Advertisement

Reverse Genetics of Influenza B Viruses

  • Aitor Nogales
  • Daniel R. Perez
  • Jefferson Santos
  • Courtney Finch
  • Luis Martínez-SobridoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1602)

Abstract

Annual influenza epidemics are caused not only by influenza A viruses but also by influenza B viruses. Initially established for the generation of recombinant influenza A viruses, plasmid-based reverse genetics techniques have allowed researchers the generation of wild type and mutant viruses from full-length cDNA copies of the influenza viral genome. These reverse genetics approaches have allowed researchers to answer important questions on the biology of influenza viruses by genetically engineering infectious recombinant viruses. This has resulted in a better understanding of the molecular biology of influenza viruses, including both viral and host factors required for genome replication and transcription. With the ability to generate recombinant viruses containing specific mutations in the viral genome, these reverse genetics tools have also allowed the identification of viral and host factors involved in influenza pathogenesis, transmissibility, host-range interactions and restrictions, and virulence. Likewise, reverse genetics techniques have been used for the implementation of inactivated or live-attenuated influenza vaccines and the identification of anti-influenza drugs and their mechanism of antiviral activity. In 2002, these reverse genetics approaches allowed also the recovery of recombinant influenza B viruses entirely from plasmid DNA. In this chapter we describe the cloning of influenza B/Brisbane/60/2008 viral RNAs into the ambisense pDP-2002 plasmid and the experimental procedures for the successful generation of recombinant influenza B viruses.

Key words

Influenza B virus Plasmid-based reverse genetics Virus rescue approaches Recombinant influenza B virus Ambisense plasmids 

Notes

Acknowledgments

Influenza B research to L.M.-S. was partially funded by the 2014 University of Rochester Research Award. J.S. and D.R.P. are funded by start-up funds from the University of Georgia and by NIH contract HHSN272201400008C.

References

  1. 1.
    Palese PS, Shaw ML (2007) orthomyxoviridae: the viruses and their replication. In: Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA (eds) Fields virology, 5th edn. Lippincott Williams and Wilkins, USAGoogle Scholar
  2. 2.
    Molinari NA, Ortega-Sanchez IR, Messonnier ML, Thompson WW, Wortley PM, Weintraub E, Bridges CB (2007) The annual impact of seasonal influenza in the US: measuring disease burden and costs. Vaccine 25(27):5086–5096. doi: 10.1016/j.vaccine.2007.03.046 CrossRefPubMedGoogle Scholar
  3. 3.
    Chen R, Holmes EC (2008) The evolutionary dynamics of human influenza B virus. J Mol Evol 66(6):655–663. doi: 10.1007/s00239-008-9119-z CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Osterhaus AD, Rimmelzwaan GF, Martina BE, Bestebroer TM, Fouchier RA (2000) Influenza B virus in seals. Science 288(5468):1051–1053CrossRefPubMedGoogle Scholar
  5. 5.
    Garcia-Sastre A (2006) Antiviral response in pandemic influenza viruses. Emerg Infect Dis 12(1):44–47. doi: 10.3201/eid1201.051186 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kilbourne ED (2006) Influenza pandemics of the 20th century. Emerg Infect Dis 12(1):9–14. doi: 10.3201/eid1201.051254 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Thompson WW, Shay DK, Weintraub E, Brammer L, Cox N, Anderson LJ, Fukuda K (2003) Mortality associated with influenza and respiratory syncytial virus in the United States. JAMA 289(2):179–186CrossRefPubMedGoogle Scholar
  8. 8.
    Li WC, Shih SR, Huang YC, Chen GW, Chang SC, Hsiao MJ, Tsao KC, Lin TY (2008) Clinical and genetic characterization of severe influenza B-associated diseases during an outbreak in Taiwan. J Clin Virol 42(1):45–51. doi: 10.1016/j.jcv.2007.11.026 CrossRefPubMedGoogle Scholar
  9. 9.
    Hite LK, Glezen WP, Demmler GJ, Munoz FM (2007) Medically attended pediatric influenza during the resurgence of the Victoria lineage of influenza B virus. Int J Infect Dis 11(1):40–47. doi: 10.1016/j.ijid.2005.10.008 CrossRefPubMedGoogle Scholar
  10. 10.
    Brotherton JM, Delpech VC, Gilbert GL, Hatzi S, Paraskevopoulos PD, McAnulty JM (2003) A large outbreak of influenza A and B on a cruise ship causing widespread morbidity. Epidemiol Infect 130(2):263–271CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    CDC (2001) From the Centers for Disease Control and Prevention. Influenza B virus outbreak in a cruise ship—Northern Europe, 2000. JAMA 285(14):1833–1834Google Scholar
  12. 12.
    DeStefano F (1982) An outbreak of influenza B at an Indiana boarding school: estimate of vaccine efficacy. Public Health Rep 97(3):269–272PubMedPubMedCentralGoogle Scholar
  13. 13.
    Fayinka OA, Balayan MS, Kirya GB, Rugyendo W (1977) An outbreak of influenza B in a closed community school in Uganda. East Afr Med J 54(1):6–8PubMedGoogle Scholar
  14. 14.
    Gordon Smith CE, Thomson WG (1956) An outbreak of influenza due to type B virus in a residential boys' school in Malaya. Med J Malaya 10(4):332–337PubMedGoogle Scholar
  15. 15.
    Liu PY, Wang LC, Lin YH, Tsai CA, Shi ZY (2009) Outbreak of influenza A and B among military recruits: evidence from viral culture and polymerase chain reaction. J Microbiol Immunol Infect 42(2):114–121PubMedGoogle Scholar
  16. 16.
    Mall S, Buchholz U, Tibussek D, Jurke A, An der Heiden M, Diedrich S, Schweiger B, Alpers K (2011) A large outbreak of influenza B-associated benign acute childhood myositis in Germany, 2007/2008. Pediatr Infect Dis J 30(8):e142–e146. doi: 10.1097/INF.0b013e318217e35600006454-201108000-00034. [pii]CrossRefPubMedGoogle Scholar
  17. 17.
    Karpathios T, Kostaki M, Drakonaki S, Garoufi A, Siahanidou S, Spirou N, Theodoridis C (1995) An epidemic with influenza B virus causing benign acute myositis in ten boys and two girls. Eur J Pediatr 154(4):334–336CrossRefPubMedGoogle Scholar
  18. 18.
    Dietzman DE, Schaller JG, Ray CG, Reed ME (1976) Acute myositis associated with influenza B infection. Pediatrics 57(2):255–258PubMedGoogle Scholar
  19. 19.
    Treanor JJ (2009) Influenza viruses, including avian influenza and swine influenza. Mandell, Douglas, and Bennett’s principles and practice of infectious diseases, 7th edn. Elsevier, OrlandoGoogle Scholar
  20. 20.
    Newland JG, Romero JR, Varman M, Drake C, Holst A, Safranek T, Subbarao K (2003) Encephalitis associated with influenza B virus infection in 2 children and a review of the literature. Clin Infect Dis 36(7):e87–e95. doi: 10.1086/368184 CrossRefPubMedGoogle Scholar
  21. 21.
    McCullers JA, Facchini S, Chesney PJ, Webster RG (1999) Influenza B virus encephalitis. Clin Infect Dis 28(4):898–900. doi: 10.1086/515214 CrossRefPubMedGoogle Scholar
  22. 22.
    Paddock CD, Liu L, Denison AM, Bartlett JH, Holman RC, Deleon-Carnes M, Emery SL, Drew CP, Shieh WJ, Uyeki TM, Zaki SR (2012) Myocardial injury and bacterial pneumonia contribute to the pathogenesis of fatal influenza B virus infection. J Infect Dis 205(6):895–905. doi:jir861 [pii]10.1093/infdis/jir861CrossRefPubMedGoogle Scholar
  23. 23.
    Wright P, Nuemann G, Kawaoka Y (2007) Orthomhxoviruses. Fields virology, 5th edn. Lippincott Williams & Wilkins, PhiladelphiaGoogle Scholar
  24. 24.
    Parola P, Colson P, Dubourg G, Million M, Charrel R, Minodier P, Raoult D (2011) Letter to the editor. Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England. Euro Surveill 16(11)Google Scholar
  25. 25.
    Scaber J, Saeed S, Ihekweazu C, Efstratiou A, McCarthy N, O’Moore E (2011) Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England. Euro Surveill 16(5)Google Scholar
  26. 26.
    Pica N, Chou YY, Bouvier NM, Palese P (2012) Transmission of influenza B viruses in the guinea pig. J Virol 86(8):4279–4287. doi:JVI.06645-11 [pii]10.1128/JVI.06645-11CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Stebbins S, Cummings DA, Stark JH, Vukotich C, Mitruka K, Thompson W, Rinaldo C, Roth L, Wagner M, Wisniewski SR, Dato V, Eng H, Burke DS (2011) Reduction in the incidence of influenza A but not influenza B associated with use of hand sanitizer and cough hygiene in schools: a randomized controlled trial. Pediatr Infect Dis J 30(11):921–926. doi: 10.1097/INF.0b013e3182218656 CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Grohskopf LA, Olsen SJ, Sokolow LZ, Bresee JS, Cox NJ, Broder KR, Karron RA, Walter EB (2014) Centers for Disease C, Prevention and control of seasonal influenza with vaccines: recommendations of the Advisory Committee on Immunization Practices (ACIP)—United States, 2014-15 influenza season. MMWR Morb Mortal Wkly Rep 63(32):691–697PubMedGoogle Scholar
  29. 29.
    Palese P, Shaw M (2007) Orthomyxoviridae: the viruses and their replication. Lippincott Williams & Wilkins, PhiladelphiaGoogle Scholar
  30. 30.
    Stoeckle MY, Shaw MW, Choppin PW (1987) Segment-specific and common nucleotide sequences in the noncoding regions of influenza B virus genome RNAs. Proc Natl Acad Sci U S A 84(9):2703–2707CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Baker SF, Nogales A, Finch C, Tuffy KM, Domm W, Perez DR, Topham DJ, Martinez-Sobrido L (2014) Influenza A and B virus intertypic reassortment through compatible viral packaging signals. J Virol 88(18):10778–10791. doi: 10.1128/JVI.01440-14 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Jackson D, Elderfield RA, Barclay WS (2011) Molecular studies of influenza B virus in the reverse genetics era. J Gen Virol 92(Pt 1):1–17. doi: 10.1099/vir.0.026187-0 CrossRefPubMedGoogle Scholar
  33. 33.
    McCullers JA, Saito T, Iverson AR (2004) Multiple genotypes of influenza B virus circulated between 1979 and 2003. J Virol 78(23):12817–12828. doi: 10.1128/JVI.78.23.12817-12828.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Kanegae Y, Sugita S, Endo A, Ishida M, Senya S, Osako K, Nerome K, Oya A (1990) Evolutionary pattern of the hemagglutinin gene of influenza B viruses isolated in Japan: cocirculating lineages in the same epidemic season. J Virol 64(6):2860–2865PubMedPubMedCentralGoogle Scholar
  35. 35.
    Simonsen L, Spreeuwenberg P, Lustig R, Taylor RJ, Fleming DM, Kroneman M, Van Kerkhove MD, Mounts AW, Paget WJ, Teams GLC (2013) Global mortality estimates for the 2009 Influenza Pandemic from the GLaMOR project: a modeling study. PLoS Med 10(11):e1001558. doi: 10.1371/journal.pmed.1001558 CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Taubenberger JK, Kash JC (2010) Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7(6):440–451. doi: 10.1016/j.chom.2010.05.009 CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Yen HL, Webster RG (2009) Pandemic influenza as a current threat. Curr Top Microbiol Immunol 333:3–24. doi: 10.1007/978-3-540-92165-3_1 PubMedGoogle Scholar
  38. 38.
    Neumann G, Watanabe T, Ito H, Watanabe S, Goto H, Gao P, Hughes M, Perez DR, Donis R, Hoffmann E, Hobom G, Kawaoka Y (1999) Generation of influenza A viruses entirely from cloned cDNAs. Proc Natl Acad Sci U S A 96(16):9345–9350CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Fodor E, Devenish L, Engelhardt OG, Palese P, Brownlee GG, Garcia-Sastre A (1999) Rescue of influenza A virus from recombinant DNA. J Virol 73(11):9679–9682PubMedPubMedCentralGoogle Scholar
  40. 40.
    Jackson D, Cadman A, Zurcher T, Barclay WS (2002) A reverse genetics approach for recovery of recombinant influenza B viruses entirely from cDNA. J Virol 76(22):11744–11747CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Hoffmann E, Mahmood K, Yang CF, Webster RG, Greenberg HB, Kemble G (2002) Rescue of influenza B virus from eight plasmids. Proc Natl Acad Sci U S A 99(17):11411–11416. doi: 10.1073/pnas.172393399 CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Martinez-Sobrido L, Garcia-Sastre A (2010) Generation of recombinant influenza virus from plasmid DNA. J Vis Exp (42). doi: 10.3791/2057
  43. 43.
    Engelhardt OG (2013) Many ways to make an influenza virus--review of influenza virus reverse genetics methods. Influenza Other Respir Viruses 7(3):249–256. doi: 10.1111/j.1750-2659.2012.00392.x CrossRefPubMedGoogle Scholar
  44. 44.
    Nogales A, Baker SF, Ortiz-Riano E, Dewhurst S, Topham DJ, Martinez-Sobrido L (2014) influenza a virus attenuation by codon deoptimization of the NS gene for vaccine development. J Virol 88(18):10525–10540. doi: 10.1128/JVI.01565-14 CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Nogales A, Baker SF, Martinez-Sobrido L (2014) Replication-competent influenza A viruses expressing a red fluorescent protein. Virology 476C:206–216. doi: 10.1016/j.virol.2014.12.006 Google Scholar
  46. 46.
    Martinez-Sobrido L, Cadagan R, Steel J, Basler CF, Palese P, Moran TM, Garcia-Sastre A (2010) Hemagglutinin-pseudotyped green fluorescent protein-expressing influenza viruses for the detection of influenza virus neutralizing antibodies. J Virol 84(4):2157–2163. doi: 10.1128/JVI.01433-09 CrossRefPubMedGoogle Scholar
  47. 47.
    Nogales A, Baker SF, Domm W, Martinez-Sobrido L (2015) Development and applications of single-cycle infectious influenza A virus (sciIAV). Virus Res. doi: 10.1016/j.virusres.2015.07.013 Google Scholar
  48. 48.
    Hoffmann E, Neumann G, Kawaoka Y, Hobom G, Webster RG (2000) A DNA transfection system for generation of influenza A virus from eight plasmids. Proc Natl Acad Sci U S A 97(11):6108–6113. doi: 10.1073/pnas.100133697 CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    DuBridge RB, Tang P, Hsia HC, Leong PM, Miller JH, Calos MP (1987) Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system. Mol Cell Biol 7(1):379–387CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Heix J, Grummt I (1995) Species specificity of transcription by RNA polymerase I. Curr Opin Genet Dev 5(5):652–656CrossRefPubMedGoogle Scholar
  51. 51.
    Ortiz-Riano E, Cheng BY, Carlos de la Torre J, Martinez-Sobrido L (2013) Arenavirus reverse genetics for vaccine development. J Gen Virol 94(Pt 6):1175–1188. doi: 10.1099/vir.0.051102-0 CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Nerome K, Kumihashi H, Nerome R, Hiromoto Y, Yokota Y, Ueda R, Omoe K, Chiba M (1999) Evaluation of immune responses to inactivated influenza vaccines prepared in embryonated chicken eggs and MDCK cells in a mouse model. Dev Biol Stand 98:53–63. discussion 73–74PubMedGoogle Scholar
  53. 53.
    Gupta SK, Haigh BJ, Griffin FJ, Wheeler TT (2013) The mammalian secreted RNases: mechanisms of action in host defence. Innate Immun 19(1):86–97. doi: 10.1177/1753425912446955 CrossRefPubMedGoogle Scholar
  54. 54.
    Gaush CR, Smith TF (1968) Replication and plaque assay of influenza virus in an established line of canine kidney cells. Appl Microbiol 16(4):588–594PubMedPubMedCentralGoogle Scholar
  55. 55.
    Baker SF, Guo H, Albrecht RA, Garcia-Sastre A, Topham DJ, Martinez-Sobrido L (2013) protection against lethal influenza with a viral mimic. J Virol 87(15):8591–8605. doi: 10.1128/JVI.01081-13 CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Reed LJM, H. (1938) A simple method of estimating fifty percent endpoints. Am J Hygiene 27:493–497Google Scholar
  57. 57.
    Quinlivan M, Zamarin D, Garcia-Sastre A, Cullinane A, Chambers T, Palese P (2005) Attenuation of equine influenza viruses through truncations of the NS1 protein. J Virol 79(13):8431–8439. doi: 10.1128/JVI.79.13.8431-8439.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Skehel JJ, Hay AJ (1978) Nucleotide sequences at the 5' termini of influenza virus RNAs and their transcripts. Nucleic Acids Res 5(4):1207–1219CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Massin P, Rodrigues P, Marasescu M, van der Werf S, Naffakh N (2005) Cloning of the chicken RNA polymerase I promoter and use for reverse genetics of influenza A viruses in avian cells. J Virol 79(21):13811–13816. doi: 10.1128/JVI.79.21.13811-13816.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Murakami S, Horimoto T, Yamada S, Kakugawa S, Goto H, Kawaoka Y (2008) Establishment of canine RNA polymerase I-driven reverse genetics for influenza A virus: its application for H5N1 vaccine production. J Virol 82(3):1605–1609. doi: 10.1128/JVI.01876-07 CrossRefPubMedGoogle Scholar
  61. 61.
    Wang Z, Duke GM (2007) Cloning of the canine RNA polymerase I promoter and establishment of reverse genetics for influenza A and B in MDCK cells. Virol J 4:102. doi: 10.1186/1743-422X-4-102 CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Murakami S, Horimoto T, Ito M, Takano R, Katsura H, Shimojima M, Kawaoka Y (2012) Enhanced growth of influenza vaccine seed viruses in vero cells mediated by broadening the optimal pH range for virus membrane fusion. J Virol 86(3):1405–1410. doi: 10.1128/JVI.06009-11 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Aitor Nogales
    • 1
  • Daniel R. Perez
    • 2
  • Jefferson Santos
    • 2
  • Courtney Finch
    • 3
  • Luis Martínez-Sobrido
    • 1
    Email author
  1. 1.Department of Microbiology and ImmunologyUniversity of Rochester School of Medicine and DentistryRochesterUSA
  2. 2.Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary MedicineUniversity of GeorgiaAthensUSA
  3. 3.Division of Viral ProductsOffice of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug AdministrationSilver SpringUSA

Personalised recommendations