A method for the unbiased quantification of reassortment in segmented viruses

Abstract The diversification of segmented viruses via reassortment is important to understand due to the contributions of reassortment to viral evolution and emergence. Methods for the quantification of reassortment have been described, but are often cumbersome and best suited for the analysis of reassortment between highly divergent parental strains. While it is useful to understand the potential of divergent parents to reassort, outcomes of such heterologous reassortment are driven by differential selection acting on the progeny and are typically strain specific. To quantify reassortment, a system free of differential selection is needed. We have generated such a system for influenza A virus and for mammalian orthoreovirus by constructing well-matched parental viruses carrying small genetic tags. The method utilizes high-resolution melt technology for the identification of reassortant viruses. Ease of sample preparation and data analysis enables streamlined genotyping of a large number of virus clones. The method described here thereby allows quantification of the efficiency of unbiased reassortment and can be applied to diverse segmented viruses. Highlights Genetic tagging of viruses can be achieved without altering fitness High-resolution melt can detect single nucleotide differences in viruses Unbiased reassortment of influenza A virus and mammalian orthoreovirus can be quantified