. Frazer, 1999. Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J. Virol., 73: 4972-4982.
Direct Link  |  

Zhou, J.H., J. Zhang, H.T. Chen, L.N. Ma and Y.S. Liu, 2010. Analysis of synonymous codon usage in foot-and-mouth disease virus. Vet. Res. Commun., 34: 393-404.

Zhou, J.H., Z.L. Gao, J. Zhang, H.T. Chen and Z. Pejsak et al., 2012. Comparative the codon usage between the three main viruses in pestivirus genus and their natural susceptible livestock. Virus Genes, 44: 475-481.
CrossRef  |