Besides evolving through nucleotide substitution, viruses frequently also evolve by genetic recombination which can occur when related viral variants co-infect the same cells. Viruses with segmented or multipartite genomes can additionally evolve via the reassortment of genomic components. Various computational techniques are now available for identifying and characterizing recombination and reassortment. While these techniques have revealed both that all well studied segmented and multipartite virus species show some capacity for reassortment, and that recombination is common in many multipartite species, they have indicated that recombination is either rare or does not occur in species with segmented genomes. Reassortment and recombination can make it very difficult to study segmented/multipartite viruses using metagenomics-based approaches. Notable challenges include, both the accurate identification and assignment of genomic components to individual genomes, and the differentiation between natural ‘real’ recombination events and artifactual ‘fake’ recombination events arising from the inaccurate de novo assembly of genome component sequences determined using short read sequencing.
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