Genetic variability: The key problem in the prevention and therapy of RNA-based virus infections

Medicinal Research Reviews

Volumn 23, Issue 4, 2003, Pages 488-518

  Figlerowicz, Magdalena ^b   Alejska, Magdalena ^a   Kurzyńska Kokorniak, Anna ^a   Figlerowicz, Marek ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b POZNAN UNIVERSITY OF MEDICAL SCIENCES   (Poland)

Author keywords

Error prone replication; Genetic reassortment; Genetic variability; RNA recombination; RNA based viruses; Viral infections prevention and therapy

Indexed keywords

ABACAVIR; ACICLOVIR; ALPHA INTERFERON; AMANTADINE; AMPRENAVIR; ANTIVIRUS AGENT; DELAVIRDINE; DIDANOSINE; EFAVIRENZ; FOSCARNET; GANCICLOVIR; IDOXURIDINE; INDINAVIR; LAMIVUDINE; LOPINAVIR; NELFINAVIR; NEVIRAPINE; NUCLEOSIDE DERIVATIVE; RIBAVIRIN; RIMANTADINE; RITONAVIR; SAQUINAVIR; STAVUDINE; TRIFLURIDINE; VIDARABINE; VIRUS VACCINE; ZALCITABINE; ZIDOVUDINE;

GENE REARRANGEMENT; GENETIC VARIABILITY; HUMAN; IMMUNIZATION; INFECTION CONTROL; NONHUMAN; POINT MUTATION; RETROVIRUS; REVIEW; RNA RECOMBINATION; RNA VIRUS INFECTION; VIRUS REPLICATION;

BASE SEQUENCE; DNA REPLICATION; GENOME, VIRAL; HUMANS; IMMUNIZATION, PASSIVE; MODELS, GENETIC; MUTATION; POINT MUTATION; REASSORTANT VIRUSES; RECOMBINATION, GENETIC; RETROVIRIDAE; RNA VIRUS INFECTIONS; RNA VIRUSES; RNA, VIRAL; VACCINES, DNA; VARIATION (GENETICS);

EID: 0038469912     PISSN: 01986325     EISSN: None     Source Type: Journal    
DOI: 10.1002/med.10045     Document Type: Review

References (214)

1. Whitton JL, Oldstone MBA. Immune response to virus. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 345-374.
2. Ahmed R, Nathanson N. Immune response to viral infections. In: Viral pathogenesis and immunity. Philadelphia: Lippincott Wuilliams & Wilkins; 2002. p 53-69.
3. Nash T. Immunity to viruses. In: Roitt J, Brostoff J, Male D, editors. Immunology. London: Harcourt Publishers, Ltd.; 2001. p 235-244.
4. Murphy BR, Chanock RM. Immunization against virus diseases. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third Edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 476-497.
5. Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, Van de Pol S. Rapid evolution of RNA genomes. Science 1982;215:1577-1585.
6. Pathak VK, Hu W-S. "Might as well Jump!" Temple switching by retroviral reverse transcriptase, defective genome formation, and recombination. Sem Virol 1997;8:141-150.
7. Holland J, DelaTorre JC, Steinhauer DA. RNA virus populations as quasispecies. In: Holland J, editor. Genetic diversity of RNA viruses. Springer Verlag: Heidelberg; 1992. p 1-20.
8. Domingo E, Holland J, Biebricher C, Eigen M. Quasi-species: The concept and the word. In: Gibbs AG, Calisher CH, Garcia-Arenal F, editors. Molecular basis of virus evolution. Cambridge: Cambridge University Press; 1995. p 181-191.
9. Eigen M. On the nature of virus quasispecies. Trends Microbiol 1996;4:216-217.
10. Domingo E, Escarmis C, Sevilla N, Baranowski E. Population dynamics in the evolution of RNA viruses. Adv Exp Med Biol 1998;440:721-727.
11. Zeitlin L, Cone RA, Moench TR, Whaley KJ. Preventing infectious diseases with passive immunization. Microbes Infect 2000;2:701-708.
12. Sawyer LA. Antibodies for the prevention and treatment of viral diseases. Antiviral Res 2000;47:55-77.
13. Nydegger UE, Mohacsi PJ, Escher R, Morell A. Clinical use of intravenous immunoglobulins. Vox Sanguinis 2000;78(Suppl 2):191-195.
14. Zeitlin L, Cone RA, Whaley KJ. Using monoclonal antibodies to prevent mucosal transmission of epidemic infectious diseases. Emerg Infect Dis 1999;5:54-64.
15. Fenner F, Henderson DA, Arita I, Jezek Z, Ladny ID. Smallpox and its eradication. Geneva, Switzerland: World Health Organization; 1988.
16. Sabin AB. Oral poliovirus vaccine: History of its development and use and current challenge to eliminate poliomyelitis from the world. J Infect Dis 1985;151:420-436.
17. Ada G. Vaccines and vaccination. N Engl J Med 2001;345:1042-1053.
18. Horstmann DM. Viral vaccines and their ways. Rev Infect Dis 1979;1:502-516.
19. Horstmann DM. Control of poliomyelitis: Continuing paradox. J Infect Dis 1982;146:540-551.
20. Baez M, Palese P, Kilbourne ED. Gene composition of high-yielding influenza vaccine strains obtained by recombination. J Infect Dis 1980;141:362-369.
21. Andre FE, D'Hondt E, Delem A, Safary A. Clinical assessment of the safety and efficacy of an inactivated hepatitis A vaccine: Rationale and summary of findings. Vaccine 1992;10:160-168.
22. Krugman S. The newly licensed hepatitis B vaccine: Characteristics and indications for use. JAMA 1982;247:2012-2015.
23. Szmuness W, Stevens CE, Harley HJ, Zang EA, Oleszko WR, William DC, Sadovsky R, Morrison JM, Kellner A. N Hepatitis B vaccine demonstration of efficacy in a controlled clinical trial in a high-risk population in the Unites States. Engl J Med 1980;303:833-841.
24. Dong J, Hunter E. Analysis of retroviral assembly using a vaccinia/T7-polymerase complementation system. Virology 1993;194:192-199.
25. Gonzalez SA, Affranchino JL, Gelderblom HR, Burny A. Assembly of the matrix protein of Simian immunodeficiency virus in to virus-like particles. Virology 1993;194:548-556.
26. Kleid DG, Yansura D, Small B, Dowbenko D, Moore DM, Grubman MJ, McKercher PD, Morgan DO, Robertson BH, Bachrach HL. Cloned viral protein vaccine for foot-and-mouth disease: Response in cattle and swine. Science 1981;214:1125-1129.
27. Lin Y-L, Borenstein LA, Ahmed R, Wettstein FQ. Cotton tail rabbit papillomavirus L1 protein-based vaccines: Protection is achieved only with a full-length, nondenatured product. J Virol 1993;67:4154-4162.
28. van Drunen Little-van den Hurk S, Parker MD, Massie B. Protection of cattle from BHV-1 infection by immunization with recombinant glycoprotein gIV. Vaccine 1993;11:25-35.
29. Lasky LA, Dowbenko D, Simonsen C, Berman PW. Production of a herpes simplex virus subunit vaccine by genetically engineered mammalian cell lines. In: Lerner RA, Chanock RM, editors. Modern approaches to vaccines. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1984. p 189-194.
30. Imamura T, Araki M, Miyanohara A, Nakao J, Yonemura H, Ohtomo N, Matsubara K. Expression of hepatitis B virus middle and large surface antigen genes in Sacharomyces cerevisiae. J Virol 1987;61:3543-3549.
31. Luckow VA, Summers MD. Trends in the development of baculovirus expression vectors. Biotechnology 1988;6:47-55.
32. Kapusta J, Modelska A, Figlerowicz M, Pniewski T, Letellier M, Lisowa O, Yusibov V, Koprowski H, Płucienniczak A, Legocki AB. A plant-derived edible vaccine against hepatitis B virus. FASEB J 1999;13:1796-1799.
33. Bittle JL, Houghten RA, Alexander H, Shinnick TM, Sutcliffe JG, Lerner RA, Rowlands DJ, Brown F. Protection against foot-and-mouth disease by immunization with a chemically synthesized peptide predicted from the viral nucleotide sequence. Nature 1982;298:30-33.
34. Langbeheim H, Arnon R, Sela M. Antiviral effect on MS-2 coliphage obtained with a synthetic antigen. Proc Natl Acad Sci USA 1976;73:4636-4640.
35. Gaulton GN, Sharpe AH, Chang DW, Fields BN, Greene MI. Syngeneic monoclonal internal image anti-idiotops as prophylactic vaccines. J Immunol 1986;137:2930-2936.
36. McClintock PR, Prabhakar BS, Notkins AL. Anti-idiotypic antibodies to monoclonal antibodies that neutralize coxackievirus B4 do not recognize viral receptors. Virology 1986;150:352-360.
37. Reagan KJ, Wunner WH, Wiktor TJ, Koprowski H. Anti-idiotypic antibodies induce neutralizing antibodies to rabies virus glycoprotein. J Virol 1983;48:660-666.
38. Uytdehaag FGCM, Osterhaus ADME. Induction of neutralizing antibodies in mice against poliovirus type II with monoclonal anti-idiotipic antibodies. J Immunol 1985;134:1225-1229.
39. Tang D-C, DeVit M, Johnston SA. Genetic immunization is a simple method for eliciting an immune response. Science 1992;356:152-154.
40. Schirmbeck R, Reimann J. Revealing the potential of DNA-based vaccination: Lesson learned from the hepatitis B virus surface antigen. Biol Chem 2001;382:543-552.
41. Hirsch MS, Kaplan JC, D'Aquila RT. Antiviral agents. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 431-466.
42. Richman DD. HIV chemotherapy. Nature 2001;410:995-1001.
43. Air GM, Luo M. Structure-guided therapeutic strategies. In: Chiu W, Burnett RM, Garcea RL, editors. Structural biology of viruses. New York: Oxford University Press; 1997. p 411-431.
44. Prisbe EJ, Chen MS. Design of nucleoside analog inhibitors of herpes virus polymerases. Methods Enzymol 1996;275:425-439.
45. Tucker TJ, Lumma WC, Culberson JC. Development of nonnucleoside HIV reverse transcriptase inhibitors. Methods Enzymol 1996;275:440-471.
46. Hoge CN, Straatsma TP, McCammon JA, Wlodawer A. Rational design of HIV protease inhibitors. In: Chiu W, Burnett RM, Garcea RL, editors. Structural biology of viruses. New York: Oxford University Press; 1997. p 451-473.
47. Lam PYS, Jadhav PK, Eyermann CJ, Hodge CN, Ru Y, Bacheler LT, Meek JL, Otto MJ, Rayner MM, Wong YN. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994;263:380-384.
48. Drach DJ. Purine nucleoside analogs as antiviral agents. In: DeClercq E, Walker RT, editors. Targets for the design of antiviral drugs. New York: Plenum Press; 1984.
49. Chen H, Brown D, Gold L. Novel methods of generating specific oligonucleotide inhibitors of viral polymerases. Methods Enzymol 1996;275:503-522.
50. Ellington S, Szostak J. In vitro selection of RNA molecules that bind specific ligands. Nature 1990;346:818-820.
51. Uhlenback OC. A small catalytic oligoribonucleotide. Nature 1987;328:596-600.
52. Sarver N, Cantin EM, Chang PS, Zaia JA, Ladne PA, Stephens DA, Rossi JJ. Ribozymes as potential anti-HIV-1 therapeutic agents. Science 1990;247:1222-1225.
53. Dropulic B, Lin NH, Martin MA, Jeang K-T. Functional characterization of a U5 ribozyme: Intracellular suppression of human immunodeficiency virus type 1 expression. J Virol 1992;66:1432-1441.
54. Ojwang JO, Hempel A, Looney DJ, Wong-Staal F, Rappaport J. Inhibition of human immunodeficiency virus type 1 expression by a hairpin ribozyme. Proc Natl Acad Sci USA 1992;89:10802-10806.
55. Shippy R, Lockner R, Farnsworth M, Hampel A. The hairpin ribozyme. Discovery, mechanism, and development for gene therapy. Mol Biotechnol 1999;12:117-129.
56. Vilcek J, Le J. Immunology of cytokines: An introduction. In: Thomson AW, editor. The cytokine handbook. Second edition. London: Academic Press; 1994. p 1-19.
57. Vilcek J, Sen GC. Interferons and other cytokines. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third Edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 375-399.
58. Bazan JF. A novel family of growth factor receptors: A common binding domain in the growth hormone, prolactin, erythropoietin and IL-6 receptors, and the p75 IL-2 receptor β-chain. Biochem Biophys Res Commun 1989;164:788-795.
59. Chong KL, Feng L, Schappert K, Meurs E, Donahue TF, Friesen JD, Hovanessian AG, Williams BR. Human p68 kinase exhibits growth suppression in yeast and homology to the translational regulator GCN2. EMBO J 1992;11:1553-1562.
60. Ruff-Jamison S, Chen K, Cohen S. Induction by EGF and interferon-α of tyrosine phosphorylated DNA-binding proteins in mouse liver nuclei. Science 1993;261:1733-1736.
61. Sadowski HB, Shuai K, Darnell JE, Gilman MZ. A common nuclear signal transduction pathway activated by growth factor and cytokine receptors. Science 1993;261:1739-1744.
62. Campbell IL. Cytokines in viral diseases. Curr Opin Immunol 1991;3:486-491.
63. De Maeyer E, De Maeyer-Guignard J. Interferons and other regulatory cytokines. New York: John Wiley and Sons; 1988.
64. Finter NB, Oldham RK. Interferon: In vivo and clinical studies. Vol. 4. Amsterdam: Elsevier; 1985.
65. Havell EA, Hayes TG, Vilcek J. Synthesis of two distinct interferons by human fibroblasts. Virology 1978;89:330-334.
66. Nabel GJ. Challenges and opportunities for development of an AIDS vaccine. Nature 2001;410:1002-1007.
67. Gagneten S, Feinstone SM. Hepatitis C vaccines. In: Liang TJ, Hoofnagle JH, editors. Biomedical research reports. Hepatitis C. San Diego: Academic Press; 2000. p 469-486.
68. Oxford JS, Al-Jabri AA, Stein CA, Levantis P. Analysis of resistance mutants of viral polymerases. Methods Enzymol 1996;275:555-600.
69. Mchutchinson JG, Schalm SW. Therapy of chronic hepatitis C. In: Liang TJ, Hoofnagle JH, editors. Biomedical research reports. Hepatitis C. San Diego: Academic Press; 2000. p 203-240.
70. Gooding LR. Virus proteins that counteract host immune defenses. Cell 1992;71:5-7.
71. Andersson M, Paabo S, Nilsson T, Peterson PA. Impaired intracellular transport of class I MHC antigens as a possible means for adenoviruses to evade immune surveillance. Cell 1985;43:215-222.
72. Jennings SR, Rice PL, Kloszewski WD, Anderson RW, Thompson KL, Tevethia SS. Effect of verpes simplex virus types 1 and 2 on surface expression of class I major histocompatibility antigens on infected cells. J Virol 1985;56:757-766.
73. Rinaldo CR, Jr. Modulation of major histocompatibility complex antigen expression by viral infection. Am J Pathol 1994;144:637-650.
74. Paabo S, Nilsson T, Peterson PA. Adenoviruses of subgenera B, C, D, and E modulate cell-surface expression of major histocompatibility complex class antigens. Proc Natl Acad Sci USA 1986;83:9665-9669.
75. Scholz M, Hamann A, Blaheta RA, Auth MKH, Encke A, Markus BH. Cytomegalovirus- and interferon-related effects on human endothelial cells: Cytomegalovirus infection reduces upregulation of HLA class II antigen expression after treatment with interferon 7. Hum Immunol 1992;35:230-238.
76. Sedmak DD, Guglielmo AM, Knight DA, Birmingham DJ, Huang EH, Waldman WJ. Cytomegalovirus inhibits major histocompatibility class II expression on infected endothelial cells. Am J Pathol 1994;144:683.
77. Marrack P, Kappler J. Subversion of the immune system by pathogens. Cell 1994;76:323-332.
78. Spriggs MK. Cytokine and citokine receptor genes captured by viruses. Curr Opin Immunol 1994;6:526-529.
79. Batschelet E, Domingo E, Weissmann C. The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate. Gene 1976;1:27-32.
80. Domingo E, Flavell RA, Weissmann C. In vitro site-directed mutagenesis: Generation and properties of an infectious extracistronic mutant of bacteriophage Qbeta. Gene 1976;1:3-25.
81. Domingo E, Sabo D, Taniguchi T, Weissmann C. Nucleotide sequence heterogeneity of an RNA phage population. Cell 1978;13:735-744.
82. Eigen M, Schuster P. The hypercycle: A principles of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften 1977;64:541-565.
83. Eigen M, McCaskill J, Schuster P. Molecular quasi-species. J Phys Chem 1988;92:6881-6891.
84. Mansky LM. Retrovirus mutation rates and their role in genetic variation. J Gen J Gen Virol 1998;79:1337-1345.
85. Drake JW, Holland JJ. Mutation rates among RNA viruses. Proc Natl Acad Sci USA 1999;96:13910-13913.
86. Coffin JM. Retroviridae: The viruses and their replication. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third Edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 1767-1848.
87. Britten RJ. Rates of DNA sequence evolution differ between taxonomic groups. Science 1986;231:1393-1398.
88. Smith DB, Inglis SC. The mutation rate and variability of eukaryotic viruses: An analytical review. J Gen Virol 1987;68:2729-2740.
89. Parvin JD, Moscona A, Pan WT. Measurement of the mutation rates of animal viruses: Influenza A virus and poliovirus type 1. J Virol 1986;59:377-383.
90. Steinhauer DA, Holland JJ. Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA. J Virol 1986;57:219-228.
91. Ward CD, Stokes MAM, Flanegan JB. Direct measurement of the poliovirus RNA polymerase error frequency in vitro. J Virol 1988;62:558-562.
92. Mansky LM, Temin HM. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 1995;69:5087-5094.
93. Kim T, Mudry RA, Jr., Rexrode CA, Pathak VK. Retroviral mutation rates and A-to-G hypermutation during different stages of retroviral replication. J Virol 1996;70:7594-7602.
94. Pathak VK, Temin HM. Broad spectrum of in vivo forward mutations, hypermutations, and hotspots in a retroviral shuttle vector after a single replication cycle: Substitutions, frameshifts, and hypermutations. Proc Natl Acad Sci USA 1990;87:6019-6023.
95. Pathak VK, Temin HM. Broad spectrum of in vivo forward mutations, hypermutations, and hotspots in a retroviral shuttle vector after a single replication cycle: Deletions and deletions with insertions. Proc Natl Acad Sci USA 1990;87:6024-6028.
96. Drake JW, Charlesworth B, Charlesworth D, Crow JF. Rates of spontaneous mutation. Genetics 1998;148:1667-1686.
97. Elena SF, Moya A. Effect of population patchiness and migration rates on the adaptation and divergence of vesicular stomatitis virus quasispecies populations. J Evol Biol 1999;12:1078-1088.
98. Holland JJ, Domingo E, de la Torre JC, Steinhauer DA. Mutation frequencies at defined single codon sites in vesicular stomatitis virus and poliovirus can be increased only slightly by chemical mutagenesis. J Virol 1990;64:3960-3962.
99. Ohman N, Bass BL. RNA editing. In: Soll D, Nishimura S, Moore PB, editors. Comprehensive natural products chemistry. Prebiotic chemistry, molecular fossils, nucleosides, and RNA. Oxford: Elsevier Science, Ltd.; 1999. 97-108.
100. Bass BL, Weintraub H. A developmentally regulated activity that unwinds RNA duplexes. Cell 1987;48:607-613.
101. Rebagliati MR, Melton DA. Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity Cell 1987;48:599-605.
102. Bass BL. RNA editing and hypermutation by adenosine deamination. Trends Biochem Sci 1997;22:157-162.
103. Maas S, Melcher T, Seeburg PH. Mammalian RNA-dependent deaminases and edited mRNAs. Curr Opin Cell Biol 1997;9:343-349.
104. Casey JL, Gerin JL. J Hepatitis D virus RNA editing: Specific modification of adenosine in the antigenomic RNA. Virology 1995;69:7593-7600.
105. Lai MM. The molecular biology of hepatitis delta virus. Annu Rev Biochem 1995;64:259-286.
106. Hirst GK. Genetic recombination with Newcastle disease virus, poliovirus, and influenza. Cold Spring Harbor Symp Quant Biol 1962;27:303-309.
107. Ledinko N. Genetic recombination with poliovirus type 1 studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain. Virology 1963;20:107-119.
108. Pringle CR. Evidence of genetic recombination in foot-and-mouth disease virus. Virology 1965;25:48-54.
109. Lai MMC. RNA recombination in animal and plant viruses. Microbiol Rev 1992;56:61-79.
110. Simon AE, Bujarski JJ. RNA-RNA recombination and evolution in virus-infected plants. Annu Rev Phytopathol 1994;32:337-362.
111. Coffin JM. Structure, replication, and recombination of retrovirus genomes. Some unifying hypotheses. J Gen Virol 1979;199:47-59.
112. Zhang J, Temin HM. Rate and mechanism of nonhomologous recombination during a single cycle of retroviral replication. Science 1993;259:234-238.
113. Khatchikian D, Orlich M, Rott R. Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the hemagglutinin gene of an influenza virus. Nature 1989;340:156-157.
114. Mindich L, Qiao X, Onodera S, Gottlieb P, Strassman J. Heterologous recombination in the dsRNA bacteriophage φ6. J Virol 1992;66:2605-2610.
115. Onodera S, Qiao X, Gottlieb P, Strassman J, Frilander M, Mindich L. RNA structure and heterologous recombination in the dsRNA bacteriophage φ6. J Virol 1993;67:4914-4922.
116. Suzuki Y, Gojobori T, Nakagomi O. Intragenic recombination in rotaviruses. FEBS Lett 1998;427:183-187.
117. Plyusnin A, Kukkonen SKJ, Plyusnina A, Vapalahti O, Vaheri A. Transfection-mediated generation of functionally competent Tula hantivirus with recombinant S RNA segment 2002;21:1497-1503.
118. Meyers G, Tautz N, Dubovi EJ, Thiel H-J. Viral cytopathogenenicity correlated with integration of ubiquitin-coding sequences. Virology 1991;180:602-616.
119. Green AM, Allison RF. Recombination between viral RNA and transgenic plant transcripts. Science 1994;263:1423-1425.
120. Kirkegaard K, Baltimore D. The mechanism of RNA recombination in poliovirus. Cell 1986;47:433-443.
121. Figlerowicz M, Nagy PD, Bujarski JJ. A mutation in the putative RNA polymerase gene inhibits nonhomologous, but not homologous, genetic recombination in RNA virus. Proc Natl Acad Sci USA 1997;94:2073-2078.
122. Figlerowicz M, Nagy PD, Tang N, Kao CC, Bujarski JJ. Mutations in the N-terminus of the brome mosaic virus polymerase affect genetic RNA-RNA recombination. J Virol 1998;72:9192-9200.
123. Stuhlmann H, Berg P. Homologous recombination of copackage retrovirus RNAs during reverse transcription. J Virol 1992;66:2378-2381.
124. Figlerowicz M, Bujarski JJ. RNA recombination in brome mosaic virus, a model plus stranded RNA virus. Acta Biochim Pol 1998;45:1-23.
125. Alejska M, Kurzynska-Kokorniak A, Broda M, Kierzek R, Figlerowicz M. How RNA viruses exchange their genetic material. Acta Biochim Pol 2001;48:391-407.
126. Nagy PD, Zhang C, Simon AE. Dissecting RNA recombination in vitro: Role of RNA sequences and the viral replicase. EMBO J 1998;17:2392-2403.
127. Romanova LI, Blinov VM, Tolskaya EA, Viktorova EG, Kolesnikova MS, Guseva EA, Agol VI. The primary structure of crossovers regions of intertypic poliovirus recombinants: A model of recombination between RNA genomes. Virology 1986;155:202-213.
128. Nagy PD, Bujarski JJ. Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc Natl Acad Sci USA 1993;90:6390-6394.
129. Zhang X, Lai MMC. Unusual heterogenity of leader-mRNA fusion in a murine coronavirus: Implications for the mechanism of RNA transcription and recombination. J Virol 1994;68:6626-6633.
130. Nagy PD, Simone AE. New insight into the mechanism of RNA recombination. Virology 1997;235:1-9.
131. Chetverin AB, Chetverina HV, Demidenko AA, Ugarov VI. Nonhomologous RNA recombination in a cell-free system: Evidence for a transesterification mechanism guided by secondary structure. Cell 1997;88:503-513.
132. Temin HM. Retrovirus variation and reverse transcription: Abnormal strand transfer results in retrovirus genetic variation. Proc Natl Acad Sci USA 1993;90:6900-6903.
133. Zhang J, Temin HM. Retrovirus recombination depends on the length of sequence identity and is not error prone. J Virol 1994;68:2409-2414.
134. Zhang J, Temin HM. 3′ Junctions of oncogene-virus sequence and the mechanism for formation of highly oncogenic retroviruses. J Virol 1993;67:1747-1751.
135. Rueckert RR. Picomaviridae: The viruses and their replication. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 609-654.
136. King AMQ. Genetic recombination in positive strand RNA viruses. In: Domingo P, Holland JJ, Ahlquist P, editors. RNA genetics. Vol. 2. Boca Raton: FL CRC Press; 1988. p 149-165.
137. Jarvis TC, Kirkegaard K. Poliovirus RNA recombination: Mechanistic studies in the absence of selection. EMBO J 1992;11:3135-3145.
138. Pilipenco EV, Gmyl AP, Agol VI. A model for rearrangements in RNA genomes. Nucl Acids Res 1995;23:1870-1875.
139. McIntosh K. Coronaviruses. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 1095-1103.
140. Sawicki DL, Wang T, Sawicki SG. RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus. J Gen Virol 2001;82:385-396.
141. Fu K, Baric RS. Evidence for variable rates of recombination in MHV genome. Virology 1992;189:88-102.
142. Fu K, Baric RS. Map locations of mouse hepatitis virus temperature-sensitive mutants: Confirmation of variable rates of recombination. J Virol 1994;68:7458-7466.
143. Banner LR, Keck JG, Lai MM-C. A clustering of RNA recombination sites adjacent to a hyper-variable region of the peplomer gene of murine coronavirus. Virology 1990;175:548-555.
144. Ahlquist P. Bromovirus RNA replication and transcription. Curr Opin Genet Dev 1992;2:71-76.
145. Bujarski JJ, Kaesberg P. Genetic recombination in a multipartite plant virus. Nature 1986;321:528-531.
146. Nagy PD, Bujarski JJ. Efficient system of homologous RNA recombination in brome mosaic virus: Sequence and structure requirements and accuracy of crossovers. J Virol 1995;69:131-140.
147. Nagy PD, Ogiela C, Bujarski JJ. Mapping sequences active in homologous recombination in brome mosaic virus: Prediction of recombination hot-spots. Virology 1999;254:92-104.
148. Figlerowicz M. Role of RNA structure in heteroduplex-mediated and site-specific nonhomologous recombination in brome mosaic virus. Nucl Acids Res 2000;28:1714-1723.
149. Bruyere A, Wantroba M, Flasinski S, Dzianott A, Bujarski JJ. Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. J Virol 2000;74:4214-4219.
150. Figlerowicz M, Bibiłło A. RNA motifs mediating in vivo site-specific nonhomologous recombination in (+)RNA virus enforce in vitro nonhomologous crossovers with HIV-1 reverse transcriptase. RNA 2000;6:339-351.
151. Li Y, Ball LA. Non-homologous RNA recombination during negative strand synthesis of flock house virus RNA. J Virol 1993;67:3854-3860.
152. Raju R, Subramaniam SV, Hajjou M. Genesis of Sindbis virus by in vivo recombination of nonreplicative RNA precursors. J Virol 1995;69:7391-7401.
153. Tordo N, de Haan P, Goldbach R, Poch O. Evolution of negative-stranded RNA genomes. Semin Virol 1992;3:341-357.
154. Koonin EV. Evolution of double-stranded RNA viruses: A case for polyphyletic origin from different groups of positive-stranded RNA viruses. Semin Virol 1992;3:327-340.
155. Webster RG, Laver WG, Air GM, Schild GC. Molecular mechanisms of variation in influenza viruses. Nature 1982;296:115-121.
156. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol Rev 1992;56:152-179.
157. Tobita K. Genetic recombination between influenza virus A0/NWS and A2/Hong Kong. Arch Gesamte Virusforschung 1971;34:119-130.
158. Tobita K, Kilbourne ED. Genetic recombination for antigenic markers of antigenically different strains of influenza B virus. J Virol 1974;13:347-352.
159. Racaniello VR, Palese P. Isolation of influenza C virus recombinants. J Virol 1979;32:1006-1014.
160. Galasso RT, Tyeryar TF, Jr., Cate TR. Clinical studies of influenza vaccines-1976. J Infect Dis 1977;136(Suppl 1):S341-S346.
161. Garcia-Sastre A, Palese P. Genetic manipulation of negative-strand RNA virus genomes. Annu Rev Microbiol 1993;47:765-790.
162. Gardner PS, Court SDM, Brocklebank JT, Downham MAPS, Weightman D. Virus cross-infection in paediatric wards. Br Med J 1973;2:571-575.
163. Vezza AC, Cash P, Jahrling P, Eddy G, Bishop DHL. Arenavirus recombination: The formation of recombinants between prototype Pichinde and Pichinde Munhique viruses and evidence that arenavirus S RNA codes for N polypeptide. Virology 1980;106:250-260.
164. Fields BN. Temperature-sensitive mutants of reovirus type 3: Features of genetic recombination. Virology 1971;46:142-148.
165. Fields BN, Joklik WK. Isolation and preliminary genetic and biochemical characterization of temperature-sensitive mutants of reovirus. Virology 1969;37:335-342.
166. Lamb RA, Choppen PW. The gene structure and replication of influenza virus. Ann Rev Biochem 1983;52:467-506.
167. Lamb RA. Genes and proteins of the influenza viruses. In: Krug RM, editor. The influenza viruses. New York: Plenum Press; 1969. p 1-87.
168. Burnet FN, Lind PE. Recombination of characters between two influenza virus strains. Aust J Sci 1949;12:109-110.
169. Cox NJ, Bender CA. The molecular epidemiology of influenza viruses. Semin Virol 1995;6:359-370.
170. Ghenkina DB, Ghendon YZ. Recombination and complementation between orthomyxoviruses under conditions of abortive infection. Arch Virol 1979;23:97-106.
171. Nakajima K, Sugiura A. Three-factor cross of influenza virus. Virology 1977;81:486-489.
172. Donald HB, Jsaacs A. Counts of influenza virus particles. J Gen Microbiol 1954;10:457-462.
173. Hirst GK. Mechanism of influenza recombination. I. Factors influencing recombination rates between temperature-sensitive mutants of strain WSN and the classification of mutants into complementation-recombination groups. Virology 1973;55:81-93.
174. Xu X, Guo Y, Rota PA, Hemphill M, Kendal AP, Cox N. Genetic reassortment of human influenza virus in nature. In: Hannoun C, Kendal AP, Klenk HD, Rudenko AA, editors. Options for the control of influenza. Vol. II. Amsterdam, The Netherlands: Elsevier Science Publishers; 1993. p 203-207.
175. McCullers JA, Wang GC, He S, Webster RG. Reassortment and insertion-deletion are strategies for the evolution of influenza B viruses in nature. J Virol 1999;73:7343-7348.
176. Peng G, Hongo S, Kimura H, Muraki Y, Sugawara K, Kitame F, Numazaki Y, Suzuki H, Nakamura K. Frequent occurrence of genetic reassortment between influenza C virus strains in nature. J Gen Virol 1996;77:1489-1492.
177. Ito T, Couceiro JN, Kelm S, Baum LG, Krauss S, Castrucci MR, Donatelli I, Kida H, Paulson JC, Webster RG, Kawaoka Y. Molecular basis for the generation in pigs of influenza A viruses with pandemic potential. J Virol 1998;72:7367-7373.
178. Zhou NN, Shortridge KF, Claas EC, Krauss SL, Webster RG. Rapid evolution of H5N1 influenza viruses in chickens in Hong Kong. J Virol 1999;73:3366-3374.
179. Gonzales-Scarano F, Nathanson N. Bunyaviridae. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 1473-1504.
180. Gentsch J, Bishop DHL. Recombination and complementation between temperature-sensitive mutants of a buynavirus, snowshoe hare virus. J Virol 1976;20:351-354.
181. Gensch J, Robeson G, Bishop DHL. Recombination between snowshoe hare and La Crosse bunyaviruses. J Virol 1979;31:707-717.
182. Gensch J, Wynne LR, Clewley JP, Shope RE, Bishop DHL. Formation of recombinants between snowshoe hare and La Crosse bunyaviruses. J Virol 1977;24:893-902.
183. Bowen MD, Trappier SG, Sanchez AJ, Meyer RF, Goldsmith CS, Zaki SR, Dunster LM, Peters CJ, Ksiazek TG, Nichol ST. A reassortant bunyavirus isolated from acute hemorrhagic fever cases in Kenya and Somalia. Virology 2001;291:185-190.
184. Southern PJ. Arenaviridae: The viruses and their replication. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 1505-1520.
185. Riviere Y, Oldstone MBA. Genetic reassortants of lymphocytic choriomeningitis virus: Unexpected disease and mechanism of pathogenesis. J Virol 1986;59:363-368.
186. Fields BN. Reoviridae. In: Fields BN, Knipe DM, Howley PM, et al., editors. Fields virology. Third edition. Philadelphia: Lippincott-Raven Publishers; 1996. p 1553-1555.
187. Gorman BM. On the evolution of orbiviruses. Intervirology 1983;20:169-180
188. Desselberger U. Genome rearrangements of rotaviruses. Adv Virus Res 1996;46:69-95.
189. Gouvea V, Brantly M. Is rotavirus a population of reassortants? Trends Microbiol 1995;3:159-162.
190. Wenske EA, Chanock SJ, Krata L, Fields BN. Genetic reassortment of mammalian reoviruses in mice. J Virol 1985;56:613-616.
191. Watanabe M, Nakagomi T, Koshimura Y, Nakagomi O. Direct evidence for genome segment reassortment between concurrently circulating human rotavirus strains. Arch Virol 2001;146:557-570.
192. Unicomb LE, Podder G, Gentsch JR, Woods PA, Hasan KZ, Faruque AS, Albert MJ, Glass RI. Evidence of high frequency genomic reassortment of group A rotavirus strains in Bangladesh: Emergence of type G9 in 1995. J Clin Microbiol 1999;37:1885-1891.
193. Samal SK, Livingstone CW, McConnell S, Ramig RE Analysis of mixed infection of sheep with bluetongue virus serotypes 10 and 17: Evidence for genetic reassortment in the vertebrate host. J Virol 1987;61:1086-1091.
194. Sugiyama K, Bishop DHL, Roy P. Analysis of the genomes of bluetongue viruses recovered in the United States. I. Oligonucleotide fingerprint studies that indicate the existence of naturally occurring reassortment BTV isolates. Virology 1981;114:210-217.
195. Iturriza-Gomara M, Isherwood B, Desselberger U, Gray J. Reassortment in vivo: Driving force for diversity of human rotavirus strains isolated in the United Kingdom between 1995 and 1999. J Virol 2001;75:3696-3705.
196. Cross RK, Fields BN. Use of aberrant polypeptide as a marker in three-factor crosses: Further evidence for independent reassortment as a mechanism of recombination between temperature-sensitive mutants of reovirus type 3. Virology 1979;74:345-362.
197. Krishnan T, Naik TN, Desselberger U. Molecular epidemiology of human rotaviruses: Reassortment in vivo as a mechanism for strain diversity? J Infect 1996;32:169-170.
198. Ramig RF. Genetics of the rotaviruses. Annu Rev Microbiol 1997;51:225-255.
199. Fields BN. Temperature-sensitive mutants of reovirus type 3: Features of genetic recombination. Virology 1971;46:142-148.
200. Fenner F. Myxomatosis in Australian wild rabbits - Evolutionary changes in an infectious disease. Harvey Lect 1957;53:25-55.
201. McNeill WH. Plagues and peoples: Natural history of infectious
202. Piot P, Bartos M, Ghys PD, Walker N, Schwartlander B. The global impact of HIV/AIDS. Nature 2001;410:968-973.
203. Lavanchy D, McMahon B. Worldwide prevalence and prevention of hepatitis C. In: Liang TJ, Hoofnagle JH, editors. Biomedical research reports. Hepatitis C. San Diego: Academic Press; 2000. p 185-201.
204. Desrosiers RC. HIV-1 origins: Finger on the missing link. Nature 1990;345:288-289.
205. Desrosiers RC, Daniel MD, Li Y. HIV-related lentiviruses of nonhuman primates. AIDS Res Hum Retroviruses 1989;5:465-473.
206. Sharp PM, Bailes E, Chaudhuri RR, Rodenburg CM, Santiago MO, Hahn BH. The origins of acquired immune deficiency syndrome viruses: Where and when? Philosophical transactions of the Royal Society of London - Series B. Biol Sci 2001;356:867-876.
207. Schneider J, Hunsmann G. Simian lentiviruses - The SIV group. AIDS 1988;2:1-9.
208. Farci P. Hepatitis C virus. The importance of viral heterogeneity. Clin Liver Dis 2001;5:895-916.
209. Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, Strazzera A, Chien DY, Munoz SJ, Balestrieri A, Purcell RH, Alter HJ. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science 2000;288:339-344.
210. Farci P, Strazzera R, Alter HJ, Farci S, Degioannis D, Coiana A, Peddis G, Usai F, Serra G, Chessa L, Diaz G, Balestrieri A, Purcell RH. Early changes in hepatitis C viral quasispecies during interferon therapy predict the therapeutic outcome. Proc Natl Acad Sci USA 2002;99:3081-3086.
211. Choo QL, Kuo G, Weiner AJ. Isolation of cDNA derived from blood-borne non-A, non-B viral hepatitis genome. Science 1989;244:359-362.
212. Yoo BJ, Spaete RR, Geballe AP, Selby M, Houghton M, Han JH. 5′ End-dependent translation initiation of hepatitis C viral RNA and the presence of putative positive and negative control elements within the 5′ untranslated region. Virology 1992;191:889-899.
213. Miller RH, Purcell RH. Hepatitis C virus shares amino acid sequence similarity with pestivirus and flaviviruses as well as members of two plant virus supergroups. Proc Natl Acad Sci USA 1990;87:2057-2061.
214. Bendinelli M, Vatteroni ML, Maggi F, Pistello M. Hepatitis C virus. Biology, pathogenesis, epidemiology, clinical description, and diagnosis. In: Specter S, editor. Viral hepatitis-Diagnosis, therapy, and prevention. Totowa, NJ: Humana Press; 1999. p 65-127.