huddlej
commented
1 year ago Actually, we want to scale substitution rates to match SARS-CoV-2 instead of seasonal coronaviruses, so we need a rate of ~8 x 10^-4 which is pretty close to what we already have from the MERS-CoV rate. I don't think we need to change any parameters in our simulations, but we do need to update our citations in the methods.
For our original simulations for coronaviruses, we scaled the number of generations per year to match the substitution rate of MERS-CoV which is 9.57 x 10^-4. Now that the simulations focus on seasonal coronaviruses which have a rate of 5 x 10^-4, we should inspect the substitution rate for the simulated trees and adjust the generations per year to match the expected rate.
One simple way to adjust for this change in rate would be to halve the generations per year from 30 to 15 to get a rate that is approximately half the MERS-CoV rate (i.e., get fewer substitutions accumulating in a year). If we decrease the number of generations per year, we do not need to simulate as many generations as we currently do to get as many total years.