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Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains

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Abstract

Recombination has been recognized as a major mechanism of evolution in enteroviruses. The Echovirus 30 (E-30) strain Gior was sequenced and phylogenetically compared to all available E-30 sequences to detect recombination events between the 5΄UTR and VP1 genomic regions. The comparison of phylogenetic trees of the 5΄UTR and VP1 revealed incongruences concerning strains, lineages and sub-lineages. Comparative analysis of 62 E-30 sub-genomic sequences revealed six different recombination events that almost all occurred in the same region, having a start point in the 3΄end of the 5΄ UTR and end point in VP4. The only exception was the sub-lineage of Gior for which both borders of recombination were located in the 5΄UTR. These results describe for the first time recombination events in this region in circulating EV-B strains, revealing the exact points of these recombination events, highlighting the impact of such events on the evolution and epidemiology of enteroviruses.

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Authors and Affiliations

  1. Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece

    Zaharoula Kyriakopoulou, Tilemachos G. Dimitriou, Dimitris Tsakogiannis, Dimitris Mossialos & Panayotis Markoulatos

  2. Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece

    Grigoris D. Amoutzias

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  1. Zaharoula Kyriakopoulou
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Correspondence to Zaharoula Kyriakopoulou.

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Funding

This study was funded by research grants of the Postgraduate Program “Toxicology”, of the University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology (grant number 5050).

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All authors declare that they have no conflicting or dual interests

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This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Handling Editor: Tim Skern.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online resource 1: Table describing the primers used for the complete genome sequencing of the strain Gior. (DOC 38 kb)

705_2017_3600_MOESM2_ESM.doc

Online resource 2: Table with the strains and groups of strains used in Similarity Plot. The mean distances within the groups for the region from150 to1090 nt are presented. (DOC 107 kb)

705_2017_3600_MOESM3_ESM.ppt

Online resource 3: Similarity Plot analysis for the non-recombinant E-30 groups a) e.C0 I, b)e.C0 II, c) e.C1 sub-lineage, d) e.C2 sub-lineage, e) f.C3 sub-lineage and f) d lineage. (PPT 349 kb)

705_2017_3600_MOESM4_ESM.pdf

Online resource 4: Phylogenetic trees for 5΄UTR (left) and VP1(right) genomic regions of 437 strains of E30 and other EV-B serotypes. The serotype, the name and the country of origin of each strain is presented for each sequence. (PDF 105 kb)

705_2017_3600_MOESM5_ESM.xls

Online resource 5: Annotation file for the strains included in phylogenetic analysis of online resource 4. For each sequence is presented the name of strain, the accession number, the serotype, the date and the country of origin. (XLS 157 kb)

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Kyriakopoulou, Z., Amoutzias, G.D., Dimitriou, T.G. et al. Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains. Arch Virol 163, 365–375 (2018). https://doi.org/10.1007/s00705-017-3600-1

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