On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

Given these complexities, we think it may be challenging to develop predictive models of insert stability, for different types of virus genomes under different conditions. We hope to see developments in this area, possibly linked to resurging interest in preventing and exploiting DI viruses. However, we think that experimental tests of the stability of viral constructs will remain important in the foreseeable future. Experimental evolution can detect design problems in engineered genomes by looking at fitness and evolutionary stability (Springman et al.) . As Springman and collaborators suggest, experimental evolution may also prove useful for optimizing the stability of expression vectors by ameliorating constraints for which solutions are hard to predict because we lack a mechanistic understanding, such as codon usage (Carrasco, de la Iglesia, and Elena 2007; Agashe et al. 2013) . This approach can lead to improved engineering of viral genomes, which is also of interest for designing vectors with tags to follow viral infection, and for the use of viral vectors for gene therapy as well as for vaccine vectors. Finally, for real-world applications it can be useful to determine quantitatively the impact of the loss of inserted sequences on the desired output. For example, models suggest that deletions in vector vaccines may not have a large impact on eliciting the desired immune response (Bull, Nuismer, and Antia 2019) .