The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies However, previous methods for detecting recombination and reassortment events cannot handle the computational requirements of analyzing tens of thousands of genomes, a scenario that has now emerged in the effort to track the spread of the SARS-CoV-2 virus Furthermore, the low divergence of near-identical genomes sequenced in short periods of time presents a statistical challenge not addressed by available methods In this work we present Bolotie, an efficient method designed to detect recombination and reassortment events between clades of viral genomes We applied our method to a large collection of SARS-CoV-2 genomes and discovered hundreds of isolates that are likely of a recombinant origin In cases where raw sequencing data was available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads Our findings further show that several recombinants appear to have persisted in the population
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie