where mRNA i is concentration of mRNAs for gene i, k d,mRNA is the decay rate constant of mRNA that is the same for all five viral mRNAs [54] , and pol t,i is the total concentration of the polymerases occupying on the ith gene. Our formulation for transcription assumes that the synthesis of viral mRNAs is rate-controlled by the transcription initiation as well as the elongation of polymerase. Transcription initiation rate is parameterized by the spacing between neighboring polymerases in our model. At a given polymerase elongation rate, the larger polymerase spacing indicates the lower rate of transcription initiation. Transcription initiation modulates the input of polymerases to the leader region of the genome.