Free Access
Review
Issue
Vet. Res.
Volume 41, Number 6, November–December 2010
Emerging and re-emerging animal viruses
Number of page(s) 14
DOI https://doi.org/10.1051/vetres/2010010
Published online 05 February 2010
How to cite this article Vet. Res. (2010) 41:38
  • Antia R., Regoes R.R., Koella J.C., Bergstrom C.T., The role of evolution in the emergence of infectious diseases, Nature (2003) 426:658–661. [CrossRef] [PubMed] [Google Scholar]
  • Baranowski E., Ruiz-Jarabo C.M., Domingo E., Evolution of cell recognition by viruses, Science (2001) 292:1102–1105. [CrossRef] [PubMed] [Google Scholar]
  • Baranowski E., Ruiz-Jarabo C.M., Pariente N., Verdaguer N., Domingo E., Evolution of cell recognition by viruses: a source of biological novelty with medical implications, Adv. Virus Res. (2003) 62:19–111. [CrossRef] [PubMed] [Google Scholar]
  • Batschelet E., Domingo E., Weissmann C., The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate, Gene (1976) 1:27–32. [CrossRef] [PubMed] [Google Scholar]
  • Bloomfield V.A., Crothers D.M., Tinoco J., Nucleic acids. Structures, properties, and functions, Section I, University Science Books, Sausalito, CA, 2000. [Google Scholar]
  • Bowen D.G., Walker C.M., The origin of quasispecies: cause or consequence of chronic hepatitis C viral infection?, J. Hepatol. (2005) 42:408–417. [CrossRef] [PubMed] [Google Scholar]
  • Bushman F., Lateral DNA transfer, mechanisms and consequences, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2002. [Google Scholar]
  • Ciurea A., Hunziker L., Martinic M.M., Oxenius A., Hengartner H., Zinkernagel R.M., CD4+ T-cell-epitope escape mutant virus selected in vivo, Nat. Med. (2001) 7:795–800. [CrossRef] [PubMed] [Google Scholar]
  • Chetverin A.B., Kopein D.S., Chetverina H.V., Demidenko A.A., Ugarov V.I., Viral RNA-directed RNA polymerases use diverse mechanisms to promote recombination between RNA molecules, J. Biol. Chem. (2005) 280:8748–8755. [CrossRef] [PubMed] [Google Scholar]
  • Domingo E., Díez J., Martínez M.A., Hernández J., Holguín A., Borrego B., Mateu M.G., New observations on antigenic diversification of RNA viruses. Antigenic variation is not dependent on immune selection, J. Gen. Virol. (1993) 74:2039–2045. [CrossRef] [PubMed] [Google Scholar]
  • Domingo E., Holland J.J., RNA virus mutations and fitness for survival, Annu. Rev. Microbiol. (1997) 51:151–178. [CrossRef] [PubMed] [Google Scholar]
  • Domingo E., Biebricher C., Eigen M., Holland J.J., Quasispecies and RNA virus evolution: principles and consequences, Landes Bioscience, Austin, 2001. [Google Scholar]
  • Domingo E., Quasispecies: concepts and implications for virology, Springer Verlag, 2006. [CrossRef] [Google Scholar]
  • Domingo E., Virus evolution, in: Fields Virology, 5th ed., Lappincott Williams & Wilkins, Philadelphia, 2007. [Google Scholar]
  • Domingo E., Gomez J., Quasispecies and its impact on viral hepatitis, Virus Res. (2007) 127:131–150. [CrossRef] [PubMed] [Google Scholar]
  • Domingo E., Parrish C., Holland J.J.E., Origin and evolution of viruses, 2nd ed., Elsevier, Oxford, 2008. [Google Scholar]
  • Drake J.W., Holland J.J., Mutation rates among RNA viruses, Proc. Natl. Acad. Sci. USA (1999) 96:13910–13913. [CrossRef] [Google Scholar]
  • Eckerle L.D., Lu X., Sperry S.M., Choi L., Denison M.R., High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants, J. Virol. (2007) 81:12135–12144. [CrossRef] [PubMed] [Google Scholar]
  • Eigen M., Biebricher C.K., Sequence space and quasispecies distribution, CRC Press, Boca Raton, FL, 1988. [Google Scholar]
  • Eriksson N., Pachter L., Mitsuya Y., Rhee S.Y., Wang C., Gharizadeh B., et al., Viral population estimation using pyrosequencing, PLoS Comput. Biol. (2008) 4:e1000074. [CrossRef] [PubMed] [Google Scholar]
  • Escarmís C., Dávila M., Domingo E., Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller’s ratchet, J. Mol. Biol. (1999) 285:495–505. [CrossRef] [PubMed] [Google Scholar]
  • Evans A.S., Kaslow R.A., Viral infections of humans. Epidemiology and control, Plenum Medical Book Company, New York and London, 1997. [Google Scholar]
  • Farci P., Shimoda A., Coiana A., Diaz G., Peddis G., Melpolder J.C., et al., The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies, Science (2000) 288:339–344. [CrossRef] [PubMed] [Google Scholar]
  • Ferrer-Orta C., Arias A., Escarmis C., Verdaguer N., A comparison of viral RNA-dependent RNA polymerases, Curr. Opin. Struct. Biol. (2006) 16:27–34. [CrossRef] [PubMed] [Google Scholar]
  • Figlerowicz M., Alejska M., Kurzynska-Kokorniak A., Figlerowicz M., Genetic variability: the key problem in the prevention and therapy of RNA-based virus infections, Med. Res. Rev. (2003) 23:488–518. [CrossRef] [PubMed] [Google Scholar]
  • Friedberg E.C., Walker G.C., Siede W., Wood R.D., Schultz R.A., Ellenberger T., DNA repair and mutagenesis, American Society for Microbiology, Washington, DC, 2006. [Google Scholar]
  • Gavrilin G.V., Cherkasova E.A., Lipskaya G.Y., Kew O.M., Agol V.I., Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model, J. Virol. (2000) 74:7381–7390. [CrossRef] [PubMed] [Google Scholar]
  • Gibbs M.J., Armstrong J.S., Gibbs A.J., The haemagglutinin gene, but not the neuraminidase gene, of “Spanish flu” was a recombinant, Philos. Trans. R. Soc. Lond. B Biol. Sci. (2001) 356:1845–1855. [CrossRef] [PubMed] [Google Scholar]
  • Gmyl A.P., Korshenko S.A., Belousov E.V., Khitrina E.V., Agol V.I., Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces?, RNA (2003) 9:1221–1231. [CrossRef] [PubMed] [Google Scholar]
  • González-López C., Arias A., Pariente N., Gómez-Mariano G., Domingo E., Preextinction viral RNA can interfere with infectivity, J. Virol. (2004) 78:3319–3324. [CrossRef] [PubMed] [Google Scholar]
  • González-López C., Gómez-Mariano G., Escarmís C., Domingo E., Invariant aphthovirus consensus nucleotide sequence in the transition to error catastrophe, Infect. Genet. Evol. (2005) 5:366–374. [CrossRef] [PubMed] [Google Scholar]
  • Grande-Pérez A., Lazaro E., Lowenstein P., Domingo E., Manrubia S.C., Suppression of viral infectivity through lethal defection, Proc. Natl. Acad. Sci. USA (2005) 102:4448–4452. [CrossRef] [Google Scholar]
  • Haagmans B.L., Andeweg A.C., Osterhaus A.D., The application of genomics to emerging zoonotic viral diseases, PLoS Pathog. (2009) 5:e1000557. [CrossRef] [PubMed] [Google Scholar]
  • Haydon D.T., Woolhouse M.E., Immune avoidance strategies in RNA viruses: fitness continuums arising from trade-offs between immunogenicity and antigenic variability, J. Theor. Biol. (1998) 193:601–612. [CrossRef] [PubMed] [Google Scholar]
  • He C.Q., Xie Z.X., Han G.Z., Dong J.B., Wang D., Liu J.B., et al., Homologous recombination as an evolutionary force in the avian influenza A virus, Mol. Biol. Evol. (2009) 26:177–187. [PubMed] [Google Scholar]
  • Hueffer K., Parrish C.R., Parvovirus host range, cell tropism and evolution, Curr. Opin. Microbiol. (2003) 6:392–398. [CrossRef] [PubMed] [Google Scholar]
  • Ishihama A., Mizumoto K., Kawakami K., Kato A., Honda A., Proofreading function associated with the RNA-dependent RNA polymerase from influenza virus, J. Biol. Chem. (1986) 261:10417–10421. [PubMed] [Google Scholar]
  • Khetsuriani N., Prevots D.R., Quick L., Elder M.E., Pallansch M., Kew O., Sutter R.W., Persistence of vaccine-derived polioviruses among immunodeficient persons with vaccine-associated paralytic poliomyelitis, J. Infect. Dis. (2003) 188:1845–1852. [CrossRef] [PubMed] [Google Scholar]
  • Knowles N.J., Samuel A.R., Molecular epidemiology of foot-and-mouth disease virus, Virus Res. (2003) 91:65–80. [CrossRef] [PubMed] [Google Scholar]
  • Krauss H., Weber A., Appel M., Enders B., Isenberg H.D., Schiefer H.G., et al., Zoonoses. Infectious diseases transmissible from animals to humans, ASM Press, Washington, DC, 2003. [Google Scholar]
  • Lai M.M.C., Genetic recombination in RNA viruses, Curr. Top. Microbiol. Immunol. (1992) 176:21–32. [PubMed] [Google Scholar]
  • Lazaro E., Escarmis C., Perez-Mercader J., Manrubia S.C., Domingo E., Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss, Proc. Natl. Acad. Sci. USA (2003) 100:10830–10835. [CrossRef] [Google Scholar]
  • Lea S., Hernández J., Blakemore W., Brocchi E., Curry S., Domingo E., et al., The structure and antigenicity of a type C foot-and-mouth disease virus, Structure (1994) 2:123–139. [CrossRef] [PubMed] [Google Scholar]
  • Levy J.A., HIV and the pathogenesis of AIDS, ASM Press, Washington, DC, 2007. [Google Scholar]
  • Li W., Wong S.K., Li F., Kuhn J.H., Huang I.C., Choe H., Farzan M., Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions, J. Virol. (2006) 80:4211–4219. [CrossRef] [PubMed] [Google Scholar]
  • Luytjes W., Bredenbeek P.J., Noten A.F., Horzinek M.C., Spaan W.J., Sequence of mouse hepatitis virus A59 mRNA 2: indications for RNA recombination between coronaviruses and influenza C virus, Virology (1988) 166:415–422. [CrossRef] [PubMed] [Google Scholar]
  • Mardis E.R., The impact of next-generation sequencing technology on genetics, Trends Genet. (2008) 24:133–141. [PubMed] [Google Scholar]
  • Martinez M.A., Hernandez J., Piccone M.E., Palma E.L., Domingo E., Knowles N., Mateu M.G., Two mechanisms of antigenic diversification of foot-and-mouth disease virus, Virology (1991) 184:695–706. [CrossRef] [PubMed] [Google Scholar]
  • Mascola J.R., The cat and mouse of HIV-1 antibody escape, PLoS Pathog. (2009) 5:e1000592. [CrossRef] [PubMed] [Google Scholar]
  • Maynard Smith J.M., Natural selection and the concept of a protein space, Nature (1970) 225:563–564. [CrossRef] [PubMed] [Google Scholar]
  • McFadden G., Poxvirus tropism, Nat. Rev. Microbiol. (2005) 3:201–213. [CrossRef] [PubMed] [Google Scholar]
  • Menéndez-Arias L., Molecular basis of fidelity of DNA synthesis and nucleotide specificity of retroviral reverse transcriptases, Prog. Nucleic Acid Res. Mol. Biol. (2002) 71:91–147. [CrossRef] [PubMed] [Google Scholar]
  • Mims C., Nash A., Stephen J., Mims’ pathogenesis of infectious disease, Academic Press, San Diego, 2001. [Google Scholar]
  • Minskaia E., Hertzig T., Gorbalenya A.E., Campanacci V., Cambillau C., Canard B., Ziebuhr J., Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis, Proc. Natl. Acad. Sci. USA (2006) 103:5108–5113. [CrossRef] [Google Scholar]
  • Morse S.S., The evolutionary biology of viruses, Raven Press, New York, 1994. [Google Scholar]
  • Nagy P.D., Carpenter C.D., Simon A.E., A novel 3′-end repair mechanism in an RNA virus, Proc. Natl. Acad. Sci. USA (1997) 94:1113–1118. [CrossRef] [Google Scholar]
  • Nagy P.D., Simon A.E., New insights into the mechanisms of RNA recombination, Virology (1997) 235:1–9. [CrossRef] [PubMed] [Google Scholar]
  • Nemerow G.R., Stewart P.L., Antibody neutralization epitopes and integrin binding sites on nonenveloped viruses, Virology (2001) 288:189–191. [CrossRef] [PubMed] [Google Scholar]
  • Nijhuis M., van Maarseveen N.M., Boucher C.A., Antiviral resistance and impact on viral replication capacity: evolution of viruses under antiviral pressure occurs in three phases, Handb. Exp. Pharmacol. (2009) 189:299–320. [CrossRef] [PubMed] [Google Scholar]
  • Novella I.S., Duarte E.A., Elena S.F., Moya A., Domingo E., Holland J.J., Exponential increases of RNA virus fitness during large population transmissions, Proc. Natl. Acad. Sci. USA (1995) 92:5841–5844. [CrossRef] [Google Scholar]
  • Novella I.S., Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution, Curr. Opin. Microbiol. (2003) 6:399–405. [CrossRef] [PubMed] [Google Scholar]
  • Nowak M.A., May R.M., Virus dynamics. Mathematical principles of immunology and virology, Oxford University Press Inc., New York, 2000. [Google Scholar]
  • Nowak M.A., Evolutionary dynamics, The Belknap Press of Harvard University Press, Cambridge, Massachusetts and London, England, 2006. [Google Scholar]
  • Nunez J.I., Molina N., Baranowski E., Domingo E., Clark S., Burman A., et al., Guinea pig-adapted foot-and-mouth disease virus with altered receptor recognition can productively infect a natural host, J. Virol. (2007) 81:8497–8506. [CrossRef] [PubMed] [Google Scholar]
  • Odoom J.K., Yunus Z., Dunn G., Minor P.D., Martin J., Changes in population dynamics during long-term evolution of sabin type 1 poliovirus in an immunodeficient patient, J. Virol. (2008) 82:9179–9190. [CrossRef] [PubMed] [Google Scholar]
  • Palese P., Shaw M.L., Orthomyxoviridae: the viruses and their replication, in: Knipe D.M., Howley P.M. (Eds.), Fields Virology, 5th ed., Lappincott Williams & Wilkins, Philadelphia, 2007. [Google Scholar]
  • Parrish C.R., Kawaoka Y., The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses, Annu. Rev. Microbiol. (2005) 59:553–586. [CrossRef] [PubMed] [Google Scholar]
  • Paunio M., Peltola H., Valle M., Davidkin I., Virtanen M., Heinonen O.P., Explosive school-based measles outbreak: intense exposure may have resulted in high risk, even among revaccinees, Am. J. Epidemiol. (1998) 148:1103–1110. [PubMed] [Google Scholar]
  • Peters C.J., Emerging viral diseases, in: Knipe D.M., Howley P.M. (Eds.), Fields Virology, 5th ed., Lappincott Williams & Wilkins, Philadelphia, 2007, pp. 605–625. [Google Scholar]
  • Pfeiffer J.K., Kirkegaard K., Ribavirin resistance in hepatitis C virus replicon-containing cell lines conferred by changes in the cell line or mutations in the replicon RNA, J. Virol. (2005) 79:2346–2355. [CrossRef] [PubMed] [Google Scholar]
  • Quiñones-Mateu M.E., Arts E., Virus fitness: concept, quantification, and application to HIV population dynamics, Curr. Top. Microbiol. Immunol. (2006) 299:83–140. [CrossRef] [PubMed] [Google Scholar]
  • Rocha E., Cox N.J., Black R.A., Harmon M.W., Harrison C.J., Kendal A.P., Antigenic and genetic variation in influenza A (H1N1) virus isolates recovered from a persistently infected immunodeficient child, J. Virol. (1991) 65:2340–2350. [PubMed] [Google Scholar]
  • Sanz-Ramos M., Diaz-San Segundo F., Escarmis C., Domingo E., Sevilla N., Hidden virulence determinants in a viral quasispecies in vivo, J. Virol. (2008) 82:10465–10476. [CrossRef] [PubMed] [Google Scholar]
  • Schnitzler S.U., Schnitzler P., An update on swine-origin influenza virus A/H1N1: a review, Virus Genes (2009) 39:279–292. [CrossRef] [PubMed] [Google Scholar]
  • Simmonds P., Welch J., Frequency and dynamics of recombination within different species of human enteroviruses, J. Virol. (2006) 80:483–493. [CrossRef] [PubMed] [Google Scholar]
  • Small M., Tse C.K., Walker D.M., Super-spreaders and the rate of transmission of the SARS virus, Physica D (2006) 215:146–158. [CrossRef] [MathSciNet] [Google Scholar]
  • Smolinski M.S., Hamburg M.A., Lederberg J., Microbial threats to health. Emergence, detection and response, The National Academics Press, Washington, DC, 2003. [Google Scholar]
  • Solé R., Goodwin B., Signs of life, how complexity pervades biology, Basic Books, New York, 2000. [Google Scholar]
  • Steinhauer D.A., Domingo E., Holland J.J., Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase, Gene (1992) 122:281–288. [CrossRef] [PubMed] [Google Scholar]
  • Taboga O., Tami C., Carrillo E., Núñez J.I., Rodríguez A., Saíz J.C., et al., A large-scale evaluation of peptide vaccines against foot-and-mouth disease: lack of solid protection in cattle and isolation of escape mutants, J. Virol. (1997) 71:2606–2614. [PubMed] [Google Scholar]
  • Tami C., Taboga O., Berinstein A., Nuñez J.I., Palma E.L., Domingo E., et al., Evidence of the coevolution of antigenicity and host cell tropism of foot-and-mouth disease virus in vivo, J. Virol. (2003) 77:1219–1226. [CrossRef] [PubMed] [Google Scholar]
  • Tsibris A.M., Korber B., Arnaout R., Russ C., Lo C.C., Leitner T., et al., Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo, PLoS ONE (2009) 4:e5683. [CrossRef] [PubMed] [Google Scholar]
  • Verdaguer N., Mateu M.G., Andreu D., Giralt E., Domingo E., Fita I., Structure of the major antigenic loop of foot-and-mouth disease virus complexed with a neutralizing antibody: direct involvement of the Arg-Gly-Asp motif in the interaction, EMBO J. (1995) 14:1690–1696. [PubMed] [Google Scholar]
  • Vignuzzi M., Stone J.K., Arnold J.J., Cameron C.E., Andino R., Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population, Nature (2006) 439:344–348. [CrossRef] [PubMed] [Google Scholar]
  • Villefroy P., Letourneur F., Coutsinos Z., Mortara L., Beyer C., Gras-Masse H., et al., SIV escape mutants in rhesus macaques vaccinated with NEF-derived lipopeptides and challenged with pathogenic SIVmac251, Virol. J. (2006) 3:65. [CrossRef] [PubMed] [Google Scholar]
  • Wang C., Mitsuya Y., Gharizadeh B., Ronaghi M., Shafer R.W., Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance, Genome Res. (2007) 17:1195–1201. [CrossRef] [PubMed] [Google Scholar]
  • Weaver S.C., Evolutionary influences in arboviral disease, Curr. Top. Microbiol. Immunol. (2006) 299:285–314. [CrossRef] [PubMed] [Google Scholar]
  • Webster D.R., Hekele A.G., Lauring A.S., Fisher K.F., Li H., Andino R., De Risi J.L., An enhanced single base extension technique for the analysis of complex viral populations, PLoS ONE (2009) 16:e7453. [CrossRef] [Google Scholar]
  • Woo P.C., Lau S.K., Yuen K.Y., Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections, Curr. Opin. Infect. Dis. (2006) 19:401–407. [CrossRef] [PubMed] [Google Scholar]
  • Woolhouse M.E., Webster J.P., Domingo E., Charlesworth B., Levin B.R., Biological and biomedical implications of the co-evolution of pathogens and their hosts, Nat. Genet. (2002) 32:569–577. [CrossRef] [PubMed] [Google Scholar]
  • Zhang C.Y., Wei J.F., He S.H., Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups, BMC Microbiol. (2006) 6:88. [CrossRef] [PubMed] [Google Scholar]