Skip to main content
SpringerLink
Log in

Evolution of Influenza Viruses

  • Chapter
  • First Online:
Insight into Influenza Viruses of Animals and Humans

  • 1899 Accesses

Abstract

The rate of evolution in influenza A viruses is the fastest followed by influenza B, C viruses. The key factor in the evolution of influenza B and C viruses is prolonged co-circulation of antigenically and genetically distinct lineages. However, predominantly clonal selection, and to a very limited extent co-circulation of sublineages, is responsible for the evolution of influenza A viruses. Studies on phylogenetic analysis have identified several host-specific virus lineages for various viral proteins, except HA and NA genes. The evolution of influenza A viruses particularly is influenced by several factors such as origin and evolution of HA gene, receptor specificity, antigenic drift and shift, recombination, mixing vessels, host species jumping, etc. Phylogenetic analysis has helped to compare past and present influenza viruses as well as the determination of the common ancestor of the virus. Considerable genetic diversity, divergence and antigenic drift observed in the H5N1 virus during the last 16 years of its circulation in poultry have led to the development of unified nomenclature system in which these viruses were classified into various virus clades. This is required to understand the evolutionary mechanism of the development of pandemic H5N1 strains. The discovery of new subtypes, H17N10 and H18N11, from bats has increased the repertoire of known subtypes of influenza viruses, and the known range of mammals that can be infected by these viruses. Multiple reassortments were responsible for the generation of the novel H7N9 isolates that caused disease and death in humans in 2013.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdel-Moneim AS, Afifi MA, El-Kady MF (2012) Isolation and mutation trend analysis of influenza a virus subtype H9N2 in Egypt. Virol J 9:173

    PubMed Central  PubMed  Google Scholar 

  • Abed Y, Pizzorno A, Hamelin ME et al (2011) The 2009 pandemic H1N1 D222G hemagglutinin mutation alters receptor specificity and increases virulence in mice but not in ferrets. J Infect Dis 204:1008–1016

    PubMed  CAS  Google Scholar 

  • Anhlan D, Grundmann N, Makalowski W et al (2011) Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis. RNA 17:64–73

    PubMed Central  PubMed  CAS  Google Scholar 

  • Anthony SJ, St Leger JA, Pugliares K et al (2012) Emergence of fatal avian influenza in New England harbor seals. mBio 3:e00166–00112 doi:10.1128/mBio.00166-12

  • Anton A, Pozo F, Niubo J et al (2012) Influenza A (H1N1)pdm09 virus: viral characteristics and genetic evolution. Enferm Infecc Microbiol Clin 30(4):10–17

    PubMed  Google Scholar 

  • Baigent SJ, McCauley JW (2001) Glycosylation of haemagglutinin and stalk-length of neuraminidase combine to regulate the growth of avian influenza viruses in tissue culture. Virus Res 79:177–185

    PubMed  CAS  Google Scholar 

  • Bao C, Cui L, Zhou M et al (2013) Live-animal markets and influenza A (H7N9) virus infection. N Engl J Med 368(24):2337–2339

    PubMed  CAS  Google Scholar 

  • Beigel J, Farrar J, Han A et al (2005) Avian influenza A (H5N1) infection in humans. N Engl J Med 353:1374–1385

    PubMed  Google Scholar 

  • Belser JA, Bridges CB, Katz JM et al (2009) Past, present, and possible future human infection with influenza virus A subtype H7. Emerg Infect Dis 15:859–865

    PubMed Central  PubMed  Google Scholar 

  • Belser JA, Jayaraman A, Raman R et al (2011) Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. PLoS ONE 6:e25091. doi:10.1371/journal.pone.0025091

    PubMed Central  PubMed  CAS  Google Scholar 

  • Belshe RB (2009) Implications of the Emergence of a novel H1 influenza virus. N Engl J Med 360:2667–2668

    PubMed  CAS  Google Scholar 

  • Betakova T, Nermut MV, Hay AJ (1996) The NB protein is an integral component of the membrane of influenza B virus. J Gen Virol 77:2689–2694

    PubMed  CAS  Google Scholar 

  • Bowes VA, Ritchie SJ, Byrne S et al (2004) Virus characterization, clinical presentation, and pathology associated with H7N3 avian influenza in British Columbia in broiler breeder chicken in 2004. Avian Dis 48:928–934

    PubMed  CAS  Google Scholar 

  • Brown IH (2000) The epidemiology and evolution of influenza viruses in pigs. Vet Microbiol 74:29–46

    PubMed  CAS  Google Scholar 

  • Burleigh LM, Calder LJ, Skehel JJ et al (2005) Influenza A viruses with mutations in the M1 helix six domain display a wide variety of morphological phenotypes. J Virol 79:1262–1270

    PubMed Central  PubMed  CAS  Google Scholar 

  • Campitelli L, Di Martino A, Spagnolo D et al (2008) Molecular analysis of avian H7 influenza viruses circulating in Eurasia in 1999-2005: detection of multiple reassortant virus genotypes. J Gen Virol 89:48–59

    PubMed  CAS  Google Scholar 

  • Cappuccio JA, Pena L, Dibarbora M et al (2011) Outbreak of swine influenza in Argentina reveals a non-contemporary human H3N2 virus highly transmissible among pigs. J Gen Virol 92:2871–2878

    PubMed Central  PubMed  CAS  Google Scholar 

  • Capua I, Alexander DJ (2002) Avian influenza and human health. Acta Trop 83:1–6

    PubMed  Google Scholar 

  • Chakrabarti AK, Pawar SD, Cherian SS et al (2009) Characterization of the influenza A H5N1 viruses of the 2008–2009 outbreaks in India reveals a third introduction and possible endemicity. PLoS ONE 4(11):e7846

    PubMed Central  PubMed  Google Scholar 

  • Chambers TM, Hinshaw VS, Kawaoka Y et al (1991) Influenza viral infection of swine in the United States 1988–1989. Arch Virol 116:261–265

    PubMed  CAS  Google Scholar 

  • Chan JFW, To KKW, Tse H et al (2013) Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol 21(10):544–555

    PubMed  CAS  Google Scholar 

  • Chen LM, Blixt O, Stevens J et al (2012) In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity. Virology 422(1):105–113

    PubMed  CAS  Google Scholar 

  • Chen GW, Chang SC, Mok CK (2006) Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis 12(9):1353–1360

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chen Y, Liang W, Yang S et al (2013) Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet 381(9881):1916–1925

    PubMed  CAS  Google Scholar 

  • Choi YK, Lee JH, Erickson G et al (2004) H3N2 influenza virus transmission from swine to turkeys, United States. Emerg Infect Dis 10:2156–2160

    PubMed Central  PubMed  Google Scholar 

  • Choi JG, Kang HM, Jeon WJ et al (2013) Characterization of Clade 2.3. 2.1 H5N1 highly pathogenic avian influenza viruses isolated from wild birds (Mandarin Duck and Eurasian Eagle Owl) in 2010 in Korea. Viruses 5(4):1153–1174

    Google Scholar 

  • Christman MC, Kedwaii A, Xu J et al (2011) Pandemic (H1N1) 2009 virus revisited: an evolutionary retrospective. Infect Genet Evol 11:803–811

    PubMed Central  PubMed  Google Scholar 

  • Chutinimitkul S, Herfst S, Steel J et al (2010) Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza A (H1N1) virus affects receptor binding. J Virol 84:11802–11813

    PubMed Central  PubMed  CAS  Google Scholar 

  • Class EC, Osterhaus AD, van Beek R et al (1998) Human influenza A H1N1 virus related to a highly pathogenic avian influenza virus. Lancet 351:467–472

    Google Scholar 

  • Cobey S, Pascual M, Dieckmann U (2010) Ecological factors driving the long-term evolution of influenza’s host range. Proc Biol Sci 277(1695):2803–2810

    PubMed Central  PubMed  Google Scholar 

  • Connor RJ, Kawaoka Y, Webster RG et al (1994) Receptor specificity in human, avian, and equine H2 and H3 influenza virus isolates. Virology 205:17–23

    PubMed  CAS  Google Scholar 

  • Couceiro JN, Paulson JC, Baum LG (1993) Influenza virus strains selectively recognize sialyloligosaccharides on human respiratory epithelium: the role of the host cell in selection of hemagglutinin receptor specificity. Virus Res 29:155–165

    PubMed  CAS  Google Scholar 

  • Cowling BJ, Jin L, Lau EH et al (2013) Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a population-based study of laboratory-confirmed cases. Lancet 382(9887):129–137. doi:10.1016/S0140-6736(13)61171-X

    PubMed  Google Scholar 

  • Cox NJ, Fuller F, Kaverin N et al (2000) Family Orthomyxoviridae. In: van Regenmortel MHV, Fauquet CM, Bishop DHL et al (eds) Virus taxonomy. Academic Press, London pp 585–597

    Google Scholar 

  • Crawford PC, Dubovi EJ, Castleman WL et al (2005) Transmission of equine influenza virus to dogs. Science 51:407–421

    Google Scholar 

  • Crispe E, Finlaison DS, Hurt AC et al (2011) Infection of dogs with equine influenza virus: evidence for transmission from horses during the Australian outbreak. Aust Vet J 89(Suppl 1):27–28. doi:10.1111/j.1751-0813.2011.00734.x

    PubMed  Google Scholar 

  • Croville G, Soubies SM, Barbieri B et al (2012) Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing. J Clin Microbiol 50:2881–2887

    PubMed Central  PubMed  CAS  Google Scholar 

  • Daly JM, Blunden AS, Macrae S et al (2008) Transmission of equine influenza virus to English foxhounds. Emerg Infect Dis 14:461–464

    PubMed Central  PubMed  Google Scholar 

  • de Jong MD, Tran TT, Truong HK et al (2005) Oseltamivir resistance during treatment of influenza A (H5N1) infection. N Engl J Med 353:2667–2672

    PubMed  Google Scholar 

  • de Vries RP, Zhu X, McBride R et al (2014) Hemagglutinin receptor specificity and structural analyses of respiratory droplet-transmissible H5N1 viruses. J Virol 88(1):768–773

    PubMed  Google Scholar 

  • Desvaux S, Marx N, Ong S et al (2009) Highly pathogenic avian influenza virus (H5N1) outbreak in captive wild birds and cats, Cambodia. Emerg Infect Dis 15:475–478

    PubMed Central  PubMed  Google Scholar 

  • Dos Reis M, Hay AJ, Goldstein RA (2009) Using non-homogenous models of nucleotide substitution to identify host shift events: applications to the origin of the 1918 Spanish Influenza pandemic virus. J Mol Biol 69(4):333–345

    Google Scholar 

  • Domingo E, Sheldon J, Perales C (2012) Viral quasispecies evolution. Microbiol Mol Biol Rev 76(2):159–216. doi:10.1128/MMBR.05023-11

    PubMed Central  PubMed  CAS  Google Scholar 

  • Dubey SC, Nagarajan S, Tosh C et al (2009) Avian influenza: a long known disease and its current threat. Ind J Anim Sci 79:113–140

    Google Scholar 

  • Ducatez MF, Hause B, Stigger-Rosser E et al (2011) Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis 17:1624–1629

    PubMed Central  PubMed  Google Scholar 

  • Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9:267–276

    PubMed  CAS  Google Scholar 

  • Ebrahimi SM, Ziapour S, Tebianian M et al (2011) Study of infection with an Iranian field-isolated H9N2 avian influenza virus in vaccinated and unvaccinated Japanese Quail. Avian Dis 55(2):195–200

    PubMed  Google Scholar 

  • Enami M, Enami K (1996) Influenza virus haemagglutinin and neuraminidase glycoproteins stimulate the membrane association of the matrix protein. J Virol 70:6653–6657

    PubMed Central  PubMed  CAS  Google Scholar 

  • Enserink M, Kaiser J (2004) Avian flu finds new mammal hosts. Science 305:1385

    PubMed  CAS  Google Scholar 

  • Fernandes ND, Downard KM (2014) Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry. J Mass Spectrom 49(1):93–102

    PubMed  CAS  Google Scholar 

  • Fitch W, Bush R, Bender C et al (2000) Predicting the evolution of human influenza A. J Hered 91(3):183–185

    PubMed  CAS  Google Scholar 

  • Fonville JM, Burke DF, Lewis NS et al (2013) Quantifying the fitness advantage of polymerase substitutions in influenza A/H7N9 viruses during adaptation to humans. PLoS ONE 8(9):e76047

    PubMed Central  PubMed  CAS  Google Scholar 

  • Fouchier RA, Schneeberger PM, Rozendaal FW et al (2004) Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome. Proc Natl Acad Sci USA 101:1356–1361

    PubMed Central  PubMed  CAS  Google Scholar 

  • Freeman S, Herron JC (2007) Evolutionary Analysis. Pearson Education International 4th Edn, Benjamin Cummings Publishing Company, San Francisco. ISBN-10: 0132275848, ISBN-13: 9780132275842 pp 1–800

    Google Scholar 

  • Fuhrmann C (2010) The effects of weather and climate on the seasonality of influenza: what we know and what we need to know. Genography Compass 4(7):718–730. doi:10.1111/j.1749-8198.2010.00343x

    Google Scholar 

  • Fuller TL, Gilbert M, Martin V et al (2013) Predicting hotspots for influenza virus reassortment. Emerg Infect Dis 19(4):581–588

    PubMed Central  PubMed  Google Scholar 

  • Gabriel G, Klingel K, Otte A (2011) Differential use of importin-alpha isoforms governs cell tropism and host adaptation of influenza virus. Nat Commun 2:156

    PubMed Central  PubMed  Google Scholar 

  • Gammelin M, Altmuller A, Reinhardt U et al (1990) Phylogenetic analysis of nucleoproteins suggests that human influenza A viruses emerged from a 19th-century avian ancestor. Mol Biol Evol 7:194–200

    PubMed  CAS  Google Scholar 

  • Gao R, Cao B, Hu Y et al (2013) Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 368:1888–1897

    PubMed  CAS  Google Scholar 

  • Garten RJ, Davis CT, Russell CA et al (2009) Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 325(5937):197–201

    PubMed Central  PubMed  CAS  Google Scholar 

  • Giannecchini S, Campitelli L, Calzoletti L et al (2006) Comparison of in vitro replication features of H7N3 influenza viruses from wild ducks and turkeys: potential implications for interspecies transmission. J Gen Virol 87:171–175

    PubMed  CAS  Google Scholar 

  • Goot JA, Koch G, Jong MCM et al (2003) Transmission dynamics of low and high pathogenicity A/Chicken/Pennsylvania/83 avian influenza viruses. Avian Dis 47:939–941

    PubMed  Google Scholar 

  • Gorman O, Donis R, Kawaoka Y et al (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(10):4893–4902 PMC 247979.PMID 2398532

    Google Scholar 

  • Gray GC, Kayali G (2009) Facing pandemic influenza threats: the importance of including poultry and swine workers in preparedness plans. J Poult Sci 88:880–884

    CAS  Google Scholar 

  • Gray GC, McCarthy T, Capuano AW et al (2007) Swine workers and swine influenza virus infections. Emerg Infect Dis 13:1871–1878

    PubMed Central  PubMed  Google Scholar 

  • Guan Y, Shortridge KF, Krauss S et al (1999) Molecular characterization of H9N2 influenza viruses: were they the donors of internal genes H5N1 viruses in Hong Kong? Proc Natl Acad Sci USA 96:9363–9367

    PubMed Central  PubMed  CAS  Google Scholar 

  • Guo CT, Takahashi N, Yagi H et al (2007) The quail and chicken intestine have sialyl-galactose sugar chains responsible for the binding of influenza A viruses to human type receptors. Glycobiology 17:713–724

    PubMed  CAS  Google Scholar 

  • Guo Y, Li JW, Cheng I (1999) Discovery of humans infected by avian influenza A (H9N2) virus. Chin J Exp Clin Virol 15:105–108

    Google Scholar 

  • Hall C (2004) Impact of avian influenza on US poultry trade relations-2002: H5 or H7 low pathogenic avian influenza. Ann NY Acad Sci 1026:47–53

    PubMed  Google Scholar 

  • Han J, Niu F, Meihua Jin M et al (2013) Clinical presentation and sequence analyses of HA and NA antigens of the novel H7N9 viruses. Emerg Microbes Infec 2:e23. doi:10.1038/emi.2013.28

  • Hao W (2011) Evidence of intra-segmental homologous recombination in influenza A virus. Gene 481(2):57–64

    PubMed  CAS  Google Scholar 

  • Hensley SE, Das SR, Bailey AL et al (2009) Hemagglutinin receptor binding avidity drives influenza A virus antigenic drift. Science 326:734–736

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hinshaw VS, Bean WJ, Webster RG et al (1984) Are seals frequently infected with avian influenza viruses? J Virol 51:863–865

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hinshaw VS, Webster RG, Easterday BC et al (1981) Replication of avian influenza A viruses in mammals. Infect Immun 34:354–361

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hirst M, Astell CR, Griffith M et al (2004) Novel avian influenza H7N3 strain outbreak, British Columbia. Emerg Infect Dis 10:2192–2195

    PubMed Central  PubMed  CAS  Google Scholar 

  • Holmes E, Ghedin E, Miller N et al (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3(9):1579–1589

    CAS  Google Scholar 

  • Holsinger LJ, Nichani D, Pinto LH et al (1994) Influenza A virus M2 ion channel protein: a structure-function analysis. J Virol 68:1551–1563

    PubMed Central  PubMed  CAS  Google Scholar 

  • Horimoto T, Kawaoka Y (1994) Reverse genetics provides direct evidence for a correlation of haemagglutinin cleavability and virulence of an avian influenza virus. J Virol 68:3120–3128

    PubMed Central  PubMed  CAS  Google Scholar 

  • Horimoto T, Kawaoka Y (2001) Pandemic threat posed by avian influenza A viruses. Clin Microbiol Rev 14:129–149

    PubMed Central  PubMed  CAS  Google Scholar 

  • Horimoto T, Rivera E, Pearson J et al (1995) Origin and molecular changes associated with emergence of a highly pathogenic H5N2 influenza virus in Mexico. Virol NY 213:223–230

    CAS  Google Scholar 

  • Hu YJ, Tu PC, Lin CS et al (2014) Identification and chronological analysis of genomic signatures in influenza A viruses. PLoS ONE 9(1):e84638

    PubMed Central  PubMed  Google Scholar 

  • Hulse DJ, Ramirez KM, Humberd J et al (2005) Role of domestic ducks in the propagation and biological evolution of highly pathogenic H5N1 influenza viruses in Asia. Proc Natl Acad Sci USA 102:10682–10687

    Google Scholar 

  • Imai M, Kawaoka Y (2012) The role of receptor binding specificity in interspecies transmission of influenza viruses. Curr Opin Virol 2:160–167

    PubMed  CAS  Google Scholar 

  • Ince WL, Gueye-Mbaye A, Bennink JR et al (2013) Reassortment complements spontaneous mutation in influenza A virus NP and M1 genes to accelerate adaptation to a New Host. J Virol 87(8):4330–4338

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ip DK, Liao Q, Wu P et al (2013) Detection of mild to moderate influenza A/H7N9 infection by China’s national sentinel surveillance system for influenza-like illness: case series. BMJ 346:f3693

    PubMed Central  PubMed  Google Scholar 

  • Ito T (2000) Interspecies transmission and receptor recognition of influenza A viruses. Microbiol Immunol 44:423–430

    PubMed  CAS  Google Scholar 

  • Ito T, Couceiro JNSS, Kelm S et al (1998) Molecular basis for the generation in pigs of influenza A viruses with pandemic potential. J Virol 72:7367–7373

    PubMed Central  PubMed  CAS  Google Scholar 

  • Jones JC, Baranovich T, Zaraket H et al (2013) Human H7N9 influenza A viruses replicate in swine respiratory tissue explants. J Virol 2013 Sep 11. [Epub ahead of print]

    Google Scholar 

  • Kalthoff D, Globig A, Beer M (2010) Highly pathogenic avian influenza as a zoonotic agent. Vet Microbiol 140(3–4):237–245

    PubMed  Google Scholar 

  • Kang HM, Batchuluun D, Kim MC et al (2011) Genetic analyses of H5N1 avian influenza virus in Mongolia, 2009 and its relationship with those of eastern Asia. Vet Microbiol 147:170–175

    PubMed  CAS  Google Scholar 

  • Karasin AI, Schutten MM, Cooper LA et al (2000) Genetic characterisation of H3N2 influenza viruses isolated from pigs in North America, 1977–1999: evidence for wholly human and reassortant virus genotypes. Virus Res 68:71–85

    PubMed  CAS  Google Scholar 

  • Kawaoka Y, Krauss S, Webster RG (1989) Avain-to-human S transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics. J Virol 63:4603–4608

    PubMed Central  PubMed  CAS  Google Scholar 

  • Keawcharoen J, Oraveerakul K, Kuiken T et al (2004) Avian influenza H5N1 in tigers and leopards. Emerg Infect Dis 10:2189–2191

    PubMed Central  PubMed  Google Scholar 

  • Khatchikian D, Orlich M, Rott R (1989) Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340:156–157

    PubMed  CAS  Google Scholar 

  • Klingeborn B, Englund L, Rott R et al (1985) An avian influenza A virus killing a mammalian species- the mink. Brief report. Arch Virol 86:347–351

    PubMed  CAS  Google Scholar 

  • Koopmans M, Wilbrink B, Conyn M et al (2004) Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in The Netherlands. Lancet 363:587–593

    PubMed  Google Scholar 

  • Krossoy B, Hordvik I, Nilsen F et al (1999) The putative polymerase sequence of infectious salmon anemia virus suggests a new genus within the Orthomyxoviridae. J Virol 73:2136–2142

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kuchipudi SV, Nelli R, White GA et al (2009) Differences in influenza virus receptors in chickens and ducks: implications for interspecies transmission. J Mol Genet Med 3:143–151

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kuiken T, Fouchier R, Rimmelzwaan G et al (2011) Pigs, poultry, and pandemic influenza: how zoonotic pathogens threaten human health. Adv Exp Med Biol 719:59–66. doi:10.1007/978-1-4614-0204-6_6

    PubMed  Google Scholar 

  • Kuiken T, Holmes EC, McCauley J et al (2006) Host species barriers to influenza virus infections. Science 312:394–397

    PubMed  CAS  Google Scholar 

  • Kuiken T, Rimmelzwaan G, van Riel D (2004) Avian H5N1 influenza in cats. Science 306:241

    PubMed  CAS  Google Scholar 

  • Kuntz-Simon G, Madec F (2009) Genetic and antigenetic evolution of swine influenza viruses in Europe and evaluation of their zoonotic potential. Zoonoses Public Health 56:310–325

    PubMed  CAS  Google Scholar 

  • Lam TTY, Wang J, Shen Y et al (2013) The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature doi:10.1038/nature12515

  • Lambert LC, Fauci AS (2010) Influenza vaccines for the future. N Engl J Med 363:2036–2044

    PubMed  CAS  Google Scholar 

  • Lebarbenchon C, Brown JD, Stallknecht DE (2013) Evolution of influenza A virus H7 and N9 subtypes, Eastern Asia. Emerg Infec Dis J 19(10):1635–1638

    Google Scholar 

  • Lebarbenchon C, Stallknecht DE (2011) Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin. Virol J 8:328. doi:10.1186/1743-422X-8-328

    PubMed Central  PubMed  CAS  Google Scholar 

  • Li KS, Guan Y, Wang J et al (2004) Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in Eastern Asia. Nature 430:209–213

    PubMed  CAS  Google Scholar 

  • Li ML, Rao P, Krug RM (2001) The active sites of influenza cap dependent endonuclease are on different polymerase subunits. EMBO J 20:2078–2086

    PubMed Central  PubMed  CAS  Google Scholar 

  • Li Q, Sun X, Li Z et al (2012) Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus. Proc Natl Acad Sci USA 109:18897–18902

    PubMed Central  PubMed  CAS  Google Scholar 

  • Li Y, Liu L, Zhang Y et al (2011) New avian influenza virus (H5N1) in wild birds, Qinghai, China. Emerg Infect Dis 17:265–267

    PubMed Central  PubMed  Google Scholar 

  • Li J, Yu X, Pu X et al (2013) Environmental connections of novel avian-origin H7N9 influenza virus infection and virus adaptation to the human. Sci China Life Sci. 56(6):485–492. doi:10.1007/s11427-013-4491-3

    PubMed  CAS  Google Scholar 

  • Lin YP, Xiong X, Wharton SA et al (2012) Evolution of the receptor binding properties of the influenza A (H3N2) hemagglutinin. Proc Natl Acad Sci USA 109(52):21474–21479

    PubMed Central  PubMed  CAS  Google Scholar 

  • Lin JH, Chiu SC, Lin YC et al (2013) Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan. PLoS ONE 8(4):e61957. doi:10.1371/journal.pone.0061957

    PubMed Central  PubMed  CAS  Google Scholar 

  • Liu D, Shi W, Shi Y et al (2013a) Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural and coalescent analyses. Lancet 381:1926–1932

    PubMed  Google Scholar 

  • Liu Q, Lu L, Sun Z et al (2013) Genomic signature and protein sequence analysis of a novel influenza A (H7N9) virus that causes an outbreak in humans in China. Microbes Infect 15(6 7):432–439

    Google Scholar 

  • Liu S, Kang J, Chen J et al (2009). Field. In: Dawn (eds) Panorama phylogenetic diversity and distribution of type A influenza virus. PLoS ONE 4(3):1–20

    Google Scholar 

  • Liu Y, Childs RA, Matrosovich T et al (2010) Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A (H1N1) 2009 influenza virus. J Virol 84:12069–12074

    PubMed Central  PubMed  Google Scholar 

  • Long JS, Howard WA, Núñez A et al (2013) The effect of the PB2 mutation 627 K on highly pathogenic H5N1 avian influenza virus is dependent on the virus lineage. J Virol 87(18):9983–9996

    PubMed Central  PubMed  CAS  Google Scholar 

  • Luo GX, Luytjes W, Enami M et al (1991) The polyadenylation signal of influenza virus RNA involves a stretch of uridines followed by the RNA duplex of the panhandle structure. J Virol 65:2861–2867

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ma W, Kahn RE, Richt JA (2009) The pig as a mixing vessel for influenza viruses: human and veterinary implications. J Mol Genet Med 1:158–166

    Google Scholar 

  • Ma W, Vincent AL, Gramer MR et al (2007) Identification of H2N3 influenza A viruses from swine in the United States. Proc Natl Acad Sci USA 104:20949–20954

    PubMed Central  PubMed  CAS  Google Scholar 

  • Makarova NV, Ozaki H, Kida H et al (2003) Replication and transmission of influenza viruses in Japanese quail. Virology 310:8–15

    PubMed  CAS  Google Scholar 

  • Malik Peiris JS (2009) Avian influenza viruses in humans. Rev Sci Tech 28(1):161–173

    PubMed  CAS  Google Scholar 

  • Mancini DA, Mendonca RM, Pereira AS et al (2012) Influenza viruses in adult dogs raised in rural and urban areas in the state of São Paulo, Brazil. Rev Inst Med Trop Sao Paulo 54(6):311–314

    PubMed  Google Scholar 

  • Manz B, Schwemmle M, Brunotte L (2013) Adaptation of avian Influenza A virus polymerase in mammals to overcome the host species barrier. J Virol 87(13):7200–7209

    PubMed Central  PubMed  Google Scholar 

  • Matrosovich M, Krauss S, Webster RG (2001) H9N2 influenza A viruses from poultry in Asia have human-like receptor specificity. Virology 281:156–162

    PubMed  CAS  Google Scholar 

  • Matrosovich M, Stech J, Klenk HD (2009) Influenza receptors, polymerase and host range. Rev SciTech 28:203–217

    CAS  Google Scholar 

  • Matrosovich M, Tuzikov A, Bovin N et al (2000) Early alterations of the receptor-binding properties of H1, H2 and H3 avian influenza virus hemagglutinins after their introduction into mammals. J Virol 74:8502–8512

    PubMed Central  PubMed  CAS  Google Scholar 

  • Matrosovich M, Zhau N, Kawaoka Y et al (1999) The surface glycoprotein of H5 influenzaviruses isolated from humans, chickens, and wild aquatic birds have distinguishable properties. J Virol 73:1146–1155

    PubMed Central  PubMed  CAS  Google Scholar 

  • Matsui S (2005) Protecting human and ecological health under viral threats in Asia. Water Sci Technol 51:91–97

    PubMed  CAS  Google Scholar 

  • Mehle A, Dugan VG, Taubenberger JK et al (2012) Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol 86:1750–1757

    PubMed Central  PubMed  CAS  Google Scholar 

  • Memorandum WHO (1980) A revision of the system of nomenclature for influenza viruses. Bull WHO 58:585–591

    Google Scholar 

  • Mok CK, Lee HH, Lestra M et al (2014) Amino-acid substitutions in polymerase basic protein 2 gene contributes to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. J Virol 8 Jan 2014. (Epub ahead of print)

    Google Scholar 

  • Moreno A, Chiapponi C, Boniotti MB et al (2012) Genomic characterization of H1N2 swine influenza viruses in Italy. Vet Microbiol 156:265–276

    PubMed  CAS  Google Scholar 

  • Murcia PR, Baillie GJ, Daly J et al (2010) Intra- and inter-host evolutionary dynamics of equine influenza virus. J Virol 84(14):6943–6954

    PubMed Central  PubMed  CAS  Google Scholar 

  • Murcia PR, Hughes J, Battista P et al (2012) Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathog 8(5):e1002730

    PubMed Central  PubMed  CAS  Google Scholar 

  • Musa OI, Salaudeen AG, Akanbi AA II et al (2009) Risk factors, threats and prevention of highly pathogenic avian influenza (hpai) in African countries. Afr J Cln Exper Microbiol 10(2):99–116

    Google Scholar 

  • Nagarajan S, Tosh C, Smith DK et al (2012) Avian influenza (H5N1) virus of clade 2.3.2 in domestic poultry in India. PLoS ONE 7:e31844

    PubMed Central  PubMed  CAS  Google Scholar 

  • Nava GM, Attene-Ramos MS, Ang JK et al (2009) Origins of the new influenza A (H1N1) virus: time to take action. Euro Surveill 14(22):pii=19228

    Google Scholar 

  • Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford

    Google Scholar 

  • Nei M, Xu P, Glazko G (2001) Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc Natl Acad Sci USA 98:2497–2502

    PubMed Central  PubMed  CAS  Google Scholar 

  • Nelson MI, Gramer MR, Vincent AL et al (2012a) Global transmission of influenza viruses from humans to swine. J Gen Virol 93:2195–2203

    PubMed Central  PubMed  CAS  Google Scholar 

  • Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8:196–205

    PubMed  CAS  Google Scholar 

  • Nelson MI, Vincent AL, Kitikoon P et al (2012b) Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009–2011. J Virol 86:8872–8878

    PubMed Central  PubMed  CAS  Google Scholar 

  • Neumann G, Kawaoka Y (2006) Host range restriction and pathogenicity in the context of influenza pandemic. Emerg Infect Dis 12:881–886

    PubMed Central  PubMed  Google Scholar 

  • Newman AP, Reisdorf E, Beinemann J et al (2008) Human case of swine influenza A (H1N1) triple reassortant virus infection, Wisconsin. Emerg Infect Dis 14:1470–1472

    PubMed Central  PubMed  Google Scholar 

  • Nguyen-Van-Tam JS, Nair P, Acheson P et al (2006) Outbreak of low pathogenicity H7N3 avian influenza in UK, including associated case of human conjunctivitis. Euro Surveill 11(E060504):2

    PubMed  Google Scholar 

  • Noronha JM, Liu M, Squires RB et al (2012) Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction. J Virol 86(10):5857–5866

    PubMed Central  PubMed  CAS  Google Scholar 

  • Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team (2009) Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 360:2605–2615

    Google Scholar 

  • OIE (2005) www.oie.int

  • Olofsson S, Kumlin U, Dimock K et al (2005) Avian influenza and sialic acid receptors: more than meets the eye? Lancet Infect Dis 5:184–188

    PubMed  CAS  Google Scholar 

  • Olsen CW, Brammer L, Easterday BC et al (2002) Serologic evidence of H1 swine influenza virus infection in swine farm residents and employees. Emerg Infect Dis 8:814–819

    PubMed Central  PubMed  Google Scholar 

  • Olsen CW, Karasin AI, Carman S et al (2006) Triple reassortant H3N2 influenza A viruses, Canada, 2005. Emerg Infect Dis 12:1132–1135

    PubMed Central  PubMed  Google Scholar 

  • Orlich M, Gottwald H, Rott R (1994) Nonhomologous recombination between haemagglutinin gene and the nucleoprotein gene of an influenza virus. Virology 204:462–465

    PubMed  CAS  Google Scholar 

  • Panigrahy B, Senne DA, Pedersen JC (2002) Avian influenza virus subtypes inside and outside the live bird markets, 1993–2000: a spatial and temporal relationship. Avian Dis 46:298–307

    PubMed  Google Scholar 

  • Parry J (2013) H7N9 avian flu infects humans for the first time. BMJ 346:f2151

    PubMed  Google Scholar 

  • Pasik J, Handel K, Robinson J et al (2005) Intersegmental recombination between the haemmagglutinin and the matrix genes was responsible for the emergence of a highly pathogenic H7N3 avian influenza virus in British Columbia. J Gen Virol 86:727–731

    Google Scholar 

  • Paterson D, Fodor E (2012) Emerging roles for the influenza A virus nuclear export protein (NEP). PLoS Pathog 8(12):e1003019. doi:10.1371/journal.ppat.1003019

    PubMed Central  PubMed  CAS  Google Scholar 

  • Peiris JS, Guan Y, Markwell D et al (2001) Cocirculation of avian H9N2 and contemporary human H3N2 influenza A viruses in pigs in South-Eastern China: potential for genetic reassortment? J Virol 75:9679–9686

    PubMed Central  PubMed  CAS  Google Scholar 

  • Peiris JSM, de Jong MD, Guan Y (2007) Avian influenza virus (H5N1): a threat to human health. Clin Microbiol Rev 20:243–267

    PubMed Central  PubMed  Google Scholar 

  • Peiris M, Yuen KY, Leung CW et al (1999) Human infection with influenza H9N2. Lancet 354:916–917

    PubMed  CAS  Google Scholar 

  • Perdue ML, Swayne DE (2005) Public health risk from avian influenza viruses. Avian Dis 49:317–327

    PubMed  Google Scholar 

  • Perez DR, Lim W, Seiler JP et al (2003a) Role of quail in the interspecies transmission of H9 influenza A viruses: molecular changes on HA that correspond to adaptation from ducks to chickens. J Virol 77:3148–3156

    PubMed Central  PubMed  CAS  Google Scholar 

  • Perez DR, Webby RJ, Hoffmann E et al (2003b) Land-based birds as potential disseminators of avian/mammalian reassortant influenza A viruses. Avian Dis 47:1114–1117

    PubMed  CAS  Google Scholar 

  • Permin A (2004) Avian influenza is spreading. Now avian influenza is also in pigs. Dan Vet 87:10–11

    Google Scholar 

  • Qi X, Qian YH, Bao CJ et al (2013) Probable person to person transmission of novel avian influenza A (H7N9) virus in Eastern China, 2013: epidemiological investigation. BMJ 347:f4752

    PubMed Central  PubMed  Google Scholar 

  • Quiñones-Parra S, Grant E, Loh L et al (2014) Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities. Proc Natl Acad Sci USA doi:10.1073/pnas.1322229111

  • Radomski JP, PÅ‚oÅ„ski P, Zagórski-Ostoja W (2014) The hemagglutinin mutation E391 K of pandemic 2009 influenza revisited. Mol Phylogenet Evol 70:29–36

    PubMed  CAS  Google Scholar 

  • Rahnama L, Aris-Brosou S (2013) Phylodynamics of the emergence of influenza viruses after cross-species transmission. PLoS ONE 8(12):e82486

    PubMed Central  PubMed  Google Scholar 

  • Rambaut A, Pybus OG, Nelson MI et al (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615–619

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ramirez SKM, Hulse DJ, Govorkova EA et al (2005) Are ducks contributing to the endemicity of highly pathogenic H5N1 influenza virus in Asia? J Virol 79:11269–11279

    Google Scholar 

  • Ramos I, Krammer F, Hai R et al (2013) H7N9 influenza viruses interact preferentially with α2,3-linked sialic acids and bind weakly to α2, 6-linked sialic acids. J Gen Virol 15 Aug 2013. (Epub ahead of print)

    Google Scholar 

  • Ranst M, Lemey P (2013) Genesis of avian-origin H7N9 influenza A viruses. Lancet 381(9881):1883–1885

    PubMed  Google Scholar 

  • Reid AH, Fanning TG, Hultin JV et al (1999) Origin and evolution of the 1918 Spanish influenza virus hemagglutinin gene. Proc Natl Acad Sci USA 96:1651–1656

    PubMed Central  PubMed  CAS  Google Scholar 

  • Reid SM, Shell WM, Barboi G et al (2011) First reported incursion of highly pathogenic notifiable avian influenza A H5N1 viruses from clade 2.3.2 into European poultry. Transbound Emerg Dis 58:76–78

    PubMed Central  PubMed  CAS  Google Scholar 

  • Renzette N, Caffrey DR, Zeldovich KB et al (2014) Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol 88(1):272–281

    PubMed  CAS  Google Scholar 

  • Reperant LA, Kuiken T, Osterhaus AD (2012) Adaptive pathways of zoonotic influenza viruses: from exposure to establishment in humans. Vaccine 30:4419–4434

    PubMed  Google Scholar 

  • Resa-Infante P, Gabriel G (2013) The nuclear import machinery is a determinant of influenza virus host adaptation. BioEssays 35:23–27

    PubMed  CAS  Google Scholar 

  • Roberts NA (2001) Treatment of influenza with neuraminidase inhibitors: virological implications. Philos Trans R Soc Lond B Biol Sci 356:1895–1897

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rogers GN, D’Souza BL (1989) Receptor binding properties of human and animal H1 influenza virus isolates. Virology 173:317–322

    PubMed  CAS  Google Scholar 

  • Rogers GN, Paulson JC (1983) Receptor determinants of human and animal influenza virus isolates: differences in receptor specificity of the H3 hemagglutinin based on species of origin. Virology 127:361–373

    PubMed  CAS  Google Scholar 

  • Rogers GN, Paulson JC, Daniels RS et al (1983) Single amino acid substitutions in influenza hemagglutinin change receptor binding specificity. Nature 304:76–78

    PubMed  CAS  Google Scholar 

  • Rolling T, Koerner I, Zimmermann P et al (2009) Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice. J Virol 83:6673–6680

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rudge JW, Coker R (2013) Human to human transmission of H7N9. BMJ: Brit Med J 347. BMJ 347:f4730 doi:10.1136/bmj.f4730

  • Ruigrok RW, Barge A, Durrer P et al (2000) Membrane interaction of influenza virus M1 protein. Virology 267:289–298

    PubMed  CAS  Google Scholar 

  • Russell CA, Jones TC, Barr IG et al (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science 320:340–346

    PubMed  CAS  Google Scholar 

  • Salvatore M, Basler CF, Parisien JP et al (2002) Effects of influenza A virus NS1 protein on protein expression: the NS1 protein enhances translation and is not required for shutoff of host protein synthesis. J Virol 76:1206–1212

    PubMed Central  PubMed  CAS  Google Scholar 

  • Sandie R, Aris-Brosou S (2014) Predicting the emergence of H3N2 influenza viruses reveals contrasted modes of evolution of HA and NA antigens. J Mol Evol 78:1–12

    PubMed  CAS  Google Scholar 

  • Sanz-Ezquerro JJ, de la Luna S, Ortin J et al (1995) Individual expression of influenza virus PA protein induces degradation of coexpressed proteins. J Virol 69:2420–2426

    PubMed Central  PubMed  CAS  Google Scholar 

  • Scheiffele P, Roth MG, Simons K (1997) Interaction of influenza virus haemmagglutinin with sphingolipid-cholesterol membrane domain via its transmembrane domain. EMBO J 16:5501–5508

    PubMed Central  PubMed  CAS  Google Scholar 

  • Scholtissek C (1990) Pigs as mixing vessels for the creation of new pandemic influenza A viruses. Med Principles Pract 2:65–71

    Google Scholar 

  • Scholtissek C (1995) Molecular evolution of influenza viruses. Virus Genes 11(2–3):209–215. doi:10.1007/BF01728660

    PubMed  CAS  Google Scholar 

  • Scholtissek C, Rohde W, von Hoyningen V, Rott R (1978) On the origin of the human influenza virus subtypes H2N2 and H3N2. Virology 87:13–20

    PubMed  CAS  Google Scholar 

  • Schultz U, Fitch WM, Ludwig S et al (1991) Evolution of pig influenza viruses. Virology 183:61–73

    PubMed  CAS  Google Scholar 

  • Shi B, Xia S, Yang GJ et al (2013c) Inferring the potential risks of H7N9 infection by spatiotemporally characterizing bird migration and poultry distribution in eastern. China Infect Dis Poverty 2:8. doi:10.1186/2049-9957-2-8

  • Shi J Z, Deng G H, Liu P H, et al (2013b) Isolation and characterization of H7N9 viruses from live poultry markets—Implication of the source of current H7N9 infection in humans. Chin Sci Bull doi:10.1007/s11434-013-5873-4

  • Shi Y, Zhang W, Wang F et al (2013a) Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses. Science 342(6155):243–247

    PubMed  CAS  Google Scholar 

  • Shinde V, Bridges CB, Uyeki TM et al (2009) Triple-reassortant swine influenza A (H1) in humans in the United States, 2005–2009. N Engl J Med 360(25):2616–2625

    PubMed  CAS  Google Scholar 

  • Shirogane Y, Watanabe S, Yanagi Y (2013) Cooperation: another mechanism of viral evolution. Trends Microbiol 21(7):320–324

    PubMed  CAS  Google Scholar 

  • Shortridge KF, Peiris JSM, Guan Y (2003) The next influenza pandemic: lessons from Hong Kong. Soc Appl Microbiol Symp Series 32:70–79

    Google Scholar 

  • Simonsen L, Viboud C, Grenfell B et al (2007) The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol Biol Evol 24(8):1811–1820

    PubMed  CAS  Google Scholar 

  • Smith GJD, Vijayakrishna D, Bahl J et al (2009) Origin and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122–1126

    PubMed  CAS  Google Scholar 

  • Solovyov A, Palacios G, Briese T et al (2009) Cluster analysis of the origins of the new influenza A (H1N1) virus. Euro Surveill 14(21):pii=19224

    Google Scholar 

  • Song D, Kang B, Lee C et al (2008) Transmission of avian influenza virus (H3N2) to dogs. Emerg Infect Dis 14:741–746

    PubMed Central  PubMed  Google Scholar 

  • Songserm T, Amonsin A, Jam-on R et al (2006) Fatal avian influenza A H5N1 in a dog. Emerg Infect Dis 12:1744–1747

    PubMed Central  PubMed  Google Scholar 

  • Steinhauer DA (2013) Influenza: pathways to human adaptation. Nature 499(7459):412–413

    PubMed  CAS  Google Scholar 

  • Stevens J, Blixt O, Glaser L et al (2006) Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol 355:1143–1155

    PubMed  CAS  Google Scholar 

  • Stower H (2014) Flu host evasion. Nat Rev Genet 15 doi:10.1038/nrg3639

  • Suarez DL (2000) Evolution of avian influenza viruses. Vet Microbiol 74:15–27

    PubMed  CAS  Google Scholar 

  • Suarez DL, Senne DA, Banks J et al (2004) Recombination resulting in virulence shift in avian influenza outbreak, Chile. Emerg Infect Dis 10:693–699

    PubMed Central  PubMed  CAS  Google Scholar 

  • Subbarao K, Klimov A, Katz J et al (1998) Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness. Science 279:393–396

    PubMed  CAS  Google Scholar 

  • Sugimura T, Yonemochi H, Ogawa T et al (1980) Isolation of a recombinant influenza virus (Hsw1 N2) from swine in Japan. Arch Virol 66:271–274

    PubMed  CAS  Google Scholar 

  • Sun X, Shi Y, Lu X et al (2013) Bat-derived influenza hemagglutinin H17 does not bind canonical avian or human receptors and most likely uses a unique entry mechanism. Cell Rep 3(3):769–778

    PubMed  CAS  Google Scholar 

  • Suzuki Y (2005) Sialobiology of influenza—molecular mechanism of host range variation of influenza viruses (review). Biol Pharm Bull 28:399–408

    PubMed  CAS  Google Scholar 

  • Suzuki Y, Nei M (2002) Origin and evolution of influenza virus haemagglutinin gene. Mol Bio Evol 19(4):501–509

    Google Scholar 

  • Swayne DE, Halvorson DA (2003) Influenza. In: Saif YM, Barnes HJ, Fadly AM, Glisson JR, McDougald LR, Swayne DE (eds) Diseases of poultry, 11th edn. Iowa State University Press, Ames, pp 135–160

    Google Scholar 

  • Swayne DE, Suarez DL (2000) Highly pathogenic avian influenza. Rev Sci Tech Int Epiz 19:463–482

    CAS  Google Scholar 

  • Tang RB, Chen HL (2013) An overview of the recent outbreaks of the avian-origin influenza A (H7N9) virus in the human. J Chin Med Assoc 76(5):245–248

    PubMed  Google Scholar 

  • Taubenberger JK, Kash JC (2010) Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7:440–451

    PubMed Central  PubMed  CAS  Google Scholar 

  • Tefsen B, Lu G, Zhu Y et al (2013) The N-terminal domain of PA from bat-derived influenza-like virus H17N10 has endonuclease activity. J Virol 27 Nov 2013 (Epub ahead of print)

    Google Scholar 

  • Thanawongnuwech R, Amonsin A, Tantilertcharoen R et al (2005) Probable tiger-to-tiger transmission of avian influenza H5N1. Emerg Infect Dis 11:699–701

    PubMed Central  PubMed  Google Scholar 

  • Thiry E, Zicola A, Addie D et al (2007) Highly pathogenic avian influenza H5N1 virus in cats and other carnivores. Vet Microbiol 122:25–31

    PubMed  CAS  Google Scholar 

  • Thontiravong A, Kitikoon P, Wannaratana S et al (2012) Quail as a potential mixing vessel for the generation of new reassortant influenza A viruses. Vet Microbiol 160(3–4):305–313

    PubMed  CAS  Google Scholar 

  • Thornley M (2004) Avian influenza ravages Thai tigers. Aust Vet J 82:652

    PubMed  Google Scholar 

  • To KKW, Ng KHL, Que T et al (2012) Avian influenza A H5N1 virus: a continuous threat to humans. Emerg Microbes Infect 1:e25

    PubMed Central  Google Scholar 

  • Tombari W, Paul M, Bettaieb J et al (2013) Risk factors and characteristics of low pathogenic avian influenza virus isolated from commercial poultry in Tunisia. PLoS ONE 2013; 8(1):e53524. doi:10.1371/journal.pone.0053524. (Epub 11 Jan 2013)

  • Tong S, Li Y, Rivailler P et al (2012) A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci USA 109:4269–4274

    PubMed Central  PubMed  CAS  Google Scholar 

  • Tong S, Zhu X, Li Y et al (2013) New world bats harbor diverse influenza A viruses. PLoS Pathog 9(10):e1003657. doi:10.1371/journal.ppat.1003657

    PubMed Central  PubMed  Google Scholar 

  • Tosh C, Murugkar HV, Nagarajan S et al (2011a) Emergence of amantadine-resistant avian influenza H5N1 virus in India. Virus Genes 42:10–15

    PubMed  CAS  Google Scholar 

  • Tosh C, Nagarajan S, Murugkar HV et al (2011b) Phylogenetic evidence of multiple introduction of H5N1 virus in Malda district of West Bengal, India in 2008. Vet Microbiol 148:132–139

    PubMed  CAS  Google Scholar 

  • Trifonov V, Khiabanian H, Rabadan R (2009) Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus. N Engl J Med 361:115–119

    PubMed  CAS  Google Scholar 

  • Tweed SA, Skowronski DM, David ST et al (2004) Human illness from avian influenza H7N3, British Columbia. Emerg Infect Dis 10:2196–2199

    PubMed Central  PubMed  Google Scholar 

  • Uyeki TM, Cox NJ (2013) Global concerns regarding novel influenza A (H7N9) virus infections. New Engl J Med 368(20):1862–1864. doi:10.1056/NEJMp1304661

    PubMed  CAS  Google Scholar 

  • van Riel D, Leijten LME, de Graaf M et al (2013) Novel avian-origin influenza A (H7N9) virus attaches to epithelium in both upper and lower respiratory tract of humans. Am J Pathol 183:1137–1143

    PubMed  Google Scholar 

  • Vana G, Westover K (2008) Origin of the 1918 Spanish influenza virus: a comparative genomic analysis. Mol Phylogenet Evol 3:1100–1110

    Google Scholar 

  • Wainwrighta S, Trevenneca C, Claesa F et al (2012) Highly pathogenic avian influenza in Mexico (H7N3): a significant threat to poultry production not to be underestimated. Empres Watch Vol 26. http://www.fao.org/docrep/016/an395e/an395e.pdf

  • Watanabe Y, Ibrahim MS, Suzuki Y et al (2012) The changing nature of avian influenza A virus (H5N1). Trends Microbiol 20(1):11–20

    PubMed  CAS  Google Scholar 

  • Rj Webby, Swenson SI, Krauss SL et al (2000) Evolution of swine H3N2 influenza viruses in the United States. J Virol 74:8243–8251

    Google Scholar 

  • Webster RG, Bean WJ, Gorman OT et al (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56(1):152–179

    PubMed Central  PubMed  CAS  Google Scholar 

  • Webster RG, Guo YJ (1991) New influenza virus in horses. Nature 351(6327):527

    Google Scholar 

  • Webster RG, Hinshaw VS, Bean WJ et al (1981) Characterization of an influenza A virus from seals. Virology 113:712–724

    PubMed  CAS  Google Scholar 

  • Webster RG, Hulse DJ (2004) Microbial adaptation and change: avian influenza. Rev Sci Tech 23:453–465

    PubMed  CAS  Google Scholar 

  • Wen YM, Klenk HD (2013) H7N9 avian influenza virus - search and re-search. Emerg Microbes Infect 2:e18

    PubMed Central  Google Scholar 

  • WHO (2005) Avian influenza A (H5N1) infection in humans. N Engl J Med 353:1374–1385

    Google Scholar 

  • WHO (2009) Preparing for the second wave: lessons from current outbreaks. http://www.who.int/csr/disease/swineflu/notes/h1n1_second_wave_20090828/en/index.html. Accessed 28 Aug 2009

  • WHO/OIE/FAO H5N1 Evolution Working Group (2009) Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2·2 viruses. Influenza Respir Viruses 3:59–62. doi:10.1111/j.1750-2659.2009.00078.x. http://onlinelibrary.wiley.com/doi/10.1111/j.1750-2659.2009.00078.x/abstract

  • WHO/OIE/FAO H5N1 Evolution Working Group (2012) Continued evolution of highly pathogenic avian influenza A (H5N1): updated nomenclature. Influenza Respir Viruses, 6:1–5. doi:10.1111/j.1750-2659.2011.00298.x. http://onlinelibrary.wiley.com/doi/10.1111/j.1750-2659.2011.00298.x/abstract

  • Wikramaratna PS, Sandeman M, Recker M et al (2013) The antigenic evolution of influenza: drift or thrift? Philos Trans Roy Soc B: Biol Sci 368(1614):20120200

    Google Scholar 

  • Wilks S, de Graaf M, Smith DJ et al (2012) A review of influenza haemagglutinin receptor binding as it relates to pandemic properties. Vaccine 30(29):4369–4376

    PubMed Central  PubMed  CAS  Google Scholar 

  • Wiwanitkit V (2013) H7N9 influenza: the emerging infectious disease. N Am J Med Sci 5(7):395–398

    PubMed Central  PubMed  Google Scholar 

  • Wu A, Su C, Wang D et al (2013) Sequential reassortments underlie diverse influenza H7N9 genotypes in China. Cell Host and Microbe 10.1016/j.chom.2013.09.001 Accessed 19 Sept 2013

  • Wu YL, Shen LW, Ding YP et al (2014) Preliminary success in the characterization and management of a sudden breakout of a novel H7N9 influenza A virus. Int J Biol Sci 10(1):109–118

    PubMed Central  PubMed  Google Scholar 

  • Xiong X, Martin SR, Haire LF et al (2013) Receptor binding by an H7N9 influenza virus from humans. Nature 499(7459):496–499. doi:10.1038/nature12372

    PubMed  CAS  Google Scholar 

  • Xu C, Havers F, Wang L et al (2013a) Monitoring avian influenza A(H7N9) virus through national influenza-like illness surveillance. China Emerg Infect Dis 19(8):1289–1292

    Google Scholar 

  • Xu KM, Li KS, Smith GJD et al (2007a) Evolution and molecular epidemiology of H9N2 influenza A viruses from quail in southern China, 2000–2005. J Virol 81:2635–2645

    PubMed Central  PubMed  CAS  Google Scholar 

  • Xu KM, Smith GJD, Bahl J et al (2007b) The genesis and evolution of H9N2 influenza viruses in poultry from Southern China, 2000–2005. J Virol 81:10389–10401

    PubMed Central  PubMed  CAS  Google Scholar 

  • Xu L, Bao L, Lv Q et al (2010) A single-amino-acid substitution in the HA protein changes the replication and pathogenicity of the 2009 pandemic A (H1N1) influenza viruses in vitro and in vivo. Virol J 7:325. doi:10.1186/1743-422X-7-325

    PubMed Central  PubMed  Google Scholar 

  • Xu X, Subbarao K, Cox NJ et al (1999) Genetic characterization of the pathogenic influenza A/Goose/Guangdong/1/96/(H5N1) virus: similarity of its haemagglutinin gene to those of H5N1 viruses from 1997 outbreaks in Hong Kong. Virology 261:15–19

    PubMed  CAS  Google Scholar 

  • Xu J, Davis CT, Christman MC et al (2012) Evolutionary history and phylodynamics of influenza A and B neuraminidase (NA) genes inferred from large-scale sequence analyses. PLoS ONE 7(7):e38665. doi:10.1371/journal.pone.0038665

    PubMed Central  PubMed  CAS  Google Scholar 

  • Xu L, Bao L, Yuan J et al (2013b) Antigenicity and transmissibility of a novel clade 2.3. 2.1 avian influenza H5N1 virus. J Gen Virol 94(12):2616–2626

    PubMed  CAS  Google Scholar 

  • Yamada S, Hatta M, Staker BL et al (2010) Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 6:e1001034. doi:10.1371/journal.ppat.1001034

    PubMed Central  PubMed  Google Scholar 

  • Yamada S, Suzuki Y, Suzuki T et al (2006) Hemagglutinin nutations responsible for the binding of H5N1 influenza A viruses to human-type receptors. Nature 444:378–382

    PubMed  CAS  Google Scholar 

  • Yamada Shinya K, Takada A et al (2012) Adaptation of a duck influenza A virus in quail. J Virol 86:1411–1420

    PubMed Central  PubMed  CAS  Google Scholar 

  • Yamayoshi S, Yamada S, Fukuyama S et al (2014) Virulence-affecting amino acid changes in the PA protein of H7N9 Influenza A viruses. J Virol 88(6):3127–3134. doi: 10.1128/JVI.03155-13

    Google Scholar 

  • Yang F, Wang J, Jiang L et al (2013) A fatal case caused by novel H7N9 avian influenza A virus in China. Emerg Microbes Infect 2:e19

    PubMed Central  Google Scholar 

  • Yu JE, Yoon H, Lee HJ et al (2011) Expression patterns of influenza virus receptors in the respiratory tracts of four species of poultry. J Vet Sci 12:7–13

    PubMed Central  PubMed  Google Scholar 

  • Yu H, Cowling BJ, Feng L et al (2013) Human infection with avian influenza A H7N9 virus: an assessment of clinical severity. Lancet 382(9887):138–145. doi:10.1016/S0140-6736(13)61207-6

    PubMed  Google Scholar 

  • Yuen KY, Wong SS (2005) Human infection by avian influenza A H5N1. Hong Kong Med J 11:189–199

    PubMed  CAS  Google Scholar 

  • Zeitlin G, Maslow M (2005) Avian influenza. Curr Infect Dis Rep 7:193–199

    PubMed  Google Scholar 

  • Zell R, Bergmann S, Krumbholz A et al (2008a) Ongoing evolution of swine influenza viruses: a novel reassortant. Arch Virol 153:2085–2092

    PubMed  CAS  Google Scholar 

  • Zell R, Motzke S, Krumbholz A et al (2008b) Novel reassortant of swine influenza H1N2 virus in Germany. J Gen Virol 89:271–276

    PubMed  CAS  Google Scholar 

  • Zell R, Scholtissek C, Ludwig S (2013) Genetics, evolution, and the zoonotic capacity of European Swine influenza viruses. Curr Top Microbiol Immunol 370:29–55. doi:10.1007/82_2012_267

    PubMed  Google Scholar 

  • Zhang H, Hale BG, Xu K et al (2013) Viral and host factors required for avian H5N1 influenza A virus replication in mammalian cells. Viruses 5(6):1431–1446

    PubMed Central  PubMed  Google Scholar 

  • Zhang H, Li X, Guo J et al (2014) The PB2 E627 K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. J Gen Virol. doi:10.1099/vir.0.061721-0

    Google Scholar 

  • Zhou NN, Senne DA, Landgraf JS et al (1999) Genetic reassotment of avian, swine and human influenza A viruses in American pigs. J Virol 73:8851–8856

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhu X, Yang H, Guo Z et al (2012) Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site. Proc Natl Acad Sci USA 109:18903–18908

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhu X, Yu W, McBride R et al (2013) Hemagglutinin homologue from H17N10 bat influenza virus exhibits divergent receptor-binding and pH-dependent fusion activities. Proc Natl Acad Sci USA 110(4):1458–1463

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhuang QY, Wang SC, Wu ML et al (2013) Epidemiological and risk analysis of the H7N9 subtype influenza outbreak in China at its early stage. Chin Sci Bull 58:3183–3187. doi:10.1007/s11434-013-5880-5

    CAS  Google Scholar 

  • Zimmer SM, Burke DS (2009) Historical perspective—emergence of influenza A (H1N1) viruses. N Engl J Med 361:279–284

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Veterinary Microbiology, LLR University of Veterinary and Animal Sciences, Hisar, 125004, Haryana, India

    Sanjay Kapoor

  2. Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, 243122, Uttar Pradesh, India

    Kuldeep Dhama

Authors
  1. Sanjay Kapoor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kuldeep Dhama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sanjay Kapoor .

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Kapoor, S., Dhama, K. (2014). Evolution of Influenza Viruses. In: Insight into Influenza Viruses of Animals and Humans. Springer, Cham. https://doi.org/10.1007/978-3-319-05512-1_4

Download citation

Publish with us

Policies and ethics

Search

Navigation