Mosaic structure of foot-and-mouth disease virus genomes

1 Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK 2 Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X05, Onderstepoort 0010, South Africa 3 Agricultural Research Service, USDA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY 11944, USA Correspondence D. T. Haydon D.Haydon{at}bio.gla.ac.uk The results of a simple pairwise-scanning analysis designed to identify inter-serotype recombination fragments, applied to genome data from 156 isolates of Foot-and-mouth disease virus (FMDV) representing all seven serotypes, are reported. Large numbers of candidate recombinant fragments were identified from all parts of the FMDV genome, with the exception of the capsid genes, within which such fragments are infrequent. As expected, intertypic fragment exchange is most common between geographically sympatric FMDV serotypes. After accounting for the likelihood of intertypic convergence in highly conserved parts of the FMDV genome, it is concluded that intertypic recombination is probably widespread throughout the non-structural genes, but that recombination over the 2B/C and 3B/C gene boundaries appears to be less frequent than expected, given the large numbers of recombinant gene fragments arising in these genes. A supplementary table showing FMDV sequence data used in this study is available in JGV Online. Present address: Trinity Centre for Bioengineering, School of Engineering, Trinity College, Dublin 2, Ireland. Present address: Division of Medical Biochemistry, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.