On the stability of sequences inserted into viral genomes

Willemsen, Anouk; Zwart, Mark P

A large number of virus genomes have been engineered to carry additional sequences for a variety of purposes. Viruses are often used as vectors for heterologous gene expression in cultured cells or the natural host. For example, the baculovirus expression system is widely used for expression work (Chambers et al. 2018 ), lentiviruses show great promise for gene therapy (Milone and O'Doherty 2018) , and phage display allows for selection of desired epitopes (Wu et al. 2016) . Marker genes have also been built into viruses to facilitate tracking infection spread (Dolja, McBride, and Carrington 1992) . As viruses evolve rapidly, including the incorporation of genome-rearrangements, it is therefore unsurprising that the insertion of sequences into viral genomes often goes hand in hand with the rapid occurrence of deletions (Koonin, Dolja, and Morris 1993; Pijlman et al. 2001; Zwart et al. 2014 ). The inserted sequence, and sometimes parts of the viral genome, are then rapidly lost. This genomic instability can have economic ramifications, leading to decreases in heterologous protein expression (Kool et al. 1991; De Gooijer et al. 1992; Scholthof, Scholthof, V C The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [e-mail] and Jackson 1996) . It can also introduce limitations and complications to working with marker genes Majer, Darò s, and Zwart 2013) . Understanding the stability of inserted sequences therefore has value from an applied perspective, but it could also shed light on basic questions. First, how stable are natural virus genomes, and under what conditions do they become unstable? Second, since horizontal gene transfer (HGT) plays an important role in virus evolution, under what conditions are transferred sequences likely to be retained?