Hidden evolutionary constraints dictate the retention of coronavirus accessory genes

Genetic innovation is fundamental to the ability of viruses to adapt in the face of host immunity.Coronaviruses exhibit many mechanisms of innovation, including the acquisition of unique accessorygenes that can originate by capture of cellular genes or through duplication and divergence ofexisting viral genes. Accessory genes may be influential in dictating viral host range and cellulartropism, but little is known about how selection acts on these variable regions of virus genomes.We used experimental evolution of mouse hepatitis virus (MHV) with an inactive nativephosphodiesterase, NS2, that encodes a complementing cellular AKAP7 gene, to simulate thecapture of a host gene and found hidden patterns of constraint that determine the fate ofcoronavirus accessory genes. After courses of serial infection, AKAP7 was retained under strongselection but rapidly lost under relaxed selection. In contrast, the gene encoding inactive NS2,ORF2, remained intact, suggesting it is under cryptic evolutionary constraint.