FluRF, an automated flu virus reassortment finder based on phylogenetic trees

Reassortments are events in the evolution of the genome of influenza (flu). As reassortments have been implicated in major human pandemics of the last century, their identification has become a health priority. While such identification can be done on a small dataset by a biologist (using phylogenetic trees), databases of flu sequences are growing exponentially, so that it is imperative to develop automated identification methods. However, current methods are limited to pairwise segment comparisons. We present FluRF, a fully automated flu virus reassortment finder. FluRF is inspired by the visual approach to reassortment identification and thus uses the reconstructed phylogenetic trees of the individual segments and the full genome. We also present a simple flu evolution simulator, used to produce synthetic datasets to tune the FluRF parameters. On synthetic datasets produced by our flu evolution simulator, FluRF, tuned for a 0% false positive rate, yielded false negative rates of 10% or less. FluRF corroborated two new reassortments identified by visual analysis of 75 Human H3N2 New York flu strains from 2005-2008 and gave partial verification of reassortments found using another bioinformatics method. FluRF finds reassortments by a bottom-up search of the full-genome and segment-based phylogenetic trees for candidate clades-groups of one or more sampled viruses that are separated from the other variants from the same season. Candidate clades in each tree are tested to guarantee confidence values, using the lengths of key edges as well as other tree parameters; clades with reassortments must have validated incongruencies among segment trees. FluRF demonstrates robustness of prediction for geographically and temporally expanded datasets, and is not limited to finding reassortments with previously collected sequences. The complete source code is available from lcbb.epfl.ch/software.html.