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Journal of Virology, January 2006, p. 483-493, Vol. 80, No. 1
0022-538X/06/$08.00+0     doi:10.1128/JVI.80.1.483-493.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Frequency and Dynamics of Recombination within Different Species of Human Enteroviruses

Peter Simmonds*{dagger} and Jon Welch{dagger}

Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom

Received 7 June 2005/ Accepted 29 September 2005

Enteroviruses are members of the family Picornaviridae that cause widespread infections in human and other mammalian populations. Enteroviruses are genetically and antigenically highly variable, and recombination within and between serotypes contributes to their genetic diversity. To investigate the dynamics of the recombination process, sequence phylogenies between three regions of the genome (VP4, VP1, and 3Dpol) were compared among species A and B enterovirus variants detected in a human population-based survey in Scotland between 2000 and 2001, along with contemporary virus isolates collected in the same geographical region. This analysis used novel bioinformatic methods to quantify phylogenetic compatibility and correlations with serotype assignments of evolutionary trees constructed for different regions of the enterovirus genome. Species B enteroviruses showed much more frequent, time-correlated recombination events than those found for species A, despite the equivalence in population sampling, concordant with a linkage analysis of previously characterized enterovirus sequences obtained over longer collection periods. An analysis of recombination among complete genome sequences by computation of a phylogenetic compatibility matrix (PCM) demonstrated sharply defined boundaries between the VP2/VP3/VP1 block and sequences to either side in phylogenetic compatibility. The PCM also revealed equivalent or frequently greater degrees of incompatibility between different parts within the nonstructural region (2A-3D), indicating the occurrence of extensive recombination events in the past evolution of this part of the genome. Together, these findings provide new insights into the dynamics of species A and B enterovirus recombination and evolution and into the contribution of structured sampling to documenting reservoirs, emergence, and spread of novel recombinant forms in human populations.

* Corresponding author. Mailing address: Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom. Phone: 44 0131 650 7927. Fax: 44 0131 650 6511. E-mail: Peter.Simmonds{at}ed.ac.uk.

{dagger} Both authors contributed equally to the study.

Journal of Virology, January 2006, p. 483-493, Vol. 80, No. 1
0022-538X/06/$08.00+0     doi:10.1128/JVI.80.1.483-493.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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