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Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints

¹ Department of Medical Microbiology, Laboratory of Clinical Virology, Academic Medical Center, Amsterdam, The Netherlands
² Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
³ Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Edinburgh EH9 1AJ, UK

Correspondence
K. S. M. Benschop
k.s.benschop{at}amc.uva.nl

Human parechoviruses (HPeVs), members of the family Picornaviridae, are classified into six types. To investigate the dynamics and likelihood of recombination among HPeVs, we compared phylogenies of two distant regions (VP1 and 3Dpol) of 37 HPeV isolates (types 1 and 3–5) and prototype sequences (types 1–6). Evidence for frequent recombination between HPeV1, 4, 5 and 6 was found. The likelihood of recombination was correlated with the degree of VP1 divergence and differences in isolation dates, both indicative of evolutionary times of divergence. These temporal dynamics were found to be most similar to those of human enterovirus species B variants. In contrast, HPeV3 remained phylogenetically distinct from other types throughout the genome. As HPeV3 is equally divergent in nucleotide sequence from the other HPeV types, its genetic isolation may reflect different biology and changed cellular tropisms, arising from the deletion of the RGD motif, and likely use of a non-integrin receptor.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are EU170302–EU170304 and AM933167–AM933171 (VP1) and EU170312–EU170340 and AM933159–AM933166 (3Dpol).

A supplementary table showing HPeV sequence data is available with the online version of this paper.

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