Abstract
Enteroviruses are classified into two genetic clusters on the basis of 5′-UTR and all echoviruses (ECV) are classified together with coxsackie B viruses (CBV), coxsackie A viruses (CAV) types 2–10, 12, 14 and 16, and enteroviruses (EV) 68, 69, 71 and 73. During the present study, 5′-UTR-derived sequences constituting the largest part of the Internal Ribosome Entry Site (IRES) of ECVs were studied with respect to their possible secondary structures, which were predicted following the phenomenon of “covariance”, i.e. the existence of evolutionary pressure in favour of structural conservation in the light of nucleotide sequence variability. In this and previous studies, no correlation between overall 5′-UTR identity and the currently recognised Human Enterovirus species was found, implying that notwithstanding their divergent protein-encoding regions, these species are free to exchange 5′-UTRs by recombination. Secondary structure features which are known to be highly conserved amongst enteroviruses and specifically the GNRA tetraloop in secondary structure domain IV, involved in long-term tertiary interactions and loop B in secondary structure domain V with an as yet unknown function were also conserved in ECVs. In contrast, the C(NANCCA)G motif, which is considered to be important in virus transcription and translation, was not conserved in all ECVs and sequence patterns observed in other enterovirus groups and rhinoviruses were recorded.
Similar content being viewed by others
References
C.A. Tidona G. Darai (2001) The Springer Index of Viruses Springer New York 746–764
M.H.V. Regenmortel Particlevan C.M. Fauquet D.H.L. Bishop E.B. Carstens M.K. Estes S.M. Lemon J. Maniloff M.A. Mayo D.J. McGeoch C.R. Pringle R.B. Wickner (2000) Virus Taxonomy, Seventh Report of the International Committee on Taxonomy of Viruses Academic Press San Diego 657–664
J.L. Melnick (1990) NoChapterTitle B.N. Fields (Eds) Virology EditionNumber3 Lippincott-Raven Philadelphia 549–605
S. Diedrich G. Driesel E. Schreier (1995) J Med Virol 46 148–152 Occurrence Handle7636503
M.S. Oberste K. Maher M.A. Pallansch (2004) J Virol 78 855–867 Occurrence Handle10.1128/JVI.78.2.855-867.2004 Occurrence Handle14694117
T. Pöyry L. Kinnunen T. Hyypiä B. Brown C. Horsnell T. Hovi G. Stanway (1996) J Gen Virol 77 1699–1717 Occurrence Handle8760417
T. Hyypiä T. Hovi N.J. Knowles G. Stanway (1997) J Gen Virol 78 1–11 Occurrence Handle9010279
T. Pulli P. Koskimies T. Hyypiä (1995) Virology 212 30–38 Occurrence Handle10.1006/viro.1995.1450 Occurrence Handle7676647
N. Siafakas P. Markoulatos G. Stanway (2002) J Mol Evol 55 638–652 Occurrence Handle10.1007/s00239-002-2359-4 Occurrence Handle12486523
E.V. Pilipenko V.M. Blinov L.I. Romanova A.N. Sinyakov S.V. Malsova V.I. Agol (1989) Virology 168 201–209 Occurrence Handle10.1016/0042-6822(89)90259-6 Occurrence Handle2536978
M.A. Skinner V.R. Racaniello G. Dunn J. Cooper P.D. Minor J.W. Almond (1989) J Mol Biol 207 379–392 Occurrence Handle10.1016/0022-2836(89)90261-1 Occurrence Handle2547075
R. Andino G.E. Rieckhof D. Baltimore (1990) Cell 63 369–380 Occurrence Handle10.1016/0092-8674(90)90170-J Occurrence Handle2170027
R. Andino G.E. Rieckhof P.L. Achacoso D. Baltimore (1993) EMBO J 12 3587–3598 Occurrence Handle8253083
N. Siafakas P. Markoulatos G. Stanway G. Tzanakaki J. Kourea-Kremastinou (2002) Mol Cell Probe 16 209–216 Occurrence Handle10.1006/mcpr.2002.0414
V.M. Rivera D. Welsh J.V. Maizel (1988) Virology 165 42–50 Occurrence Handle10.1016/0042-6822(88)90656-3 Occurrence Handle2838971
A.M.Q. King F. Brown P. Christian T. Hovi T. Hyypiä N.J. Knowles S.M. Lemon P.D. Minor A.C. Palmenberg T. Skern G. Stanway (2000) NoChapterTitle M.H.V. Regenmortel ParticleVan C.M. Fauquet D.H.L. Bishop C.H. Calisher E.B. Carsten M.K. Estes S.M. Lemon J. Maniloff M.A. Mayo D.J. McGeoch C.R. Pringle R.B. Wickner (Eds) Virus Taxonomy,Seventh Report of the International Committee for the Taxonomy of Viruses Academic Press San Diego, New York 657–673
T. Pelletier G. Kaplan V.R. Racaniello N. Sonenberg (1988) Mol Cell Biol 8 1103–1112 Occurrence Handle2835660
R. Nicholson J. Pelletier S.-Y. Le N. Sonenberg (1991) J Virol 65 5886–5894 Occurrence Handle1656077
K. Meerovitch N. Sonenberg (1993) Semin Virol 4 217–227 Occurrence Handle10.1006/smvy.1993.1018
R.J. Jackson S.L. Hunt C.L. Gibbs A. Kaminski (1994) Mol Biol Rep 19 147–459 Occurrence Handle10.1007/BF00986957 Occurrence Handle7969103
A. Kaminski S.L. Hunt C.L. Gibbs R.L. Jackson (1994) NoChapterTitle J.K. Setlow (Eds) Genetic Engineering NumberInSeriesvol. 16 Plenum Press New York 115–155
G.J. Belsham N. Sonenberg (1996) Microbiol Rev 60 499–511 Occurrence Handle8840784
E. Ehrenfeld B.L. Semler (1995) Curr Top Microbiol Immunol 203 65–83 Occurrence Handle7555091
R. Klinck T. Sprules K. Gehring (1998) Biochem Biophys Res Commun 247 876–881 Occurrence Handle10.1006/bbrc.1998.8852 Occurrence Handle9647786
S.-Y. Le J.-H. Chen N. Sonenberg J.V. Maizel (1992) Virology 191 858–866 Occurrence Handle10.1016/0042-6822(92)90261-M Occurrence Handle1333125
G. Stanway (1990) J Gen Virol 71 2483–2501 Occurrence Handle2254747
A.M. Borman F.G. Deliat K.M. Kean (1994) EMBO J 13 3149–3157 Occurrence Handle8039507
J.B. Rohll N. Percy R. Ley D.J. Evans J.W. Almond W.S. Barclay (1994) J Virol 68 4384–4391 Occurrence Handle8207812
L.K. Johansen C.D. Morrow (2000) Virology 273 391–399 Occurrence Handle10.1006/viro.2000.0433 Occurrence Handle10915610
A. Szendroi M. El-Sageyer M. Takacs I. Mezey G. Berencsi (2000) Arch Virol 145 2575–2600 Occurrence Handle10.1007/s007050070009 Occurrence Handle11205106
J. Rinehart R.M. Gomez R.P. Root (1997) J Virol 71 3986–3991 Occurrence Handle9094675
J.J. Dunn J.R. Romero R. Wasserman H.A. Rotbart (2000) J Infect Dis 182 298–301 Occurrence Handle10.1086/315685 Occurrence Handle10882611
M. Gromeier D. Solecki D.D. Patel E. Wimmer (2000) Virology 273 248–257 Occurrence Handle10.1006/viro.2000.0418 Occurrence Handle10915595
J. Santti T. Hyypiä L. Kinnunen M. Salminen (1999) J Virol 73 8741–8749 Occurrence Handle10482628
B.H. Chua P.C. McMinn S.K. Lam K.B. Chua (2001) J Gen Virol 82 2629–2639 Occurrence Handle11602774
H.W. Pley K.M. Flaherty D.B. McKay (1994) Nature 372 111–113 Occurrence Handle10.1038/372111a0 Occurrence Handle7526219
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Siafakas, N., Papaventsis, D., Levidiotou-Stefanou, S. et al. Classification and Structure of Echovirus 5′-UTR Sequences. Virus Genes 31, 293–306 (2005). https://doi.org/10.1007/s11262-005-3244-1
Received:
Revised:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s11262-005-3244-1