The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication but essential for the production of infectious virus

Joseph C. Ward; Lidia Lasecka-Dykes; Chris Neil; Oluwapelumi Adeyemi; Sarah Gold; Niall McLean; Caroline Wright; Morgan R. Herod; David Kealy; Emma Warner; Donald P. King; Tobias J. Tuthill; David J. Rowlands; Nicola J. Stonehouse

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint passage 0 (figure 5B). Therefore, it appears that replicons with a single PK are at a competitive 399 disadvantage compared to those with two or more. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.10.901801 doi: bioRxiv preprint 20 of infectious virus despite being able to replicate after transfection into cells, is consistent with 448 a requirement for RNA structure within the PK region being required for virus assembly. The 5′ UTR of FMDV is unique amongst picornaviruses due to its large size and the presence 454 of multiple RNA elements, some of which still have unknown function. One of these features 455 is a series of repeated PKs varying in number from 2-4, depending on virus strain. In this study, 456 we sequentially deleted or mutated the PKs to help understand their role in the viral life cycle. 457 We also confirmed the predicted PK structures by SHAPE mapping, although there may be Although all viruses isolated to date contain at least two PKs, replicons or viruses containing a 464 single PK were still replication competent. However, replicons with more than a single PK 465 were found to have a competitive advantage over replicons with a single PK when sequentially 466 passaged. Replicons lacking all PKs displayed poor passaging potential even when co-467 transfected with yeast tRNA, reinforcing the observation of a significant impact in replication.