Comparison of intracellular and encapsidated viral RNA reveals selective constraints on reovirus recombination
Year: 2026
Type: preprint
Abstract: Recombination can generate genetic diversity among RNA viruses; yet, mechanisms governing recombination for segmented, double-stranded RNA viruses remain poorly understood. Reovirus genomes contain ten segments of double-stranded RNA. Previous analyses suggested low rates of reovirus RNA recombination and led to a proposed mechanism of recombination during minus-strand synthesis. These analyses focused on recombination events detected in genomic double-stranded RNA extracted from purified viral particles. In the current study, we looked deeper into the origins of the observed recombination events by assaying total cellular material, which comprises viral genomic material, as well as replication intermediates, mRNAs, and products of recombination that may not be eligible for packaging into virus particles. Intracellular viral RNA, which is almost exclusively plus-strand RNA, exhibited substantially higher recombination frequency than particle-associated double-stranded RNA. The diversity and frequency of identified junctions were more similar among samples of a given type (intracellular or virion-encapsidated) from distinct infections than between distinct sample types from the same infection. Although potential recombination sites are widely distributed across the genome, a more limited set was used in junctions in packaged viral RNA than in intracellular viral RNA. Together, these observations suggest recombination may occur more frequently than previously recognized during reovirus infection, and many such events likely occur during plus-strand synthesis. However, recombination products generated during viral transcription may be selectively incorporated into viral particles. Summary Recombination is an important means for RNA viruses to adapt and evolve, but recombination mechanisms for segmented, double-stranded RNA viruses are poorly understood. In previous work, we investigated recombination events in packaged viral RNA for the double-stranded RNA virus reovirus. We detected recombination relatively infrequently, and we proposed a mechanism of recombination during genomic RNA synthesis. Here, we report that recombination events are more frequent and potential recombination sites are used less selectively in viral plus-strand RNA transcripts isolated from infected cells than in viral double-stranded RNA packaged in matched purified virus particles. These findings suggest recombination is more promiscuous and widespread for double-stranded RNA viruses than previously recognized. However, the tightly coordinated assortment and packaging mechanisms of these viruses may selectively filter recombination products in the viral population.
Institution: Vanderbilt University Medical Center
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7221478511