Classification and structure of echovirus 5'-UTR sequences

• Published in: Virus genes Vol. 31; no. 3; pp. 293 - 306
• Main Authors: Siafakas, Nikolaos, Papaventsis, Dimitrios, Levidiotou-Stefanou, Stamatina, Vamvakopoulos, Nicholas C, Markoulatos, Panayotis
• Format: Journal Article
• Language: English
• Published: United States Springer Nature B.V 01.12.2005
• Subjects: 5' Untranslated Regions; Base Sequence; Coxsackievirus; DNA, Viral - genetics; Echovirus; Enterovirus; Enterovirus B, Human - classification; Enterovirus B, Human - genetics; Evolution, Molecular; Humans; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Phylogeny; Rhinovirus; RNA, Viral - chemistry; RNA, Viral - genetics; Sequence Homology, Nucleic Acid
• ISSN: 0920-8569; 1572-994X
• DOI: 10.1007/s11262-005-3244-1

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.