Source: http://www.asmscience.org/content/book/10.1128/9781555816698.ch14
Timestamp: 2019-04-24 06:33:02+00:00

Document:
In viruses, recombination may allow foreign genes to be acquired or may create a composite genome through recombination between different virus variants. The ability to identify a recombinant virus and the positions where recombination occurred is only as certain as the identification of the component parental viral genomes from which it was generated. Recombination detection thus shares many elements and is ultimately dependent on evolutionary reconstructions and, most importantly, on methods for the delineation of separate phylogenetic groups. The structure of the 5’ untranslated region (5’ UTR) of picornaviruses provides a further example of modular exchange through recombination during the evolution of separate genera within the picornavirus family. Members of the same picornavirus genus show conserved gene order and content, and over the much shorter evolutionary time scale in which species and serotypes developed, gene exchange is best documented as homologous recombination events. One of the problems with conceptualizing the process of recombination of enteroviruses and other picornaviruses revolves around the fundamentally different sequence relationships between serotypes in structural gene and nonstructural (NS) region sequences. From the evidence we have from the current range of picornaviruses infecting humans and other mammals, recombination has been a pervasive influence on both the early and contemporary evolution of these viruses. The wide range of molecular tools developed in picornavirus research, reverse genetics, and methods for in vitro and in vivo culture provides unprecedented future opportunities to explore the causes and consequences of recombination in RNA viruses.
1. Andersson, P.,, K. Edman, and, A. M. Lindberg. 2002. Molecular analysis of the echovirus 18 prototype: evidence of interserotypic recombination with echovirus 9. Virus Res. 85: 71– 83.
2. Arden, K. E.,, P. McErlean,, M. D. Nissen,, T. P. Sloots, and, I. M. Mackay. 2006. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J. Med. Virol. 78: 1232– 1240.
3. Bailly, J. L.,, D. Brosson,, C. Archimbaud,, M. Chambon,, C. Henquell, and, H. Peigue-Lafeuille. 2002. Genetic diversity of echovirus 30 during a meningitis outbreak, demonstrated by direct molecular typing from cerebrospinal fluid. J. Med. Virol. 68: 558– 567.
4. Bailly, J. L.,, A. Mirand,, C. Henquell,, C. Archimbaud,, M. Chambon,, F. Charbonne,, O. Traore, and, H. Peigue-Lafeuille. 2009. Phylogeography of circulating populations of human echovirus 30 over 50 years: nucleotide polymorphism and signature of purifying selection in the VP1 capsid protein gene. Infect. Genet. Evol. 9: 699– 708.
5. Benschop, K.,, M. de Vries,, R. Minaar,, G. Stanway,, L. van der Hoek,, K. Wolthers, and, P. Simmonds. 2010. Comprehensive full-length sequence analyses of human parechoviruses: diversity and recombination. J. Gen. Virol. 91: 145– 154.
6. Benschop, K. S.,, C. H. Williams,, K. C. Wolthers,, G. Stanway, and, P. Simmonds. 2008. Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints. J. Gen. Virol. 89: 1030– 1035.
7. Blinkova, O.,, A. Kapoor,, J. Victoria,, M. Jones,, N. Wolfe,, A. Naeem,, S. Shaukat,, S. Sharif,, M. M. Alam,, M. Angez,, S. Zaidi, and, E. L. Delwart. 2009. Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J. Virol. 83: 4631– 4641.
8. Blomqvist, S.,, A. L. Bruu,, M. Stenvik, and, T. Hovi. 2003. Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1. J. Gen. Virol. 84: 573– 580.
9. Burke, K. L.,, G. Dunn,, M. Ferguson,, P. D. Minor, and, J. W. Almond. 1988. Antigen chimaeras of poliovirus as potential new vaccines. Nature 332: 81– 82.
10. Cabrerizo, M.,, J. E. Echevarria,, I. Gonzalez,, T. de Miguel, and, G. Trallero. 2008. Molecular epidemiological study of HEV-B enteroviruses involved in the increase in meningitis cases occurred in Spain during 2006. J. Med. Virol. 80: 1018– 1024.
11. Calvert, J.,, T. Chieochansin,, K. Benschop,, E. C. McWilliam-Leitch,, J. F. Drexler,, K. Grywna,, H. da Costa Ribeiro,, C. Drosten,, H. Harvala,, Y. Poovorawan,, K. Wolthers, and, P. Simmonds. 2010. The recombination dynamics of human parecho-viruses; investigation of type-specific differences in frequency and epidemiological correlates. J. Gen. Virol. 91: 1229– 1238.
12. Cammack, N.,, A. Phillips,, G. Dunn,, V. Patel, and, P. D. Minor. 1988. Intertypic genomic rearrangements of poliovirus strains in vaccinees. Virology 167: 507– 514.
13. Chevaliez, S.,, A. Szendroi,, V. Caro,, J. Balanant,, S. Guillot,, G. Berencsi, and, F. Delpeyroux. 2004. Molecular comparison of echovirus 11 strains circulating in Europe during an epidemic of multisystem hemorrhagic disease of infants indicates that evolution generally occurs by recombination. Virology 325: 56– 70.
14. Choi, J.,, R. E. Means,, B. Damania, and, J. U. Jung. 2001. Molecular piracy of Kaposi’s sarcoma associated herpesvirus. Cytokine Growth Factor Rev. 12: 245– 257.
15. Costa-Mattioli, M.,, V. Ferre,, D. Casane,, R. Perez-Bercoff,, M. Coste-Burel,, B. M. Imbert-Marcille,, E. C. Andre,, C. Bressollette-Bodin,, S. Billaudel, and, J. Cristina. 2003. Evidence of recombination in natural populations of hepatitis A virus. Virology 311: 51– 59.
16. Cuervo, N. S.,, S. Guillot,, N. Romanenkova,, M. Combiescu,, A. Aubert-Combiescu,, M. Seghier,, V. Caro,, R. Crainic, and, F. Delpeyroux. 2001. Genomic features of intertypic recombinant Sabin poliovirus strains excreted by primary vaccinees. J. Virol. 75: 5740– 5751.
17. Furione, M.,, S. Guillot,, D. Otelea,, J. Balanant,, A. Candrea, and, R. Crainic. 1993. Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology 196: 199– 208.
18. Guillot, S.,, V. Caro,, N. Cuervo,, E. Korotkova,, M. Combiescu,, A. Persu,, A. Aubert-Combiescu,, F. Delpeyroux, and, R. Crainic. 2000. Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J. Virol. 74: 8434– 8443.
19. Han, T. H.,, J. Y. Chung,, E. S. Hwang, and, J. W. Koo. 2009. Detection of human rhinovirus C in children with acute lower respiratory tract infections in South Korea. Arch. Virol. 154: 987– 991.
20. Harvala, H.,, H. Kalimo,, J. Bergelson,, G. Stanway, and, T. Hyypia. 2005. Tissue tropism of recombinant coxsackieviruses in an adult mouse model. J. Gen. Virol. 86: 1897– 1907.
21. Harvala, H.,, H. Kalimo,, L. Dahllund,, J. Santti,, P. Hughes,, T. Hyypia, and, G. Stanway. 2002. Mapping of tissue tropism determinants in coxsackievirus genomes. J. Gen. Virol. 83: 1697– 1706.
22. Harvala, H.,, I. Robertson,, E. C. McWilliam Leitch,, K. Benschop,, K. C. Wolthers,, K. Templeton, and, P. Simmonds. 2008. Epidemiology and clinical associations of human parechovirus respiratory infections. J. Clin. Microbiol. 46: 3446– 3453.
23. Haydon, D. T.,, A. D. Bastos, and, P. Awadalla. 2004. Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments. J. Gen. Virol. 85: 1095– 1100.
24. Hellen, C. U., and, S. de Breyne. 2007. A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination. J. Virol. 81: 5850– 5863.
25. Huang, T.,, W. Wang,, M. Bessaud,, P. Ren,, J. Sheng,, H. Yan,, J. Zhang,, X. Lin,, Y. Wang,, F. Delpeyroux, and, V. Deubel. 2009. Evidence of recombination and genetic diversity in human rhinoviruses in children with acute respiratory infection. PLoS One 4: e6355.
26. Johnson, V. H., and, B. L. Semler. 1988. Defined recombinants of poliovirus and coxsackievirus: sequence-specific deletions and functional substitutions in the 5′-noncoding regions of viral RNAs. Virology 162: 47– 57.
27. Jones, M. S.,, V. V. Lukashov,, R. D. Ganac, and, D. P. Schnurr. 2007. Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J. Clin. Microbiol. 45: 2144– 2150.
28. Kapoor, A.,, J. Victoria,, P. Simmonds,, E. Slikas,, T. Chieochansin,, A. Naeem,, S. Shaukat,, S. Sharif,, M. M. Alam,, M. Angez,, C. Wang,, S. Zaidi,, R. W. Shafer,, S. Zaidi, and, E. Delwart. 2008. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc. Natl. Acad. Sci. USA 105: 20482– 20487.
29. Kendall, A.,, M. McDonald,, W. Bian,, T. Bowles,, S. C. Baumgarten,, J. Shi,, P. L. Stewart,, E. Bullitt,, D. Gore,, T. C. Irving,, W. M. Havens,, S. A. Ghabrial,, J. S. Wall, and, G. Stubbs. 2008. Structure of flexible filamentous plant viruses. J. Virol. 82: 9546– 9554.
30. Kistler, A.,, P. C. Avila,, S. Rouskin,, D. Wang,, T. Ward,, S. Yagi,, D. Schnurr,, D. Ganem,, J. L. DeRisi, and, H. A. Boushey. 2007. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J. Infect. Dis. 196: 817– 825.
31. Kistler, A. L.,, D. R. Webster,, S. Rouskin,, V. Magrini,, J. J. Credle,, D. P. Schnurr,, H. A. Boushey,, E. R. Mardis,, H. Li, and, J. L. DeRisi. 2007. Genome-wide diversity and selective pressure in the human rhinovirus. Virol. J. 4: 40.
32. Knowles, N. J. 2006. Picornaviridiae to Picornavirales: taxonomy on comparative genomics, abstr. A1. Northern Lights EUROPIC 2006. XIV Meet. Eur. Study Group Mol. Biol. Picornaviruses, Saariselka, Inari, Finland. Academic Press, London, England.
33. Lamson, D.,, N. Renwick,, V. Kapoor,, Z. Liu,, G. Palacios,, J. Ju,, A. Dean,, K. St. George,, T. Briese, and, W. I. Lipkin. 2006. MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004–2005. J. Infect. Dis. 194: 1398– 1402.
34. Lau, S. K.,, C. C. Yip,, H. W. Tsoi,, R. A. Lee,, L. Y. So,, Y. L. Lau,, K. H. Chan,, P. C. Woo, and, K. Y. Yuen. 2007. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J. Clin. Microbiol. 45: 3655– 3664.
35. Lee, W. M.,, C. Kiesner,, T. Pappas,, I. Lee,, K. Grindle,, T. Jartti,, B. Jakiela,, R. F. Lemanske, Jr.,, P. A. Shult, and, J. E. Gern. 2007. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS One 2: e966.
36. Lemon, S. M.,, R. W. Jansen, and, E. A. Brown. 1992. Genetic, antigenic and biological differences between strains of hepatitis A virus. Vaccine 10 (Suppl. 1) : S40– S44.
37. Lindberg, A. M.,, P. Andersson,, C. Savolainen,, M. N. Mulders, and, T. Hovi. 2003. Evolution of the genome of human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. J. Gen. Virol. 84: 1223– 1235.
38. Lu, H. H.,, X. Li,, A. Cuconati, and, E. Wimmer. 1995. Analysis of picornavirus 2A pro proteins: separation of proteinase from translation and replication functions. J. Virol. 69: 7445– 7452.
39. Lukashev, A. N. 2005. Role of recombination in evolution of enteroviruses. Rev. Med. Virol. 15: 157– 167.
40. Lukashev, A. N.,, O. E. Ivanova,, T. P. Eremeeva, and, L. V. Gmyl. 2008. Analysis of echovirus 30 isolates from Russia and new independent states revealing frequent recombination and re-emergence of ancient lineages. J. Clin. Microbiol. 46: 665– 670.
41. Lukashev, A. N.,, V. A. Lashkevich,, G. A. Koroleva,, J. Ilonen, and, A. E. Hinkkanen. 2004. Recombination in uveitis-causing enterovirus strains. J. Gen. Virol. 85: 463– 470.
42. Mackay, I. M. 2008. Human rhinoviruses: the cold wars resume. J. Clin. Virol. 42: 297– 320.
43. McErlean, P.,, L. A. Shackelton,, S. B. Lambert,, M. D. Nissen,, T. P. Sloots, and, I. M. Mackay. 2007. Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis. J. Clin. Virol. 39: 67– 75.
44. McGeoch, D. J.,, F. J. Rixon, and, A. J. Davison. 2006. Topics in herpesvirus genomics and evolution. Virus Res. 117: 90– 104.
45. McWilliam Leitch, C.,, J. W. Bendig,, M. Cabrerizo,, J. Cardosa,, T. Hyypia,, O. E. Ivanova,, A. Kelly,, A. C. M. Kroes,, A. N. Lukashev,, A. Macadam,, P. McMinn,, M. Roivainen,, G. Trallero,, D. J. Evans, and, P. Simmonds. 2009. Transmission networks and population turnover of echovirus 30. J. Virol. 83: 2109– 2118.
46. Minor, P. D.,, A. John,, M. Ferguson, and, J. P. Icenogle. 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.
47. Mirand, A.,, C. Henquell,, C. Archimbaud,, H. Peigue-Lafeuille, and, J. L. Bailly. 2007. Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events. J. Gen. Virol. 88: 166– 176.
48. Murdin, A. D.,, H. H. Lu,, M. G. Murray, and, E. Wimmer. 1992. Poliovirus antigenic hybrids simultaneously expressing antigenic determinants from all three serotypes. J. Gen. Virol. 73: 607– 611.
49. Naitow, H.,, J. Tang,, M. Canady,, R. B. Wickner, and, J. E. Johnson. 2002. L-A virus at 3.4 Å resolution reveals particle architecture and mRNA decapping mechanism. Nat. Struct. Biol. 9: 725– 728.
50. Norder, H.,, L. Bjerregaard, and, L. O. Magnius. 2002. Open reading frame sequence of an Asian enterovirus 73 strain reveals that the prototype from California is recombinant. J. Gen. Virol. 83: 1721– 1728.
51. Oberste, M. S.,, K. Maher,, M. L. Kennett,, J. J. Campbell,, M. S. Carpenter,, D. Schnurr, and, M. A. Pallansch. 1999. Molecular epidemiology and genetic diversity of echovirus type 30 (E30): genotypes correlate with temporal dynamics of E30 isolation. J. Clin. Microbiol. 37: 3928– 3933.
52. Oberste, M. S.,, K. Maher,, D. R. Kilpatrick, and, M. A. Pallansch. 1999. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J. Virol. 73: 1941– 1948.
53. Oberste, M. S.,, K. Maher, and, M. A. Pallansch. 2004. Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven serotypes. J. Virol. 78: 855– 867.
54. Oberste, M. S.,, S. Penaranda,, K. Maher, and, M. A. Pallansch. 2004. Complete genome sequences of all members of the species Human enterovirus A. J. Gen. Virol. 85: 1597– 1607.
55. Oberste, M. S.,, S. Penaranda, and, M. A. Pallansch. 2004. RNA recombination plays a major role in genomic change during circulation of coxsackie B viruses. J. Virol. 78: 2948– 2955.
56. Oprisan, G.,, M. Combiescu,, S. Guillot,, V. Caro,, A. Combiescu,, F. Delpeyroux, and, R. Crainic. 2002. Natural genetic recombination between co-circulating heterotypic enteroviruses. J. Gen. Virol. 83: 2193– 2200.
57. Palmenberg, A. C.,, D. Spiro,, R. Kuzmickas,, S. Wang,, A. Djikeng,, J. A. Rathe,, C. M. Fraser-Liggett, and, S. B. Liggett. 2009. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324: 55– 59.
58. Renwick, N.,, B. Schweiger,, V. Kapoor,, Z. Liu,, J. Villari,, R. Bull-mann,, R. Miething,, T. Briese, and, W. I. Lipkin. 2007. A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany. J. Infect. Dis. 196: 1754– 1760.
59. Rohll, J. B.,, D. H. Moon,, D. J. Evans, and, J. W. Almond. 1995. The 3′ untranslated region of picornavirus RNA: features required for efficient genome replication. J. Virol. 69: 7835– 7844.
60. Rohll, J. B.,, N. Percy,, R. Ley,, D. J. Evans,, J. W. Almond, and, W. S. Barclay. 1994. The 5′-untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J. Virol. 68: 4384– 4391.
61. Santti, J.,, H. Harvala,, L. Kinnunen, and, T. Hyypia. 2000. Molecular epidemiology and evolution of coxsackievirus A9. J. Gen. Virol. 81: 1361– 1372.
62. Santti, J.,, T. Hyypia,, L. Kinnunen, and, M. Salminen. 1999. Evidence of recombination among enteroviruses. J. Virol. 73: 8741– 8749.
63. Savolainen, C.,, P. Laine,, M. N. Mulders, and, T. Hovi. 2004. Sequence analysis of human rhinoviruses in the RNA-dependent RNA polymerase coding region reveals large within- species variation. J. Gen. Virol. 85: 2271– 2277.
64. Savolainen, C.,, T. Hovi, and, M. N. Mulders. 2001. Molecular epidemiology of echovirus 30 in Europe: succession of dominant sublineages within a single major genotype. Arch. Virol. 146: 521– 537.
65. Savolainen-Kopra, C.,, S. Blomqvist,, T. Smura,, M. Roivainen,, T. Hovi,, D. Kiang,, I. Kalra,, S. Yagi,, J. K. Louie,, H. Boushey,, J. Boothby, and, D. P. Schnurr. 2009. 5′ noncoding region alone does not unequivocally determine genetic type of human rhinovirus strains. J. Clin. Microbiol. 47: 1278– 1280.
66. Semler, B. L.,, V. H. Johnson, and, S. Tracy. 1986. A chimeric plasmid from cDNA clones of poliovirus and coxsackievirus produces a recombinant virus that is temperature-sensitive. Proc. Natl. Acad. Sci. USA 83: 1777– 1781.
67. Simmonds, P. 2006. Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J. Virol. 80: 11124– 11140.
68. Simmonds, P., and, J. Welch. 2006. Frequency and dynamics of recombination within different species of human enteroviruses. J. Virol. 80: 483– 493.
69. Stanway, G.,, P. J. Hughes,, G. D. Westrop,, D. M. Evans,, G. Dunn,, P. D. Minor,, G. C. Schild, and, J. W. Almond. 1986. Construction of poliovirus intertypic recombinants by use of cDNA. J. Virol. 57: 1187– 1190.
70. Tapparel, C.,, T. Junier,, D. Gerlach,, S. Cordey,, S. Van Belle,, L. Perrin,, E. M. Zdobnov, and, L. Kaiser. 2007. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics 8: 224.
71. Tapparel, C.,, T. Junier,, D. Gerlach,, S. Van Belle,, L. Turin,, S. Cordey,, K. Muhlemann,, N. Regamey,, J. D. Aubert,, P. M. Soccal,, P. Eigenmann,, E. Zdobnov, and, L. Kaiser. 2009. New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerg. Infect. Dis. 15: 719– 726.
72. Tosh, C.,, D. Hemadri, and, A. Sanyal. 2002. Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus. J. Gen. Virol. 83: 2455– 2460.
73. van Kuppeveld, F. J.,, P. J. van den Hurk,, W. van der Vliet,, J. M. Galama, and, W. J. Melchers. 1997. Chimeric coxsackie B3 virus genomes that express hybrid coxsackievirus-poliovirus 2B proteins: functional dissection of structural domains involved in RNA replication. J. Gen. Virol. 78: 1833– 1840.
74. Yang, C. F.,, H. Y. Chen,, J. Jorba,, H. C. Sun,, S. J. Yang,, H. C. Lee,, Y. C. Huang,, T. Y. Lin,, P. J. Chen,, H. Shimizu,, Y. Nishimura,, A. Utama,, M. Pallansch,, T. Miyamura,, O. Kew, and, J. Y. Yang. 2005. Intratypic recombination among lineages of type 1 vaccine-derived poliovirus emerging during chronic infection of an immunodeficient patient. J. Virol. 79: 12623– 12634.
75. Zoll, J.,, J. M. Galama, and, F. J. van Kuppeveld. 2009. Identification of potential recombination breakpoints in human parechoviruses. J. Virol. 83: 3379– 3383.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.