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Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events

¹ Université d'Auvergne, Laboratoire de Virologie-EA3843, UFR Médecine, 28 place Henri-Dunant, F-63001 Clermont-Ferrand, France
² CHU Clermont-Ferrand, Laboratoire de Virologie, Centre de Biologie, F-63003 Clermont-Ferrand, France

Correspondence
Jean-Luc Bailly
j-luc.bailly{at}u-clermont1.fr

In an earlier report, different variants of echovirus 30 (E-30), an enterovirus serotype, were identified during two outbreaks in 1997 and 2000. Here, the diversity of E-30 was investigated over a longer period (1991–2005) and the variations in four genomic segments were determined in 52 isolates involved in meningitis cases, to characterize the evolutionary processes underlying the emergence of lineages. Phylogenetic analysis of the VP1 sequences showed that five phylogenetic variants succeeded one another. When a partial 3CD segment was examined, the five variants split further into 10 lineages. Phylogenetic groupings observed with both the VP1 and 3CD sequences were clearly related to the calendar time of virus isolation. The rapid turnover of lineages during the study period was not associated with variations in amino acid residues in either the VP1 or the 3CD sequences, indicating major evolutionary contraints in E-30. The variation patterns were examined further along a subgenomic segment of 4878 nt in 13 virus isolates, representative of the 10 lineages. Breakpoints detected in the similarity profiles were investigated by bootscanning and maximum-likelihood phylogenetic analysis of virus genes. Evidence of several past recombination events was observed in the middle of the genome and predicted recombination crossover sites were mapped with precision. The contribution of recombination to the evolution of E-30 is substantial. It is associated tightly with the emergence of new genetic lineages and certain recombinants have undergone epidemic spread.

The GenBank/EMBL/DDBJ accession numbers for the 133 sequences determined in this work are AM236601–AM236624, AM236921–AM236924, AM236927, AM236991–AM237042, AM237043–AM237081 and AM237316–AM237328.

Supplementary tables showing echovirus 30 strains analysed in this study and parameters determined for the rate matrix of the GTR model, and a supplementary figure showing a schematic representation of the enterovirus genome and primers used for RT-PCR amplification and sequencing, are available in JGV Online.

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