1887

Abstract

Seasonal influenza viruses circulating between 1918 and 2009 harboured two prevalent genetic variations in the NS1 coding region. A glutamic acid (E)-to-lysine (K) exchange at position 196 was reported to diminish the capacity of NS1 to control interferon induction. Furthermore, alterations at position 231 determine a carboxy-terminal extension of seven amino acids from 230 to 237 residues. Sequence analyses of NS1 of the last 90 years suggest that variations at these two positions are functionally linked. To determine the impact of the two positions on viral replication , we used a mouse-adapted variant of A/Hong Kong/01/68 (maHK68) (H3N2). maHK68 encodes an NS1 of 237 amino acids with lysine at position 196. A panel of recombinant maHK68 viruses was generated encoding NS1 variants that differed at positions 196 and 231. Our analyses showed a clear effect of the K-196-to-E exchange on interferon induction and virus virulence. These effects were further modulated by the loss of the seven-amino-acid extension. We propose that the combination of NS1 E-196 with the short C-terminal variant conferred a fitness advantage that is reflected by increased virulence . Notably, this particular NS1 constellation was observed for the pandemic 1918 H1N1 virus.

Funding
This study was supported by the:
  • Georg Kochs , Deutsche Forschungsgemeinschaft , (Award KO 1579/5-2)
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001422
2020-05-14
2020-06-04
Loading full text...

Full text loading...

/deliver/fulltext/jgv/10.1099/jgv.0.001422/jgv001422.html?itemId=/content/journal/jgv/10.1099/jgv.0.001422&mimeType=html&fmt=ahah

References

  1. Taubenberger JK, Kash JC. Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 2010; 7:440–451 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Buonagurio DA, Nakada S, Parvin JD, Krystal M, Palese P et al. Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in NS gene. Science 1986; 232:980–982 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Ludwig S, Schultz U, Mandler J, Fitch WM, Scholtissek C. Phylogenetic relationship of the nonstructural (NS) genes of influenza A viruses. Virology 1991; 183:566–577 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Kawaoka Y, Krauss S, Webster RG. Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics. J Virol 1989; 63:4603–4608 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Scholtissek C, Rohde W, Von Hoyningen V, Rott R. On the origin of the human influenza virus subtypes H2N2 and H3N2. Virology 1978; 87:13–20 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Wendel I, Matrosovich M, Klenk HD. Snapshot: evolution of human influenza A viruses. Cell Host Microbe 2015a; 17:416–416.e1 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Neumann G, Kawaoka Y. Host range restriction and pathogenicity in the context of influenza pandemic. Emerg Infect Dis 2006; 12:881–886 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Ayllon J, García-Sastre A. The NS1 protein: a multitasking virulence factor. Curr Top Microbiol Immunol 2015; 386:73–107 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Gack MU, Albrecht RA, Urano T, Inn K-S, Huang I-C et al. Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Cell Host Microbe 2009; 5:439–449 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Krug RM. Functions of the influenza A virus NS1 protein in antiviral defense. Curr Opin Virol 2015; 12:1–6 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J et al. Influenza virus infection causes global RNAPII termination defects. Nat Struct Mol Biol 2018; 25:885–893 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. García-Sastre A, Egorov A, Matassov D, Brandt S, Levy DE et al. Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. Virology 1998; 252:324–330 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Kochs G, Martínez-Sobrido L, Lienenklaus S, Weiss S, García-Sastre A et al. Strong interferon-inducing capacity of a highly virulent variant of influenza A virus strain PR8 with deletions in the NS1 gene. J Gen Virol 2009; 90:2990–2994 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Bornholdt ZA, Prasad BVV. X-Ray structure of NS1 from a highly pathogenic H5N1 influenza virus. Nature 2008; 456:985–988 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Hale BG. Conformational plasticity of the influenza A virus NS1 protein. J Gen Virol 2014; 95:2099–2105 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Donelan NR, Basler CF, García-Sastre A. A recombinant influenza A virus expressing an RNA-binding-defective NS1 protein induces high levels of beta interferon and is attenuated in mice. J Virol 2003; 77:13257–13266 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Steidle S, Martínez-Sobrido L, Mordstein M, Lienenklaus S, García-Sastre A et al. Glycine 184 in nonstructural protein NS1 determines the virulence of influenza A virus strain PR8 without affecting the host interferon response. J Virol 2010; 84:12761–12770 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Wang W, Riedel K, Lynch P, Chien CY, Montelione GT et al. RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids. RNA 1999; 5:195–205 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. Muñoz-Moreno R, Martínez-Romero C, Blanco-Melo D, Forst CV, Nachbagauer R et al. Viral fitness landscapes in diverse host species reveal multiple evolutionary lines for the NS1 gene of influenza A viruses. Cell Rep 2019; 29:3997–4009 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  20. Lohrmann F, Dijkman R, Stertz S, Thiel V, Haller O et al. Emergence of a C-terminal seven-amino-acid elongation of NS1 in around 1950 conferred a minor growth advantage to former seasonal influenza A viruses. J Virol 2013; 87:11300–11303 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  21. Westgeest KB, Russell CA, Lin X, Spronken MIJ, Bestebroer TM et al. Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011. J Virol 2014; 88:2844–2857 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  22. Kuo R-L, Zhao C, Malur M, Krug RM. Influenza A virus strains that circulate in humans differ in the ability of their NS1 proteins to block the activation of IRF3 and interferon-β transcription. Virology 2010; 408:146–158 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  23. Brown EG, Liu H, Kit LC, Baird S, Nesrallah M. Pattern of mutation in the genome of influenza A virus on adaptation to increased virulence in the mouse lung: identification of functional themes. Proc Natl Acad Sci U S A 2001; 98:6883–6888 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  24. Wendel I, Rubbenstroth D, Doedt J, Kochs G, Wilhelm J et al. The avian-origin PB1 gene segment facilitated replication and transmissibility of the H3N2/1968 pandemic influenza virus. J Virol 2015b; 89:4170–4179 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Haller O, Arnheiter H, Gresser I, Lindenmann J. Genetically determined, interferon-dependent resistance to influenza virus in mice. J Exp Med 1979; 149:601–612 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Hoffmann E, Neumann G, Kawaoka Y, Hobom G, Webster RG. A DNA transfection system for generation of influenza A virus from eight plasmids. Proc Natl Acad Sci U S A 2000; 97:6108–6113 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. Site-Directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 1989; 77:51–59 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Grimm D, Staeheli P, Hufbauer M, Koerner I, Martínez-Sobrido L et al. Replication fitness determines high virulence of influenza A virus in mice carrying functional Mx1 resistance gene. Proc Natl Acad Sci U S A 2007; 104:6806–6811 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  29. Staeheli P, Grob R, Meier E, Sutcliffe JG, Haller O. Influenza virus-susceptible mice carry Mx genes with a large deletion or a nonsense mutation. Mol Cell Biol 1988; 8:4518–4523 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  30. Staeheli P, Dreiding P, Haller O, Lindenmann J. Polyclonal and monoclonal antibodies to the interferon-inducible protein Mx of influenza virus-resistant mice. J Biol Chem 1985; 260:1821–1825[PubMed][PubMed]
    [Google Scholar]
  31. Mordstein M, Kochs G, Dumoutier L, Renauld J-C, Paludan SR et al. Interferon-lambda contributes to innate immunity of mice against influenza A virus but not against hepatotropic viruses. PLoS Pathog 2008; 4:e1000151 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Reed LJ, Muench H. A simple method of estimating fifty percent endpoints. Am J Hyg 1938; 27:493–497
    [Google Scholar]
  33. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L et al. The influenza virus resource at the National center for biotechnology information. J Virol 2008; 82:596–601 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  35. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19:1572–1574 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  36. Salomon R, Staeheli P, Kochs G, Yen H-L, Franks J et al. Mx1 gene protects mice against the highly lethal human H5N1 influenza virus. Cell Cycle 2007; 6:2417–2421 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  37. Tumpey TM, Szretter KJ, Van Hoeven N, Katz JM, Kochs G et al. The Mx1 gene protects mice against the pandemic 1918 and highly lethal human H5N1 influenza viruses. J Virol 2007; 81:10818–10821 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  38. Lienenklaus S, Cornitescu M, Zietara N, Łyszkiewicz M, Gekara N et al. Novel reporter mouse reveals constitutive and inflammatory expression of IFN-beta in vivo. J Immunol 2009; 183:3229–3236 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  39. Staeheli P, Haller O, Boll W, Lindenmann J, Weissmann C. Mx protein: constitutive expression in 3T3 cells transformed with cloned Mx cDNA confers selective resistance to influenza virus. Cell 1986; 44:147–158 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  40. Bouvier NM, Lowen AC. Animal models for influenza virus pathogenesis and transmission. Viruses 2010; 2:1530–1563 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  41. Ping J, Dankar SK, Forbes NE, Keleta L, Zhou Y et al. PB2 and hemagglutinin mutations are major determinants of host range and virulence in mouse-adapted influenza A virus. J Virol 2010; 84:10606–10618 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  42. Gabriel G, Herwig A, Klenk H-D. Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. PLoS Pathog 2008; 4:e11 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  43. Albo C, Valencia A, Portela A. Identification of an RNA binding region within the N-terminal third of the influenza A virus nucleoprotein. J Virol 1995; 69:3799–3806 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  44. Kong W, Liu L, Wang Y, He Q, Wu S et al. C-Terminal elongation of NS1 of H9N2 influenza virus induces a high level of inflammatory cytokines and increases transmission. J Gen Virol 2015; 96:259–268 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  45. Noah DL, Twu KY, Krug RM. Cellular antiviral responses against influenza A virus are countered at the posttranscriptional level by the viral NS1A protein via its binding to a cellular protein required for the 3' end processing of cellular pre-mRNAS. Virology 2003; 307:386–395 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  46. Wang X, Basler CF, Williams BRG, Silverman RH, Palese P et al. Functional replacement of the carboxy-terminal two-thirds of the influenza A virus NS1 protein with short heterologous dimerization domains. J Virol 2002; 76:12951–12962 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  47. Aramini JM, Ma L-C, Zhou L, Schauder CM, Hamilton K et al. Dimer interface of the effector domain of non-structural protein 1 from influenza A virus: an interface with multiple functions. J Biol Chem 2011; 286:26050–26060 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  48. Bornholdt ZA, Prasad BVV. X-Ray structure of influenza virus NS1 effector domain. Nat Struct Mol Biol 2006; 13:559–560 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  49. Kerry PS, Ayllon J, Taylor MA, Hass C, Lewis A et al. A transient homotypic interaction model for the influenza A virus NS1 protein effector domain. PLoS One 2011; 6:e17946 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  50. Xia S, Monzingo AF, Robertus JD. Structure of NS1A effector domain from the influenza A/Udorn/72 virus. Acta Crystallogr D Biol Crystallogr 2009; 65:11–17 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  51. Melén K, Kinnunen L, Fagerlund R, Ikonen N, Twu KY et al. Nuclear and nucleolar targeting of influenza A virus NS1 protein: striking differences between different virus subtypes. J Virol 2007; 81:5995–6006 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  52. Marión RM, Zürcher T, de la Luna S, Ortín J. Influenza virus NS1 protein interacts with viral transcription-replication complexes in vivo. J Gen Virol 1997; 78:2447–2451 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  53. Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S et al. Large-Scale sequence analysis of avian influenza isolates. Science 2006; 311:1576–1580 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  54. Marazzi I, Ho JSY, Kim J, Manicassamy B, Dewell S et al. Suppression of the antiviral response by an influenza histone mimic. Nature 2012; 483:428–433 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  55. Hutchinson EC, Denham EM, Thomas B, Trudgian DC, Hester SS et al. Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry. PLoS Pathog 2012; 8:e1002993 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  56. Kochs G, García-Sastre A, Martínez-Sobrido L. Multiple anti-interferon actions of the influenza A virus NS1 protein. J Virol 2007; 81:7011–7021 [CrossRef][PubMed][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001422
Loading
/content/journal/jgv/10.1099/jgv.0.001422
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error