EVA: Examining foodborne virus evolution using the Enteric Virus Analysis tool
Graham Etherington1, Ian Roberts2, Jo Dicks, Vic Rayward-Smith
1Graham.Etherington@bbsrc.ac.uk, John Innes Centre; 2Ian.Roberts@bbsrc.ac.uk, Institute of Food Research
Foodborne viruses infect 1 million people in the UK and 23 million people in the USA each year. We wish to understand more about their origin, evolution and molecular mechanisms employed to invade the gastrointestinal tract of the host. A software environment (EVA), integrating novel and existing software has been designed to address these problems. Here we describe the software environment, examine the evolution of viral sequences as related to host phylogeny (Co-phylogeny mapping) and introduce new software developed to examine recombination events in viral sequences.
Co-Phylogeny Mapping determines host (mammalian) and parasite (virus) phylogeny. All the potentially optimal solutions (termed a ‘Jungle’) are produced and the ‘cost’ of each tree is calculated. The maps with the lowest costs are put forward. The program uses TreeMap® developed by Mike Charleston, University of Oxford.
Recombination Analysis Tool (RAT) is a Java based application designed to examine recombination in viral sequences. The program takes a DNA or protein alignment file with any number of sequences, and examines the sequences in relation to a given ‘test sequence’ (also part of the alignment file). Using a sliding window (of a given size) it produces pairwise comparisons between the test sequence and the remaining sequences, and then plots them to a dialog window. RAT also contains a search feature that examines all the sequences in the alignment and reports potential areas of recombination for each sequence.
Using these approaches within an integrated software environment has many advantages. Here we describe new information concerning evolution of a particular class of foodborne viruses that has arisen from such studies.