Open Access Research article

Rooting human parechovirus evolution in time

Nuno R Faria, Michel de Vries, Formijn J van Hemert, Kimberley Benschop and Lia van der Hoek*

Author Affiliations

Department of Medical Microbiology, CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

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BMC Evolutionary Biology 2009, 9:164  doi:10.1186/1471-2148-9-164

Published: 15 July 2009



The Picornaviridae family contains a number of important pathogenic viruses, among which the recently reclassified human parechoviruses (HPeVs). These viruses are widespread and can be grouped in several types. Understanding the evolutionary history of HPeV could answer questions such as how long the circulating lineages last shared a common ancestor and how the evolution of this viral species is shaped by its population dynamics. Using both strict and relaxed clock Bayesian phylogenetics we investigated 1) the substitutions rates of the structural P1 and capsid VP1 regions and 2) evolutionary timescale of currently circulating HPeV lineages.


Our estimates reveal that human parechoviruses exhibit high substitution rates for both structural P1 and capsid VP1 regions, respectively 2.21 × 10-3 (0.48 – 4.21 × 10-3) and 2.79 × 10-3 (2.05 – 3.66 × 10-3) substitutions per site per year. These are within the range estimated for other picornaviruses. By employing a constant population size coalescent prior, the date of the most recent common ancestor was estimated to be at around 1600 (1427–1733). In addition, by looking at the frequency of synonymous and non-synonymous substitutions within the VP1 gene we show that purifying selection constitutes the dominating evolutionary force leading to strong amino acid conservation.


In conclusion, our estimates provide a timescale for the evolution of HPeVs and suggest that genetic diversity of current circulating HPeV types has arisen about 400 years ago.