Self-replicating RNA

Methods in Molecular Biology

Volumn 1499, Issue , 2017, Pages 15-35

  Tews, Birke Andrea ^a   Meyers, Gregor ^a  

^a FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

Author keywords

Alphavirus; Classical swine fever virus; Flavivirus; Pestivirus; Positive strand RNA virus; Self replicating RNA

Indexed keywords

COMPLEMENTARY DNA; GENOMIC RNA; RECOMBINANT RNA; RNA VACCINE; VIRUS RNA; VIRUS VACCINE; VIRUS VECTOR; VACCINE;

ALPHAVIRUS; CORONAVIRIDAE; FLAVIVIRIDAE; FLAVIVIRUS; GENE EXPRESSION; GENE MAPPING; NONHUMAN; PESTIVIRUS; REPLICON; REVERSE GENETICS; RNA REPLICATION; TOGAVIRIDAE; VACCINATION; VIRUS GENOME; VIRUS PARTICLE; VIRUS STRAIN; ANIMAL; GENETICS; HUMAN; IMMUNOLOGY; RNA VIRUS;

ANIMALS; HUMANS; REPLICON; RNA VIRUSES; RNA, VIRAL; VACCINES;

EID: 85007236147     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6481-9_2     Document Type: Chapter

References (83)

1. Colter JS, Bird HH, Brown RA (1957) Infectivity of ribonucleic acid from Ehrlich ascites tumour cells infected with Mengo encephalitis. Nature 179(4565):859–860
2. Colter JS, Bird HH, Moyer AW, Brown RA (1957) Infectivity of ribonucleic acid isolated from virus-infected tissues. Virology 4(3):522–532
3. Sprunt K, Redman WM, Alexander HE (1959) Infectious ribonucleic acid derived from enteroviruses. Proc Soc Exp Biol Med Soc Exp Biol Med 101:604–608
4. Holland JJ, Hoyer BH, Mc LL, Syverton JT (1960) Enteroviral ribonucleic acid. I. Recovery from virus and assimilation by cells. J Exp Med 112:821–839
5. Holland JJ, Mc LL, Hoyer BH, Syverton JT (1960) Enteroviral ribonucleic acid. II. Biological, physical, and chemical studies. J Exp Med 112:841–864
6. Ketler A, Hamparian VV, Hilleman MR (1962) Characterization and classification of ECHO 28-rhinovirus-coryzavirus agents. Proc Soc Exp Biol Med Soc Exp Biol Med 110:821–831
7. Dimmock NJ (1966) Biophysical studies of a rhinovirus. Extraction and assay of infectious ribonucleic acid. Nature 209(5025):792–794
8. Mogler MA, Kamrud KI (2015) RNA-based viral vectors. Expert Rev Vaccines 14(2):283-312. doi:10.1586/14760584.2015.979798
9. Conzelmann KK, Meyers G (1996) Genetic engineering of animal RNA viruses. Trends Microbiol 4(10):386–393. doi:10.1016/0966-842X(96)10062-7
10. Racaniello VR, Baltimore D (1981) Cloned poliovirus complementary DNA is infectious in mammalian cells. Science 214(4523):916–919
11. Ahlquist P, French R, Janda M, Loesch-Fries LS (1984) Multicomponent RNA plant virus infection derived from cloned viral cDNA. Proc Natl Acad Sci U S A 81(22):7066–7070
12. Mizutani S, Colonno RJ (1985) In vitro synthesis of an infectious RNA from cDNA clones of human rhinovirus type 14. J Virol 56(2):628–632
13. Baltimore D (1971) Expression of animal virus genomes. Bacteriol Rev 35(3):235–241
14. Semler BL, Dorner AJ, Wimmer E (1984) Production of infectious poliovirus from cloned cDNA is dramatically increased by SV40 transcription and replication signals. Nucleic Acids Res 12(12):5123–5141
15. Moormann RJ, van Gennip HG, Miedema GK, Hulst MM, van Rijn PA (1996) Infectious RNA transcribed from an engineered full- length cDNA template of the genome of a pestivirus. J Virol 70(2):763–770
16. Meyers G, Tautz N, Becher P, Thiel HJ, Kümmerer BM (1996) Recovery of cytopathogenic and noncytopathogenic bovine viral diarrhea viruses from cDNA constructs. J Virol 70(12):8606–8613
17. Meyers G, Thiel HJ, Rümenapf T (1996) Classical swine fever virus: recovery of infectious viruses from cDNA constructs and generation of recombinant cytopathogenic defective interfering particles. J Virol 70(3):1588–1595
18. Ruggli N, Tratschin JD, Mittelholzer C, Hofmann MA (1996) Nucleotide sequence of classical swine fever virus strain Alfort/187 and transcription of infectious RNA from stably cloned full-length cDNA. J Virol 70(6): 3478–3487
19. Rice CM, Grakoui A, Galler R, Chambers TJ (1989) Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation. New Biol 1(3):285–296
20. Becher P, Orlich M, König M, Thiel HJ (1999) Nonhomologous RNA recombination in bovine viral diarrhea virus: molecular characterization of a variety of subgenomic RNAs isolated during an outbreak of fatal mucosal disease. J Virol 73(7):5646–5653
21. Becher P, Orlich M, Thiel HJ (2001) RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease. J Virol 75(14):6256–6264. doi:10.1128/JVI.75.14.6256-6264.2001
22. Becher P, Tautz N (2011) RNA recombination in pestiviruses: cellular RNA sequences in viral genomes highlight the role of host factors for viral persistence and lethal disease. RNA Biol 8(2):216–224
23. Meyers G, Rümenapf T, Thiel HJ (1989) Ubiquitin in a togavirus. Nature 341:491
24. Meyers G, Thiel HJ (1996) Molecular characterization of pestiviruses. Adv Virus Res 47:53–117
25. Gallei A, Pankraz A, Thiel HJ, Becher P (2004) RNA recombination in vivo in the absence of viral replication. J Virol 78(12):6271–6281. doi:10.1128/JVI.78.12.6271-6281.2004
26. Gmyl AP (2003) Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9(10):1221–1231. doi:10.1261/rna.5111803
27. Koetzner CA, Parker MM, Ricard CS, Sturman LS, Masters PS (1992) Repair and mutagenesis of the genome of a deletion mutant of the coronavirus mouse hepatitis virus by targeted RNA recombination. J Virol 66(4):1841–1848
28. Liao CL, Lai MMC (1992) RNA recombination in a coronavirus - recombination between viral genomic RNA and transfected RNA fragments. J Virol 66(10):6117–6124
29. van der Most RG, Heijnen L, Spaan WJ, de Groot RJ (1992) Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs. Nucleic Acids Res 20(13):3375–3381
30. Masters PS, Rottier PJ (2005) Coronavirus reverse genetics by targeted RNA recombination. Curr Top Microbiol Immunol 287:133–159
31. Almazan F, Gonzalez JM, Penzes Z, Izeta A, Calvo E, Plana-Duran J, Enjuanes L (2000) Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome. Proc Natl Acad Sci U S A 97(10):5516–5521
32. Yount B, Curtis KM, Baric RS (2000) Strategy for systematic assembly of large RNA and DNA genomes: transmissible gastroenteritis virus model. J Virol 74(22):10600–10611
33. Casais R, Thiel V, Siddell SG, Cavanagh D, Britton P (2001) Reverse genetics system for the avian coronavirus infectious bronchitis virus. J Virol 75(24):12359–12369. doi:10.1128/JVI.75.24.12359-12369.2001
34. Racaniello VR, Baltimore D (1981) Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc Natl Acad Sci U S A 78(8):4887–4891
35. Rice CM, Levis R, Strauss JH, Huang HV (1987) Production of infectious RNA transcripts from Sindbis virus cDNA clones: mapping of lethal mutations, rescue of a temperature-sensitive marker, and in vitro mutagenesis to generate defined mutants. J Virol 61(12):3809–3819
36. Sosnovtsev S, Green KY (1995) RNA transcripts derived from a cloned full-length copy of the feline calicivirus genome do not require VpG for infectivity. Virology 210(2):383–390. doi:10.1006/viro.1995.1354
37. Chumakov KM (1996) PCR engineering of viral quasispecies: a new method to preserve and manipulate genetic diversity of RNA virus populations. J Virol 70(10):7331–7334
38. Rasmussen TB, Reimann I, Hoffmann B, Depner K, Uttenthal A, Beer M (2008) Direct recovery of infectious pestivirus from a full-length RT-PCR amplicon. J Virol Methods 149(2):330–333. doi:10.1016/j. jviromet.2008.01.029
39. Cello J, Paul AV, Wimmer E (2002) Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297(5583):1016–1018. doi:10.1126/science.1072266
40. Beall A, Yount B, Lin CM, Hou Y, Wang Q, Saif L, Baric R (2016) Characterization of a pathogenic full-length cDNA clone and transmission model for porcine epidemic diarrhea virus strain PC22A. MBio 7(1):e01451–15. doi:10.1128/mBio.01451-15
41. Bushell M, Sarnow P (2002) Hijacking the translation apparatus by RNA viruses. J Cell Biol 158(3):395–399
42. Firth AE, Brierley I (2012) Non-canonical translation in RNA viruses. J Gen Virol 93(Pt 7):1385–1409. doi:10.1099/vir.0.042499-0
43. Lopez-Lastra M, Ramdohr P, Letelier A, Vallejos M, Vera-Otarola J, Valiente-Echeverria F (2010) Translation initiation of viral mRNAs. Rev Med Virol 20(3):177–195. doi:10.1002/rmv.649
44. Sosnovtsev SV, Belliot G, Chang KO, Onwudiwe O, Green KY (2005) Feline calicivirus VP2 is essential for the production of infectious virions. J Virol 79(7):4012–4024
45. Thumfart JO, Meyers G (2002) Feline calicivirus: recovery of wild-type and recombinant viruses after transfection of cRNA or cDNA constructs. J Virol 76(12):6398–6407
46. Schnell MJ, Mebatsion T, Conzelmann KK (1994) Infectious rabies viruses from cloned cDNA. EMBO J 13(18):4195–4203
47. Gonzalez JM, Penzes Z, Almazan F, Calvo E, Enjuanes L (2002) Stabilization of a fulllength infectious cDNA clone of transmissible gastroenteritis coronavirus by insertion of an intron. J Virol 76(9):4655–4661. doi:10.1128/jvi.76.9.4655-4661.2002
48. Tautz N, Tews BA, Meyers G (2015) The molecular biology of pestiviruses. Adv Virus Res 93:47–160. doi:10.1016/bs.aivir. 2015.03.002
49. Meyers G, Ege A, Fetzer C, von Freyburg M, Elbers K, Carr V, Prentice H, Charleston B, Schürmann EM (2007) Bovine viral diarrhoea virus: prevention of persistent foetal infection by a combination of two mutations affecting the Erns RNase and the Npro protease. J Virol 81(7):3327–3338
50. Masters PS (2006) The molecular biology of coronaviruses. Adv Virus Res 66:193–292. doi:10.1016/S0065-3527(06)66005-3
51. Ziebuhr J (2004) Molecular biology of severe acute respiratory syndrome coronavirus. Curr Opin Microbiol 7(4):412–419. doi:10.1016/j. mib.2004.06.007
52. Yount B, Roberts RS, Sims AC, Deming D, Frieman MB, Sparks J, Denison MR, Davis N, Baric RS (2005) Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice. J Virol 79(23):14909–14922. doi:10.1128/JVI.79.23.14909-14922.2005
53. DeDiego ML, Alvarez E, Almazan F, Rejas MT, Lamirande E, Roberts A, Shieh WJ, Zaki SR, Subbarao K, Enjuanes L (2007) A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo. J Virol 81(4):1701–1713. doi:10.1128/JVI.01467-06
54. Dediego ML, Pewe L, Alvarez E, Rejas MT, Perlman S, Enjuanes L (2008) Pathogenicity of severe acute respiratory coronavirus deletion mutants in hACE-2 transgenic mice. Virology 376(2):379–389. doi:10.1016/j. virol.2008.03.005
55. Lamirande EW, DeDiego ML, Roberts A, Jackson JP, Alvarez E, Sheahan T, Shieh WJ, Zaki SR, Baric R, Enjuanes L, Subbarao K (2008) A live attenuated severe acute respiratory syndrome coronavirus is immunogenic and efficacious in golden Syrian hamsters. J Virol 82(15):7721–7724. doi:10.1128/JVI.00304-08
56. Netland J, DeDiego ML, Zhao J, Fett C, Alvarez E, Nieto-Torres JL, Enjuanes L, Perlman S (2010) Immunization with an attenuated severe acute respiratory syndrome coronavirus deleted in E protein protects against lethal respiratory disease. Virology 399(1):120-128. doi:10.1016/j.virol.2010.01.004
57. Beer M, Reimann I, Hoffmann B, Depner K (2007) Novel marker vaccines against classical swine fever. Vaccine 25(30):5665–5670
58. Koenig P, Lange E, Reimann I, Beer M (2007) CP7_E2alf: a safe and efficient marker vaccine strain for oral immunisation of wild boar against Classical swine fever virus (CSFV). Vaccine 25(17):3391–3399
59. Leifer I, Lange E, Reimann I, Blome S, Juanola S, Duran JP, Beer M (2009) Modified live marker vaccine candidate CP7_E2alf provides early onset of protection against lethal challenge infection with classical swine fever virus after both intramuscular and oral immunization. Vaccine 27(47):6522–6529
60. Gaucher D, Therrien R, Kettaf N, Angermann BR, Boucher G, Filali-Mouhim A, Moser JM, Mehta RS, Drake DR 3rd, Castro E, Akondy R, Rinfret A, Yassine-Diab B, Said EA, Chouikh Y, Cameron MJ, Clum R, Kelvin D, Somogyi R, Greller LD, Balderas RS, Wilkinson P, Pantaleo G, Tartaglia J, Haddad EK, Sekaly RP (2008) Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 205(13):3119–3131. doi:10.1084/jem.20082292
61. Querec T, Bennouna S, Alkan S, Laouar Y, Gorden K, Flavell R, Akira S, Ahmed R, Pulendran B (2006) Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. J Exp Med 203(2):413–424. doi:10.1084/jem.20051720
62. Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, Kennedy K, Wu H, Bennouna S, Oluoch H, Miller J, Vencio RZ, Mulligan M, Aderem A, Ahmed R, Pulendran B (2009) Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 10(1):116–125. doi:10.1038/ni.1688
63. Querec TD, Pulendran B (2007) Understanding the role of innate immunity in the mechanism of action of the live attenuated Yellow Fever Vaccine 17D. Adv Exp Med Biol 590:43–53. doi:10.1007/978-0-387-34814-8_3
64. Monath TP, Guirakhoo F, Nichols R, Yoksan S, Schrader R, Murphy C, Blum P, Woodward S, McCarthy K, Mathis D, Johnson C, Bedford P (2003) Chimeric live, attenuated vaccine against Japanese encephalitis (ChimeriVax-JE): phase 2 clinical trials for safety and immunogenicity, effect of vaccine dose and schedule, and memory response to challenge with inactivated Japanese encephalitis antigen. J Infect Dis 188(8):1213–1230. doi:10.1086/378356
65. Guirakhoo F, Kitchener S, Morrison D, Forrat R, McCarthy K, Nichols R, Yoksan S, Duan X, Ermak TH, Kanesa-Thasan N, Bedford P, Lang J, Quentin-Millet MJ, Monath TP (2006) Live attenuated chimeric yellow fever dengue type 2 (ChimeriVax-DEN2) vaccine: phase I clinical trial for safety and immunogenicity: effect of yellow fever preimmunity in induction of cross neutralizing antibody responses to all 4 dengue serotypes. Hum Vaccines 2(2):60–67
66. Guirakhoo F, Weltzin R, Chambers TJ, Zhang ZX, Soike K, Ratterree M, Arroyo J, Georgakopoulos K, Catalan J, Monath TP (2000) Recombinant chimeric yellow fever-dengue type 2 virus is immunogenic and protective in nonhuman primates. J Virol 74(12):5477–5485
67. Monath TP, Arroyo J, Miller C, Guirakhoo F (2001) West Nile virus vaccine. Curr Drug Targets Infect Disord 1(1):37–50
68. Monath TP, Liu J, Kanesa-Thasan N, Myers GA, Nichols R, Deary A, McCarthy K, Johnson C, Ermak T, Shin S, Arroyo J, Guirakhoo F, Kennedy JS, Ennis FA, Green S, Bedford P (2006) A live, attenuated recombinant West Nile virus vaccine. Proc Natl Acad Sci U S A 103(17):6694–6699. doi:10.1073/pnas.0601932103
69. Pugachev KV, Guirakhoo F, Trent DW, Monath TP (2003) Traditional and novel approaches to flavivirus vaccines. Int J Parasitol 33(5-6):567–582
70. Pletnev AG, Bray M, Lai CJ (1993) Chimeric tick-borne encephalitis and dengue type 4 viruses: effects of mutations on neurovirulence in mice. J Virol 67(8):4956–4963
71. Monath TP (2011) Recombinant, chimeric, live, attenuated vaccines against Flaviviruses and Alphaviruses. In: Dormitzer PR, Mandel CW, Rappuoli R (eds) Replicating vaccines: a new generation. Springer, Basel, pp 349–438
72. Roby JA, Hall RA, Khromykh AA (2011) Nucleic acid-based infections and pseudo-infectious flavivirus vaccines. In: Dormitzer PR, Mandel CW, Rappuoli R (eds) Replicating vaccines: a new generation. Springer, Basel, pp 299–320
73. Behrens SE, Grassmann CW, Thiel HJ, Meyers G, Tautz N (1998) Characterization of an autonomous subgenomic pestivirus RNA replicon. J Virol 72(3):2364–2372
74. Lohmann V, Körner F, Koch JO, Herian U, Theilmann L, Bartenschlager R (1999) Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285:110–113
75. Reimann I, Semmler I, Beer M (2007) Packaged replicons of bovine viral diarrhea virus are capable of inducing a protective immune response. Virology 366(2):377–386
76. Kofler RM, Aberle JH, Aberle SW, Allison SL, Heinz FX, Mandl CW (2004) Mimicking live flavivirus immunization with a noninfectious RNA vaccine. Proc Natl Acad Sci U S A 101(7):1951-1956. doi:10.1073/pnas.0307145101
77. Mandl CW (2004) Flavivirus immunization with capsid-deletion mutants: basics, benefits, and barriers. Viral Immunol 17(4):461–472. doi:10.1089/vim.2004.17.461
78. Donnelly ML, Hughes LE, Luke G, Mendoza H, ten Dam E, Gani D, Ryan MD (2001) The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences. J Gen Virol 82(Pt 5):1027–1041. doi:10.1099/0022-1317-82-5-1027
79. Donnelly ML, Luke G, Mehrotra A, Li X, Hughes LE, Gani D, Ryan MD (2001) Analysis of the aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal ‘skip’. J Gen Virol 82(Pt 5):1013–1025. doi:10.1099/0022-1317-82-5-1013
80. Tautz N, Harada T, Kaiser A, Rinck G, Behrens SE, Thiel HJ (1999) Establishment and characterization of cytopathogenic and noncytopathogenic pestivirus replicons. J Virol 73(11):9422–9432
81. Baroth M, Peters Y, Schönbrunner ER, Behrens SE (2010) Stable recombinants of bovine viral diarrhea virus containing a hepatitis C virus insert. J Gen Virol 91(Pt 5):1213-1217. doi:10.1099/vir.0.016998-0
82. Agapov EV, Frolov I, Lindenbach BD, Pragai BM, Schlesinger S, Rice CM (1998) Noncytopathic Sindbis virus RNA vectors for heterologous gene expression. Proc Natl Acad Sci U S A 95:12989–12994
83. Strauss JH, Strauss EG (1994) The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 58:491–562