On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

We understand demography to be a description of the size and structure of virus populations over time. In this discussion we will consider virus populations that are divided into demes at the host or cell level. Theory suggests that demography could have major implications for the loss of inserted sequences, with small population sizes, narrow bottlenecks, and short time intervals between bottlenecks resulting in high sequence stability. Hence, the stability of the inserted sequence cannot be viewed solely as a property of a genome, rather it is a phenotype and therefore depends on the environment. In this section, we motivate this argument and present a simulation model that highlights the effects of demography on the deletion of inserted sequences.