On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

Genetic drift can also play an important role in determining the stability of inserted sequences, as inserts can have high stability if a viral population regularly passes through population bottlenecks. This idea is inspired by the empirical observation that a group IV plant virus appears to be stable when shortduration passages are used, but not in long-duration passages Zwart et al. 2014; Willemsen et al. 2016 Willemsen et al. , 2018 . Viruses pass through bottlenecks at many points during infection, in vitro and in vivo (Zwart and Elena 2015) , it is therefore important to consider these effects. Even if there is a large supply of deletions and strong selection for the deletion mutant, if deletion mutants fail to reach a frequency !/a, where a is the bottleneck size, they are unlikely to pass through the bottleneck (Willemsen et al. 2016 (Willemsen et al. , 2018 . This leads to a 'resetting' of the virus population by each bottleneck event (Fig. 1) , effectively resulting in high stability of the inserted sequences (Box 1, see also Fig. 2 ). Short passages shorten the time for deletion mutants to reach the frequency 1/a, making it more difficult for these variants to pass through bottlenecks and hereby promoting insert stability. It is important to remember that assays for detecting deletion mutants, such as deep sequencing or the polymerase chain reaction, do have limited sensitivity. Deletions may therefore also be detected more readily in longer passages, whilst low frequency mutations that will be purged by bottlenecks may not be detected (Bull, Nuismer, and Antia 2019) .