On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

A cost of the insert can arise because of the attributes of the inserted sequence (i.e. metabolic costs of expressing extra genes, toxicity of gene products), reorganization of the genome due to the insertion (i.e. disruption of the regulation of gene expression, polyprotein processing, and subgenomic RNAs), or limitations on genome size imposed by virus-particle packaging. Deletion of the inserted sequence is therefore not the only plausible class of mutation that can restore viral fitness, as other mutations can also affect fitness. These mutation types are 1, regulatory mutations (i.e. promoter mutations) that downregulate gene expression (van Opijnen, Boerlijst, and Berkhout 2006) , 2, removal of immunogenic sequence motifs (Fros et al. 2017) , 3, alteration of unfavorable secondary RNA structures (McFadden et al. 2013) , and 4, adopting a more favorable codon usage (Carrasco, de la Iglesia, and Elena 2007; Agashe et al. 2013; Cladel et al. 2013) , as synonymous mutations can have marked effects on virus fitness.