Shrinkage of Genome Size in a Plant RNA Virus upon Transfer of an Essential Viral Gene into the Host Genome

Tromas, Nicolas; Zwart, Mark P.; Forment, Javier; Elena, Santiago F.

NIRVs are thought to impact viruses by-in some casesconferring virus resistance to host organisms (Koonin, 2010) . However, these virus-derived sequences could also impact the evolution of virus populations. Here, we used an experimental model system to study the effects of NIRV expression on virus populations, using TEV and transgenic tobacco plants expressing its replicase, NIb. We found that 1) the loss of NIb cistron leads to higher within-host fitness in transgenic plants, 2) that genomic deletions quickly accumulate in a full-length virus passaged in transgenic plants, and 3) that the evolution of a virus population can be contingent upon the deletion of virus genes, although many aspects of phenotypic and molecular evolution were unchanged. Overall, our results therefore suggest that the expression of NIRVs could have far-reaching consequences for virus evolution. Moreover, these effects can occur on relatively short timescales (i.e., deletion variants were generated de novo and reached frequencies of~0.25 within four 3-week passages). These changes on short timescales support the notion that plausible epidemiological models of virus spread in NIRV-expressing host populations need to take virus evolution into consideration. For example, if large genomic deletions occur rapidly in NIRV-expressing hosts, then eventually many virus-infected hosts will only be infectious to those hosts expressing the NIRV. The generation of various classes of infectious hosts could in this case decrease viral transmission between hosts, an effect that could be further augmented by the clustering of NIRVexpressing hosts.