Genome-scale evolution and phylodynamics of equine H3N8 influenza a virus

Journal of Virology

Volumn 85, Issue 11, 2011, Pages 5312-5322

  Murcia, Pablo R ^a   Wood, James L N ^a   Holmes, Edward C ^b,c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDYLTRANSFERASE; POLYMERASE ACIDIC SEGMENT; UNCLASSIFIED DRUG;

ADAPTATION; AMINO ACID SUBSTITUTION; ARTICLE; BOTTLENECK POPULATION; CONTROLLED STUDY; GENETIC REASSORTMENT; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; HERD IMMUNITY; HORSE; INFLUENZA VIRUS A H3N8; MICROBIAL POPULATION DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLODYNAMICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES EXTINCTION; VIRUS GENOME; VIRUS MUTATION; VIRUS VIRULENCE;

CANIS FAMILIARIS; EQUIDAE; EQUINE INFLUENZA VIRUS; HUMAN INFLUENZA VIRUS; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE;

EID: 79956150523     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02619-10     Document Type: Article

References (68)

1. Adeyefa, C. A., K. Quayle, and J. W. McCauley 1994. A rapid method for the analysis of influenza virus genes: application to the reassortment of equine influenza virus genes. Virus Res. 32:391-399.
2. Allen, J. E., S. N. Gardner, E. A. Vitalis, and T. R. Slezak 2009. Conserved amino acid markers from past influenza pandemic strains. BMC Microbiol. 9:77.
3. Banbura, M. W., Y. Kawaoka, T. L. Thomas, and R. G. Webster 1991. Reassortants with equine 1 (H7N7) influenza virus hemagglutinin in an avian influenza virus genetic background are pathogenic in chickens. Virology 184:469-471.
4. Bao, Y., et al. 2008. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82:596-601.
5. Bean, W. J. 1984. Correlation of influenza A virus nucleoprotein genes with host species. Virology 133:438-442.
6. Bean, W. J., et al. 1992. Evolution of the H3 influenza virus hemagglutinin from human and nonhuman hosts. J. Virol. 66:1129-1138.
7. Bryant, N. A., et al. 2009. Antigenic and genetic variations in European and North American equine influenza virus strains (H3N8) isolated from 2006 to 2007. Vet. Microbiol. 138:41-52.
8. Bryant, N. A., et al. 2011. Isolation and characterisation of equine influenza viruses (H3N8) from Europe and North America from 2008 to 2009. Vet. Microbiol. 147:19-27.
9. Burrows, R., D. Goodridge, M. Denyer, G. Hutchings, and C. J. Frank 1982. Equine influenza infections in Great Britain, 1979. Vet. Rec. 110:494-497.
10. Chen, L. M., C. T. Davis, H. Zhou, N. J. Cox, and R. O. Donis 2008. Genetic compatibility and virulence of reassortants derived from contemporary avian H5N1 and human H3N2 influenza A viruses. PLoS Pathog. 4:e1000072.
11. Chen, R., and E. C. Holmes 2006. Avian influenza virus exhibits rapid evolutionary dynamics. Mol. Biol. Evol. 23:2336-2341.
12. Crawford, P. C., et al. 2005. Transmission of equine influenza virus to dogs. Science 310:482-485.
13. Daly, J. M., et al. 2008. Transmission of equine influenza virus to English foxhounds. Emerg. Infect. Dis. 14:461-464.
14. Daly, J. M., et al. 1996. Antigenic and genetic evolution of equine H3N8 influenza A viruses. J. Gen. Virol. 77:661-671.
15. Damiani, A. M., et al. 2008. Genetic characterization of equine influenza viruses isolated in Italy between 1999 and 2005. Virus Res. 131:100-105.
16. Drummond, A. J., and A. Rambaut 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
17. Drummond, A. J., A. Rambaut, B. Shapiro, and O. G. Pybus 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22:1185-1192.
18. Duffy, S., L. A. Shackelton, and E. C. Holmes 2008. Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 9:267-276.
19. Dunham, E. J., et al. 2009. Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses. J. Virol. 83:5485-5494.
20. Endo, A., R. Pecoraro, S. Sugita, and K. Nerome 1992. Evolutionary pattern of the H 3 haemagglutinin of equine influenza viruses: multiple evolutionary lineages and frozen replication. Arch. Virol. 123:73-87.
21. Espmark, A., L. Heller, and P. Viriden 1956. Immunological relationship between infectious cough in horses and human influenza A. Arch. Gesamte Virusforsch. 7:120-124.
22. Ferguson, N. M., A. P. Galvani, and R. M. Bush 2003. Ecological and immunological determinants of influenza evolution. Nature 422:428-433.
23. Finkelstein, D. B., et al. 2007. Persistent host markers in pandemic and H5N1 influenza viruses. J. Virol. 81:10292-10299.
24. Fitch, W. M., J. M. Leiter, X. Q. Li, and P. Palese 1991. Positive Darwinian evolution in human influenza A viruses. Proc. Natl. Acad. Sci. U.S.A. 88: 4270-4274.
25. Gorman, O. T., W. J. Bean, Y. Kawaoka, and R. G. Webster 1990. Evolution of the nucleoprotein gene of influenza A virus. J. Virol. 64:1487-1497.
26. Gorman, O. T., R. O. Donis, Y. Kawaoka, and R. G. Webster 1990. Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus. J. Virol. 64:4893-4902.
27. Grenfell, B. T., et al. 2004. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327-332.
28. Guo, Y., et al. 1992. Characterization of a new avian-like influenza A virus from horses in China. Virology 188:245-255.
29. Holmes, E. C., et al. 2005. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 3:e300.
30. Holmes, E. C., and B. T. Grenfell 2009. Discovering the phylodynamics of RNA viruses. PLoS Comput. Biol. 5:e1000505.
31. Ina, Y., and T. Gojobori 1994. Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses. Proc. Natl. Acad. Sci. U.S.A. 91:8388-8392.
32. Ito, T., O. T. Gorman, Y. Kawaoka, W. J. Bean, and R. G. Webster 1991. Evolutionary analysis of the influenza A virusMgene with comparison of the M1 and M2 proteins. J. Virol. 65:5491-5498.
33. Ito, T., et al. 1999. Replacement of internal protein genes, with the exception of the matrix, in equine 1 viruses by equine 2 influenza virus genes during evolution in nature. J. Vet. Med. Sci. 61:987-989.
34. Kawaoka, Y., W. J. Bean, and R. G. Webster 1989. Evolution of the hemagglutinin of equine H3 influenza viruses. Virology 169:283-292.
35. Kawaoka, Y., et al. 1998. Influence of host species on the evolution of the nonstructural (NS) gene of influenza A viruses. Virus Res. 55:143-156.
36. Kawaoka, Y., and R. G. Webster 1989. Origin of the hemagglutinin on A/Equine/Johannesburg/86 (H3N8): the first known equine influenza outbreak in South Africa. Arch. Virol. 106:159-164.
37. Kirkland, P. D., D. S. Finlaison, E. Crispe, and A. C. Hurt 2010. Influenza virus transmission from horses to dogs, Australia. Emerg. Infect. Dis. 16: 699-702.
38. Lai, A. C., et al. 2001. Diverged evolution of recent equine-2 influenza (H3N8) viruses in the Western Hemisphere. Arch. Virol. 146:1063-1074.
39. Lai, A. C., K. M. Rogers, A. Glaser, L. Tudor, and T. Chambers 2004. Alternate circulation of recent equine-2 influenza viruses (H3N8) from two distinct lineages in the United States. Virus Res. 100:159-164.
40. Livesay, G. J., T. O'Neill, D. Hannant, M. P. Yadav, and J. A. Mumford 1993. The outbreak of equine influenza (H3N8) in the United Kingdom in 1989: diagnostic use of an antigen capture ELISA. Vet. Rec. 133:515-519.
41. Lycett, S. J., et al. 2009. Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data. J. Virol. 83:9901-9910.
42. Morens, D. M., and J. K. Taubenberger 2010. Historical thoughts on influenza viral ecosystems, or behold a pale horse, dead dogs, failing fowl, and sick swine. In A. W. Hampson (ed.), Influenza and other respiratory viruses. Wiley, Hoboken, NJ.
43. Mumford, J. A. 1999. The equine influenza surveillance program. Adv. Vet. Med. 41:379-387.
44. Murcia, P. R., et al. 2010. Intra- and interhost evolutionary dynamics of equine influenza virus. J. Virol. 84:6943-6954.
45. Nelson, M. I., et al. 2008. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 4:e1000012.
46. Newton, J. R., et al. 2000. Immunity to equine influenza: relationship of vaccine-induced antibody in young Thoroughbred racehorses to protection against field infection with influenza A/equine-2 viruses (H3N8). Equine Vet. J. 32:65-74.
47. Newton, J. R., K. Verheyen, J. L. Wood, P. J. Yates, and J. A. Mumford 1999. Equine influenza in the United Kingdom in 1998. Vet. Rec. 145:449-452.
48. Office International des Epizooties. 2008. Expert surveillance panel on equine influenza vaccines. Conclusions and recommendations. Office International des Epizooties, Paris, France.
49. Okazaki, K., Y. Kawaoka, and R. G. Webster 1989. Evolutionary pathways of the PA genes of influenza A viruses. Virology 172:601-608.
50. Paccaud, M. F., M. Couard, F. Bürki, H. Gerbbr, and J. Löhrer 1966. Outbreak of influenza A/equi-2 in Switzerland. Nature 211:101-102.
51. Palese, P., and M. L. Shaw 2007. Orthomyxoviridae: The viruses and their replication, p. 1647-1690. In D. M. Knipe and P. M. Howley (ed.), Fields virology, 5th ed., vol. 1. Lippincott Williams & Wilkins, Philadelphia, PA.
52. Pond, S. L., and S. D. Frost 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531-2533.
53. Pond, S. L., and S. D. Frost 2005. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22:478-485.
54. Pond, S. L., S. D. Frost, and S. V. Muse 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
55. Posada, D., and K. A. Crandall 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
56. Ronquist, F., and J. P. Huelsenbeck 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
57. Saito, T., Y. Kawaoka, and R. G. Webster 1993. Phylogenetic analysis of the N8 neuraminidase gene of influenza A viruses. Virology 193:868-876.
58. Sanz-Ezquerro, J. J., T. Zurcher, S. de la Luna, J. Ortin, and A. Nieto 1996. The amino-terminal one-third of the influenza virus PA protein is responsible for the induction of proteolysis. J. Virol. 70:1905-1911.
59. Scholtens, R. G., J. H. Steele, W. R. Dowdle, W. B. Yarbrough, and R. Q. Robinson 1964. U.S. epizootic of equine influenza, 1963. Public Health Rep. 79:393-402.
60. Smith, G. J., et al. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-1125.
61. Song, M. S., et al. 2009. The polymerase acidic protein gene of influenza a virus contributes to pathogenicity in a mouse model. J. Virol. 83:12325-12335.
62. Sovinova, O., B. Tumova, F. Pouska, and J. Nemec 1958. Isolation of a virus causing respiratory disease in horses. Acta Virol. 2:52-61.
63. Swofford, D. L 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
64. Tu, J., et al. 2009. Isolation and molecular characterization of equine H3N8 influenza viruses from pigs in China. Arch. Virol. 154:887-890.
65. Tumova, B., B. C. Easterday, and A. Stumpa 1972. Simultaneous occurrence of A-equi-1 and A-equi-2 infleunza viruses in a small group of horses. Am. J. Epidemiol. 95:80-87.
66. Waddell, G. H., M. B. Teigland, and M. M. Sigel 1963. A new influenza virus associated with equine respiratory disease. J. Am. Vet. Med. Assoc. 143: 587-590.
67. Webster, R. G. 1993. Are equine 1 influenza viruses still present in horses? Equine Vet. J. 25:537-538.
68. Webster, R. G., W. J. Bean, O. T. Gorman, T. M. Chambers, and Y. Kawaoka 1992. Evolution and ecology of influenza A viruses. Microbiol. Rev. 56:152-179.