A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus

William Fitzsimmons; Robert J. Woods; John T. McCrone; Andrew Woodman; Jamie J. Arnold; Madhumita Yennawar; Richard Evans; Craig E. Cameron; Adam S. Lauring

Master Mix, Thermo 4368708). Two custom TaqMan probes (Applied Biosystems) were used to 356 quantify the number of WT and 3D G64S genomes. Duplicate wells were averaged, and relative 357 amounts of WT and 3D G64S RNA were determined by normalizing the cycle thresholds for each 358 these probes to those of the COM primer set (ΔCt = Ct Virus -Ct COM ). The normalized values for 359 virus passages 1-6 were then compared to passage 0 to obtain a ratio relative to P0 (ΔΔCt = 360 ΔCt PX -ΔCt P0 ). This relative Ct value was converted to reflect the fold change in the ratio (Δratio = The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/309880 doi: bioRxiv preprint 15 1F) were performed in the exact same manner except that serum free media were used in both 364 drug and mock passages.