Recombination and other genomic rearrangements in picornaviruses

Seminars in Virology

Volumn 8, Issue 2, 1997, Pages 77-84

  Agol, Vadim I ^a,b  

^a INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Deletions; Genomic rearrangements; Insertions; Picornavirus RNA; Recombination

Indexed keywords

VIRUS RNA;

GENE DELETION; GENE INSERTION; GENE REARRANGEMENT; GENETIC RECOMBINATION; NONHUMAN; PICORNAVIRUS; REVIEW; RNA SYNTHESIS; VIRUS GENOME;

PICORNAVIRIDAE; RNA VIRUSES;

EID: 0031457832     PISSN: 10445773     EISSN: None     Source Type: Journal    
DOI: 10.1006/smvy.1997.0112     Document Type: Article

References (67)

1. 1. Hirst, G. K. (1962) Genetic recombination with Newcastle disease virus, polioviruses, and influenza. Cold Spring Harbor Symp. Quant. Biol. 27, 303-309.
2. 2. Ledinko, N. (1963) 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 20, 107-119.
3. 3. Pringle, C. R. (1965) Evidence of genetic recombination in foot-and-mouth disease virus. Virology 25, 48-54.
4. 4. King, A. M. Q. (1988) Genetic recombination in positive strand RNA viruses. In RNA Genetics (E. Domingo, J. J. Holland, and P. Ahlquist, Eds.), Vol. 2, pp. 149-165. CRC Press, Boca Raton, FL.
5. 5. Cooper, P. D. (1977) Genetics of picornaviruses. Comp. Virol. 9, 133-207.
6. 6. Tolskaya, E. A., and Kolesnilova, M. S. (1977) Genetic analysis of the poliovirus. Vestn. Acad. Med. Nauk. SSSR 5, 3-10. [in Russian]
7. 7. McCahon, D. (1981) The genetics of aphthovirus. Arch. Virol. 69, 1-23.
8. 8. Romanova, L. I., Tolskaya, E. A., Kolesnikova, M. S., and Agol, V. I. (1980) Biochemical evidence for intertypic genetic recombination of polioviruses. FEBS Lett. 118, 109-112.
9. 9. Tolskaya, E. A., Romanova, L. I., Kolesnikova, M. S., and Agol, V. I. (1983) Intertypic recombination in poliovirus: Genetic and biochemical studies. Virology 124, 121-132.
10. 10. King, A. M. Q., McCahon, D., Slade, W. R., and Newman, J. W. I. (1982) Biochemical evidence of recombination within the unsegmented RNA genome of aphthovirus. J. Virol. 41, 66-77.
11. 11. King, A. M. Q., McCahon, D., Slade, W. R., and Newman, J. W. I. (1982) Recombination in RNA. Cell 29, 921-928.
12. 12. McCahon, D., King, A. M. Q., Roe, D. S., Slade, W. R., Newman, J. W. I., and Cleary, A. M. (1985) Isolation and biochemical characterization of intertypic recombinants of foot-and-mouth disease virus. Virus Res. 3, 87-100.
13. 13. King, A. M. Q., McCahon, D., Saunders, K., Newman, J. W. I., and Slade, W. R. (1985) Multiple sites of recombination within the RNA genome of foot-and-mouth disease virus. Virus Res. 3, 373-384.
14. 14. Saunders, K., King, A. M. Q., McCahon, D., Newman, J. W. I., Slade, W. R., and Forss, S. (1985) Recombination and oligonucleotide analysis of guanidine-resistant foot-and-mouth disease virus mutants. J. Virol. 56, 921-929.
15. 15. Agol, V. I., Grachev, V. P., Drozdov, S. G., Kolesnikova, M. S., Kozlov, V. G., Ralph, N. M., Romanova, L. I., Tolskaya, E. A., Tyufanov, A. V., and Viktorova, E. G. (1984) Construction and properties of intertypic poliovirus recombinants: first approximation mapping of the major determinants of neurovirulence. Virology 136, 41-55.
16. 16. Agol, V. I., Drozdov, S. G., Grachev, V. P., Kolesnikova, M. S., Kozlov, V. G., Ralph, N. M., Romanova, L. I., Tolskaya, E. A., Tyufanov, A. V., and Viktorova, E. G. (1985) Recombinants between attenuated and virulent strains of poliovirus type 1: Derivation and characterization of recombinants with centrally located crossover points. Virology 143, 467-477.
17. 17. Agut, H., Kean, K. M., Bellocq, C., Fichot, O., and Girard, M. (1987) Intratypic recombination of polioviruses: Evidence for multiple crossing-over sites on the viral genome. J. Virol. 61, 1722-1725.
18. 18. Emini, E. A., Leibowitz, J., Diamond, D. C., Bonin, J., and Wimmer, E. (1984) Recombination of Mahoney and Sabin strain poliovirus type 1: Analysis of in vitro phenotypic markers and evidence that resistance to guanidine maps in the nonstructural proteins. Virology 137, 74-85.
19. 19. Kew, O. M., and Nottay, B. K. (1984) Evolution of oral polio vaccine strains in humans occurs by both mutations and intramolecular recombination. In Modern Approaches to Vaccines (R. M. Channock, and R. A. Lerner, Eds.), pp. 357-367. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
20. 20. Romanova, L. I., Blinov, V. M., Tolskaya, E. A., Viktorova, E. G., Kolesnikova, M. S., Guseva, E. A., and Agol, V. I. (1986) The primary structure of crossover regions of intertypic poliovirus recombinants: A model of recombination between RNA genomes. Virology 155, 202-213.
21. 21. Kirkegaard, K., and Baltimore, D. (1986) The mechanism of recombination in poliovirus. Cell 47, 433-443.
22. 22. Lemon, S. M., Murphy, P. C., Shields, P. A., Ping, L-H., Feinstone, S. M., Cromeans, T., and Jansen, R. W. (1991) Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: Evidence for genetic recombination. J. Virol. 65, 2056-2065.
23. 23. Cole, C. N., Smoler, D., Wimmer, E., and Baltimore, D. (1971) Defective interfering particles of poliovirus. 1. Isolation and physical properties. J. Virol. 7, 478-485.
24. 24. Cole, C. N., and Baltimore, D. (1973) Defective interfering particles of poliovirus. 2. Nature of the defect. J. Mol. Biol. 76, 325-343.
25. 25. Lundquist, R. E., Sullivan, M., and Maizel, J. V., Jr. (1979) Characterization of a new isolate of poliovirus defective interfering particles. Cell 18, 759-769.
26. 26. Nomoto, A., Jacobson, A., Lee, J., Dunn, J., and Wimmer, E. (1979) Defective interfering particles of poliovirus: Mapping of the deletion and evidence that the deletions in the genome DI (1), (2), (3) are located in the same region. J. Mol. Biol. 128, 179-196.
27. 27. Kajigaya, S., Arakawa, H., Kuge, S., Koi, T., Imura, N., and Nomoto, A. (1985) Isolation and characterization of defective-interfering particles of poliovirus Sabin 1 strain. Virology 142, 307-316.
28. 28. Kuge, S., Saito, I., and Nomoto, A. (1986) Primary structure of poliovirus defective-interfering particle genomes and possible generation mechanisms of the particles. J. Mol. Biol. 192, 473-487.
29. 29. McClure, M. A., Holland, J. J., and Perrault, J. (1980) Generation of defective interfering particles in picornaviruses. Virology 100, 408-418.
30. 30. Jarvis, T. C., and Kirkegaard, K. (1991) The polymerase in its labyrinth: Mechanisms and implications of RNA recombination. Trends Genet. 7, 186-191.
31. 31. Lai, M. M. C. (1992) RNA recombination in animal and plant viruses. Microbiol. Rev. 56, 61-79.
32. 32. Wimmer, E., Hellen, C. U. T., and Cao, X. (1993) Genetics of poliovirus. Annu. Rev. Genet. 27, 353-436.
33. 33. Tolskaya, E. A., Romanova, L. I., Blinov, V. M., Viktorova, E. G., Sinyakov, A. N., Kolesnikova, M. S., and Agol, V. I. (1987) Studies on the recombination between RNA genomes of poliovirus: The primary structure and nonrandom distribution of crossover regions in the genomes of intertypic poliovirus recombinants. Virology 161, 54-61.
34. 34. King, A. M. Q. (1988) Preferred sites of recombination in poliovirus RNA: An analysis of 40 intertypic cross-over sequences. Nucleic Acids Res. 16, 11705-11723.
35. 35. Jarvis, T. C., and Kirkegaard, K. (1992) Poliovirus RNA recombination: Mechanistic studies in the absence of selection. EMBO J. 11, 3135-3145.
36. 36. Pilipenko, E. V., Gmyl, A. P., and Agol, V. I. (1995) A model for rearrangements in RNA genomes. Nucleic Acids Res. 23, 1870-1875.
37. 37. Charini, W. A., Todd, S., Gutman, B. A., and Semler, B. L. (1994) Transduction of a human RNA sequence by poliovirus. J. Virol. 68, 6547-6542.
38. 38. Wilson, B. (1988) Crossover regions in foot-and-mouth disease virus (FMDV) recombinants correspond to regions of high local secondary structure. Arch. Virol. 102, 131-139.
39. 39. Kuge, S., Kawamura, N., and Nomoto, A. (1989) Genetic variation occurring on the genome of an in vitro insertion mutant of poliovirus type 1. J. Virol. 63, 1069-1075.
40. 40. Minor, P. D., John, A., Ferguson, M., and Icenogle, J. P. (1986) Antigenic and molecular evolution of the vaccine strain of type 3 poliovirus during the period of excretion by a primary vaccinee. J. Gen. Virol. 67, 693-706.
41. 41. Cammack, N., Phillips, A., Dunn, G., Patel, V., and Minor, P. D. (1988) Intertypic genomic rearrangements of poliovirus strains in vaccinees. Virology 167, 507-514.
42. 42. Lipskaya, G. Y., Muzychenko, A. R., Kutitova, O. K., Maslova, S. V., Equestre, M., Drozdov, S. G., Perez Bercoff, R., and Agol, V. I. (1991) Frequent isolation of intertypic poliovirus recombinants with serotype 2 specificity from vaccine-associated polio cases. J. Med. Virol. 35, 290-296.
43. 43. Furione, M., Guillot, S., Otelea, D., Balanant, J., Candrea, A., and Crainic, R. (1993) Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology 196, 199-208.
44. 44. Georgescu, M. M., Delpeyroux, F., Targy-Panit, M., Balanant, J., Combiescu, M., Combiescu, A. A., Guillot, S., and Crainic, R. (1994) High diversity of poliovirus strains isolated from the central nervous system from patients with vaccine-associated paralytic poliomyelitis. J. Virol. 68, 8089-8901.
45. 45. Friedrich, F., Da-Silva, E. E., and Schatzmayr, H. G. (1996) Type 2 poliovirus recombinants isolated from vaccine-associated cases and from healthy contacts in Brazil. Acta Virol. 40, 27-33.
46. 46. Zheng, D. F., Zhang, L. B., Fang, Z. Y., Yang, C. F., Mulders, M., Pallanch, M. A., and Kew, O. M. (1993) Distribution of wild type 1 poliovirus genotypes in China. J. Infect. Dis. 168, 1361-1367.
47. 47. Georgescu, M.-M., Delpeyroux, F., and Crainic, R. (1995) Tripartite genome organization of a natural type 2 vaccine/nonvaccine recombinant poliovirus. J. Gen. Virol. 76, 2343-2348.
48. 48. Krebs, O., and Marquardt, O. (1992) Identification and characterization of foot-and-mouth disease virus O1 Burgwedel/1987 as an intertypic recombinant. J. Virol. 73, 613-619.
49. 49. Pilipenko, E. V., Blinov, V. M., Romanova, L. I., Sinyakov, A. N., Maslova, S. V., and Agol, V. I. (1989) Conserved structural domains in the 5′-untranslated region of picornaviral genomes: An analysis of the segment controlling translation and neurovirulence. Virology 168, 201-209.
50. 50. Pilipenko, E. V., Blinov, V. M., Chernov, B. K., Dmitrieva, T. M., and Agol, V. I. (1989) Conservation of the secondary structure elements of the 5′-untranslated region of cardio-and aphthovirus RNAs. Nucleic Acids Res. 17, 5701-5711.
51. 51. Brown, E. A., Day, S. P., Jansen, R. W., and Lemon, S. M. (1991) The 5′ nontranslated region of hepatitis A virus: Secondary structure and elements required for translation in vitro. J. Virol. 65, 5828-5838.
52. 52. Hyypiä, T., Horsnell, C., Maaronen, M., Khan, M., Kalkkinen, N., Auvinen, P., Kinnunen, L., and Stanway, G. (1992) A distinct picornavirus group identified by sequence analysis. Proc. Natl. Acad. Sci. USA 89, 8847-8851.
53. 53. Gorbalenya, A. E. (1995) Origin of RNA viral genomes: Approaching the problem by comparative sequence analysis. In Molecular Basis of Virus Evolution (A. J. Gibbs, C. H. Calisher, and F. Garcia-Arenal, Eds.), pp. 49-66. Cambridge Univ. Press, Cambridge, UK.
54. 54. Alexander, L., Lu, H. H., and Wimmer, E. (1994) Polioviruses containing picornavirus type 1 and/or type 2 internal ribosome entry site elements: Genetic hybrids and the expression of a foreign gene. Proc. Natl. Acad. Sci. USA 91, 1406-1410.
55. 55. Pilipenko, E. V., Gmyl, A. P., Maslova, S. V., Khitrina, E. V., and Agol, V. I. (1995) Attenuation of Theiler's murine encephalomyelitis virus by modifications of the oligopyrimidine/AUG tandem, a host-dependent translational cis element. J. Virol. 69, 864-870.
56. 56. Cao, X., Kuhn, R., and Wimmer, E. (1993) Replication of poliovirus RNA containing two VPg coding sequences leads to a specific deletion event. J. Virol. 67, 5572-5578.
57. 57. Cao, X., and Wimmer, E. (1996) Genetic variation of the poliovirus genome with two VPg coding units. EMBO J. 15, 23-33.
58. 58. Dildine, S. L., and Semler, B. L. (1989) The deletion of 41 proximal nucleotides reverts a poliovirus mutant containing a temperature-sensitive lesion in the 5′ noncoding region of genomic RNA. J. Virol. 63, 847-862.
59. 59. Pilipenko, E. V., Gmyl, A. P., Maslova, S. V., Svitkin, Y. V., Sinyakov, A. N., and Agol, V. I. (1992) Prokaryotic-like cis elements in the cap-independent internal initiation of translation on picornavirus RNA. Cell 68, 119-131.
60. 60. Haller, A. A., and Semler, B. L. (1992) Linker scanning mutagenesis of the internal ribosome entry site of poliovirus RNA. J. Virol. 66, 5075-5086.
61. 61. Gmyl, A. P., Pilipenko, E. V., Maslova, S. V., Belov, G. A., and Agol, V. I. (1993) Functional and genetic plasticities of the poliovirus genome: Quasi-infectious RNAs modified in the 5′-untranslated region yield a variety of pseudorevertants. J. Virol. 67, 6309-6316.
62. 62. Forss, S., Strebel, K., Beck, E., and Schaller, H. (1984) Nucleotide sequence and genome organization of foot-and-mouth disease virus. Nucleic Acids Res. 12, 6587-6601.
63. 63. Toyoda, H., Kohara, M., Kataoka, Y., Suganuma, T., Omata, T., Imura, N., and Nomoto, A. (1984) Complete nucleotide sequence of all three poliovirus serotype genomes. Implication for genetic relationship, gene function and antigenic determinants. J. Mol. Biol. 174, 561-586.
64. 64. Pilipenko, E. V., Blinov, V. M., and Agol, V. I. (1990) Gross rearrangements within the 5′-untranslated region of the picornaviral genomes. Nucleic Acids Res. 18, 3371-3375.
65. 65. Pilipenko, E. V., Maslova, S. V., Sinyakov, A. N., and Agol, V. I. (1992) Toward identification of cis-acting element involved in the replication of enterovirus and rhinovirus RNAs: A proposal for the existence of tRNA-like terminal structures. Nucleic Acids Res. 20, 1739-1745.
66. 66. Li, F., Browning, G. F., Studdert, M. J., and Crabb, B. S. (1996) Equine rhinovirus 1 is more closely related to foot-and-mouth disease virus than to other picornaviruses. Proc. Natl. Acad. Sci. USA 93, 990-995.
67. 67. Johnson, V. H., and Semler, B. L. (1988) Defined recombinants of poliovirus and coxsackievirus: Sequence-specific deletions and functional substitutions in the 5′-noncoding regions of viral RNA. Virology 162, 47-57.