JVI Accepts, published online ahead of print on 13 September 2006

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J. Virol. doi:10.1128/JVI.01100-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Recombination patterns in aphthoviruses mirror those found in other picornaviruses

Livio Heath, Eric van der Walt, Arvind Varsani, and Darren P. Martin^*

Department of Molecular & Cell Biology, Faculty of Science, University of Cape Town, Rondebosch, 7701, South Africa; Electron Microscopy Unit, University of Cape Town, Rondebosch, 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa

^* To whom correspondence should be addressed. Email: Darren{at}science.uct.ac.za.

Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase. There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related Picornoviruses. Here we use an extensive set of recombination detection methods to identify eighty-six unique potential recombination events amongst 125 publicly available FMDV complete genome sequences. The large number of events detected between members of different serotypes suggests that horizontal flow of sequences amongst the serotypes is both relatively common and does not incur severe fitness costs. Interestingly, the distribution of recombination breakpoints was found to be largely non-random. Whereas there are clear breakpoint cold-spots within the structural genes, two statistically significant hot-spots precisely separate these from the non-structural genes. Very similar breakpoint distributions were found for other picornovirus species in the genera, Enterovirus and Teschovirus. Our results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally interchangeable modules, supporting recent proposals that the structural and non-structural coding regions of the picornaviruses are evolving largely independently of one another.

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