We simulate the transcription and replication processes by considering the spatial-temporal distribution of template-associated polymerases. We first partition the viral genome and anti-genome templates into 40 segments, excluding their 39 and 59 end regions, which are the leader (Le) and trailer regions (Tr) for the genome, and the complementary trailer (Trc) and complementary leader regions (Lec) for the anti-genome, respectively ( Figure 9B ). For the genome template that is used for transcription as well as for replication, we specially grouped the segments into five genes ( Figure 9B ). We chose 40 as a minimum number for total segments which allows each gene to be split into a specific integer number of segments, proportional to the length of the gene. By considering the mechanisms for the interactions between polymerase and the intergenic regulatory sequences of the templates, as described below in the Transcription section, we simulated the polymerase flux into each segment over the time elapsed from the initiation of transcription on each template. Then we correlated the level of polymerase occupying each geneencoding section of the template with the synthesis rate of each corresponding viral mRNA. In a similar way, the distribution of polymerases on the replication templates was correlated with the synthesis rate of viral genome-sized RNA. Such explicit treatment of polymerase spatial distributions on the viral genome and antigenome templates was central to modeling the growth of wild-type and gene-rearranged virus strains. This treatment systematically accounts for polymerization-associated time delays and the polymerase fluxes into each template segment.