The association of recombination events in the founding and emergence of subgenogroup evolutionary lineages of human enterovirus 71

Journal of Virology

Volumn 86, Issue 5, 2012, Pages 2676-2685

  Leitch, E C McWilliam ^a   Cabrerizo, M ^b   Cardosa, J ^c   Harvala, H ^d   Ivanova, O E ^e   Koike, S ^f   Kroes, A C M ^g   Lukashev, A ^e   Perera, D ^b   Roivainen, M ^h   Susi, P ⁱ   Trallero, G ^b   Evans, D J ^j   Simmonds, P ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c UNIVERSITI MALAYSIA SARAWAK   (Malaysia)

^d ROYAL INFIRMARY OF EDINBURGH   (United Kingdom)

^e CHUMAKOV INSTITUTE OF POLIOMYELITIS AND VIRAL ENCEPHALITIDES   (Russian Federation)

^f TOKYO METROPOLITAN INSTITUTE OF MEDICAL SCIENCE   (Japan)

^g LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^h NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

ⁱ UNIVERSITY OF TURKU   (Finland)

^j UNIVERSITY OF WARWICK   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

3DPOL GENE; ARTICLE; CLADISTICS; CONTROLLED STUDY; COXSACKIE VIRUS A; COXSACKIE VIRUS A16; ECHO VIRUS; ENTEROVIRUS 71; GENETIC ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEROTYPE; UNINDEXED SEQUENCE; VIRUS GENE; VIRUS GENOME; VIRUS RECOMBINATION; VP1 GENE;

ENTEROVIRUS A, HUMAN; ENTEROVIRUS INFECTIONS; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; VIRAL PROTEINS;

COXSACKIEVIRUS; HUMAN ECHOVIRUS 9; HUMAN ENTEROVIRUS 71;

EID: 84857817153     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.06065-11     Document Type: Article

References (67)

1. Andersson P, Edman K, Lindberg AM. 2002. Molecular analysis of the echovirus 18 prototype: evidence of interserotypic recombination with echovirus 9. Virus Res. 85:71-83.
2. Bailly JL, et al. 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.
3. Benschop K, et al. 2010. Comprehensive full length sequence analyses of human parechoviruses; diversity and recombination. J. Gen. Virol. 91:151-154.
4. Benschop KS, Williams CH, Wolthers KC, Stanway G, Simmonds P. 2008. Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints. J. Gen. Virol. 89:1030-1035.
5. Bible JM, Pantelidis P, Chan PKS, Tong CYW. 2007. Genetic evolution of enterovirus 71: epidemiological and pathological implications. Rev. Med. Virol. 17:371-379.
6. Brown BA, Oberste MS, Alexander JP, Jr., Kennett ML, Pallansch MA. 1999. Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998. J. Virol. 73:9969-9975.
7. Calvert J, et al. 2010. The recombination dynamics of human parechoviruses; investigation of type-specific differences in frequency and epidemiological correlates. J. Gen. Virol. 91:1229-1238.
8. Cammack N, Phillips A, Dunn G, Patel V, Minor PD. 1988. Intertypic genomic rearrangements of poliovirus strains in vaccinees. Virology 167:507-514.
9. Cardosa MJ, et al. 2003. Molecular epidemiology of human enterovirus 71 strains and recent outbreaks in the Asia-Pacific region: comparative analysis of the VP1 and VP4 genes. Emerg. Infect. Dis. 9:461-468.
10. Chan YF, Abubakar S. 2004. Recombinant human enterovirus 71 in hand, foot and mouth disease patients. Emerg. Infect. Dis. 10:1468-1470.
11. Chang LY, et al. 2008. HLA-A33 is associated with susceptibility to enterovirus 71 infection. Pediatrics 122:1271-1276.
12. Chen KT, Chang HL, Wang ST, Cheng YT, Yang JY. 2007. Epidemiologic features of hand-foot-mouth disease and herpangina caused by enterovirus 71 in Taiwan, 1998-2005. Pediatrics 120:E244 -E252.
13. Chen TC, et al. 2006. Combining multiplex reverse transcription-PCR and a diagnostic microarray to detect and differentiate enterovirus 71 and coxsackievirus A16. J. Clin. Microbiol. 44:2212-2219.
14. Chen X, et al. 2010. Analysis of recombination and natural selection in human enterovirus 71. Virology 398:251-261.
15. Chevaliez S, et al. 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.
16. Cuervo NS, et al. 2001. Genomic features of intertypic recombinant Sabin poliovirus strains excreted by primary vaccinees. J. Virol. 75:5740-5751.
17. Ding NZ, et al. 2009. Appearance of mosaic enterovirus 71 in the 2008 outbreak of China. Virus Res. 145:157-161.
18. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
19. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
20. Furione M, et al. 1993. Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology 196:199-208.
21. Guillot S, et al. 2000. Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J. Virol. 74:8434-8443.
22. Harvala H, Wolthers K, Simmonds P. 2010. Parechoviruses in children: understanding a new infection. Curr. Opin. Infect. Dis. 23:224-230.
23. Hosoya M, et al. 2006. Genetic diversity of enterovirus 71 associated with hand, foot and mouth disease epidemics in Japan from 1983 to 2003. Pediatr. Infect. Dis. J. 25:691-694.
24. Huang SC, et al. 2008. Appearance of intratypic recombination of enterovirus 71 in Taiwan from 2002 to 2005. Virus Res. 131:250-259.
25. Huang SW, et al. 2009. Reemergence of enterovirus 71 in 2008 in Taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008. J. Clin. Microbiol. 47:3653-3662.
26. Huang YP, et al. 2010. Genetic diversity and C2-like subgenogroup strains of enterovirus 71, Taiwan, 2008. Virol. J. 7:277.
27. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23:1891-1901.
28. Kung S-H, et al. 2007. Genetic and antigenic analyses of enterovirus 71 isolates in Taiwan during 1998-2005. Clin. Microbiol. Infect. Dis. 13:782-787.
29. Lee TC, et al. 2009. Diseases caused by enterovirus 71 infection. Pediatr. Infect. Dis. J. 28:904-910.
30. Lindberg AM, Andersson P, Savolainen C, Mulders MN, Hovi T. 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.
31. Lukashev AN. 2005. Role of recombination in evolution of enteroviruses. Rev. Med. Virol. 15:157-167.
32. Lukashev AN, et al. 2005. Recombination in circulating human enterovirus B: independent evolution of structural and non-structural genome regions. J. Gen. Virol. 86:3281-3290.
33. Lukashev AN, Lashkevich VA, Koroleva GA, Ilonen J, Hinkkanen AE. 2004. Recombination in uveitis-causing enterovirus strains. J. Gen. Virol. 85:463-470.
34. Martin DP, et al. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463.
35. McMinn P, et al. 2001. Phylogenetic analysis of enterovirus 71 strains isolated during linked epidemics in Malaysia, Singapore, and Western Australia. J. Virol. 75:7732-7738.
36. McMinn P, Stratov I, Nagarajan L, Davis S. 2001. Neurological manifestations of enterovirus 71 infection in children during an outbreak of hand, foot, and mouth disease in western Australia. Clin. Infect. Dis. 32:236-242.
37. McWilliam Leitch EC, et al. 2009. Transmission networks and population turnover of echovirus 30. J. Virol. 83:2109-2118.
38. McWilliam Leitch EC, et al. 2010. Evolutionary dynamics and temporal/geographical correlates of recombination in the human enteroviruses, echovirus 9, 11, and 30. J. Virol. 84:9292-9300.
39. Minor PD, John A, Ferguson M, Icenogle JP. 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.
40. Mizuta K, et al. 2009. Cross-antigenicity among EV71 strains from different genogroups isolated in Yamagata, Japan, between 1990 and 2007. Vaccine 27:3153-3158.
41. Norder H, Bjerregaard L, Magnius LO. 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.
42. Oberste MS, Maher K, Pallansch MA. 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.
43. Oberste MS, Penaranda S, Maher K, Pallansch MA. 2004. Complete genome sequences of all members of the species human enterovirus A. J. Gen. Virol. 85:1597-1607.
44. Ooi MH, et al. 2007. Human enterovirus 71 disease in Sarawak, Malaysia: a prospective clinical, virological, and molecular epidemiological study. Clin. Infect. Dis. 44:646-656.
45. Oprisan G, et al. 2002. Natural genetic recombination between cocirculating heterotypic enteroviruses. J. Gen. Virol. 83:2193-2200.
46. Podin Y, et al. 2006. Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years. BMC Public Health 6:180.
47. Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
48. Santti J, Harvala H, Kinnunen L, Hyypia T. 2000. Molecular epidemiology and evolution of coxsackievirus A9. J. Gen. Virol. 81:1361-1372.
49. Santti J, Hyypia T, Kinnunen L, Salminen M. 1999. Evidence of recombination among enteroviruses. J. Virol. 73:8741-8749.
50. Savolainen C, Hovi T, Mulders MN. 2001. Molecular epidemiology of echovirus 30 in Europe: succession of dominant sublineages within a single major genotype. Arch. Virol. 146:521-537.
51. Schmidt NJ, Lennette EH, Ho HH. 1974. An apparently new enterovirus isolated from patients with disease of the central nervous system. J. Infect. Dis. 129:304-309.
52. Schuffenecker I, et al. 2011. Epidemiology of human enterovirus 71 infections in France, 2000-2009. J. Clin. Virol. 50:50-56.
53. Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23:7-9.
54. Shih SR, et al. 2000. Genetic analysis of enterovirus 71 isolated from fatal and non-fatal cases of hand, foot and mouth disease during an epidemic in Taiwan, 1998. Virus Res. 68:127-136.
55. Simmonds P. 2006. Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J. Virol. 80:11124-11140.
56. Simmonds P, Welch J. 2006. Frequency and dynamics of recombination within different species of human enteroviruses. J. Virol. 80:483-493.
57. Singh S, Poh CL, Chow VT. 2002. Complete sequence analyses of enterovirus 71 strains from fatal and non-fatal cases of the hand, foot and mouth disease outbreak in Singapore (2000). Microbiol. Immunol. 46:801-808.
58. Solomon T, et al. 2010. Virology, epidemiology, pathogenesis, and control of enterovirus 71. Lancet Infect. Dis. 10:778-790.
59. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
60. Stanway G, et al. 2005. Family Picornaviridae, p. 757-778. In Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (ed.), Virus taxonomy. Eighth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, London, United Kingdom.
61. Tee KK, et al. 2010. Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene J. Virol. 84:3339-3350.
62. Tu PV, et al. 2007. Epidemiologic and virologic investigation of hand, foot, and mouth disease, southern Vietnam, 2005. Emerg. Infect. Dis. 13:1733-1741.
63. van der Sanden S, van der Avoort H, Lemey P, Uslu G, Koopmans M. 2010. Evolutionary trajectory of the VP1 gene of human enterovirus 71 genogroup B and C viruses. J. Gen. Virol. 91:1949-1958.
64. van der Sanden S, et al. 2011. Detection of recombination breakpoints in the genomes of human enterovirus 71 strains isolated in the Netherlands in epidemic and non-epidemic years, 1963-2010. Infect. Genet. Evol. 11:886-894.
65. Wong SSY, Yip CCY, Lau SKP, Yuen KY. 2010. Human enterovirus 71 and hand, foot and mouth disease. Epidemiol. Infect. 138:1071-1089.
66. Yoke-Fun C, Abubakar S. 2006. Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes. BMC Microbiol. 6:74.
67. Zoll J, Galama JM, van Kuppeveld FJ. 2009. Identification of potential recombination breakpoints in human parechoviruses. J. Virol. 83:3379-3383.