Coronaviruses pp 41-48 | Cite as
Estimation of Evolutionary Dynamics and Selection Pressure in Coronaviruses
Abstract
Evolution of coronaviruses is facilitated by the strong selection, large population size, and great genetic diversity within the susceptible hosts. This predisposition is primarily due to high error rate, and limited proofreading capability of the viral polymerase and by recombination. These characteristics make coronaviruses an interesting model system to study the mechanisms involved in viral evolution and the ways viruses adapt to switch host or to gain novel functions. Here we describe the protocol to estimate selection pressures for the spike gene and evolutionary dynamics of bovine coronaviruses.
Key words
Coronaviruses Evolution Genetics Emergence Selection S geneNotes
Acknowledgement
The work at our laboratories is supported by the grant from Biotechnology and Biological Sciences Research Council (BBSRC) through Institute Strategic Programme Grant (BB/J004448/1).
References
- 1.Minskaia E, Hertzig T, Gorbalenya A et al (2006) Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc Natl Acad Sci U S A 103:5108–5113CrossRefPubMedCentralPubMedGoogle Scholar
- 2.Jackwood MW, Hall D, Handel A (2012) Molecular evolution and emergence of avian gammacoronaviruses. Infect Genet Evol 12:1305–1311CrossRefPubMedGoogle Scholar
- 3.de Groot RJ, Baker SC, Baric R et al (2012) Coronaviridae. In: King AMQ et al (eds) Virus taxonomy: classification and nomenclature of viruses: ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, Oxford, pp 806–828Google Scholar
- 4.Drake JW, Holland JJ (1999) Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96:13910–13913CrossRefPubMedCentralPubMedGoogle Scholar
- 5.Moya A, Holmes EC, Gonzalez-Candelas F (2004) The population genetics and evolutionary epidemiology of RNA viruses. Nat Rev Microbiol 2:279–288CrossRefPubMedGoogle Scholar
- 6.Vijgen L, Keyaerts E, Lemey P et al (2006) Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43. J Virol 80:7270–7274CrossRefPubMedCentralPubMedGoogle Scholar
- 7.Woo PC, Lau SK, Lam CS et al (2012) Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol 86:3995–4008CrossRefPubMedCentralPubMedGoogle Scholar
- 8.Erles K, Shiu KB, Brownlie J (2007) Isolation and sequence analysis of canine respiratory coronavirus. Virus Res 124:78–87CrossRefPubMedGoogle Scholar
- 9.Bidokhti MR, Tråvén M, Krishna NK et al (2013) Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains. J Gen Virol 94:2036–2049CrossRefPubMedGoogle Scholar
- 10.Zhang XM, Herbst W, Kousoulas KG et al (1994) Biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child. J Med Virol 44:152–161CrossRefPubMedGoogle Scholar
- 11.Munir M (2013) Bioinformatics analysis of large-scale viral sequences: From construction of data sets to annotation of a phylogenetic tree. Virulence 4:97–106CrossRefPubMedCentralPubMedGoogle Scholar
- 12.Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676–679CrossRefPubMedGoogle Scholar
- 13.Drummond AJ, Suchard MA, Xie D et al (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973CrossRefPubMedCentralPubMedGoogle Scholar