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Evolution and conservation in human parechovirus genomes

Çidem H. Williams¹

¹ Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
² Department of Virology, University of Tampere, Medical School, Tampere, Finland
³ Center for Laboratory Medicine, Tampere University Hospital, Tampere, Finland

Correspondence
Glyn Stanway
stanwg{at}essex.ac.uk

Human parechoviruses (HPeVs) are frequent pathogens with a seroprevalance of over 90 % in adults. Recent studies on these viruses have increased the number of HPeV types to eight. Here we analyse the complete genome of one clinical isolate, PicoBank/HPeV1/a, and VP1 and 3D protein sequences of PicoBank/HPeV6/a, isolated from the same individual 13 months later. PicoBank/HPeV1/a is closely related to other recent HPeV1 isolates but is distinct from the HPeV1 Harris prototype isolated 50 years ago. The availability of an increasing number of HPeV sequences has allowed a detailed analysis of these viruses. The results add weight to the observations that recombination plays a role in the generation of HPeV diversity. An important finding is the presence of unexpected conservation of codons utilized in part of the 3D-encoding region, some of which can be explained by the presence of a phylogenetically conserved predicted secondary structure domain. This suggests that in addition to the cis-acting replication element, RNA secondary structure domains in coding regions play a key role in picornavirus replication.

The GenBank/EMBL/DDBJ accession numbers for the sequence data obtained in this study are as follows: PicoBank/HPeV1/a, FM242866; PicoBank/HPeV6/a, VP1, FM242868, 3D, FM242867.

Two supplementary figures (showing the occurrence of bases and sequence alignments of HPeV strains) and two supplementary tables (showing primer sequences and the GenBank accession numbers of all sequences used in this study) are available with the online version of this paper.