On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

When stratifying by viral groups, we observe that the stability of viral genomes partially depends on the nature of the genome. Viral genomes with separately expressed nonoverlapping ORFs (group V: ssRNAÀ) appear to have less constraints imposed on sequence insertions as compared to genomes with genes encoded in one single ORF (group IV: ssRNAþ). Although the dsDNA (group I) virus genomes are extremely plastic in natural conditions, this observation is not a good predictor for stability of engineered viral genomes as inserts are generally lost. In the case of ssDNA (group II) viruses, the varying frequency of genomic segments might lead to rapid adaptive responses to inserted sequences. While in the case of segmented dsRNA (group III) viruses, sequence insertions probably perturb segmented genome assembly. When comparing the retro-transcribing viruses, the RT-ssRNA(þ) (group VI) viruses appear to successfully express sequences of interest after stable integration into the host genome, whilst the RT-dsDNA (group VII) viruses are less stable and only rarely integrate into the host genome. Multipartite viruses, represented in various groups, also present unique challenges when thinking about the stability of inserted sequences.