Poxviruses deploy genomic accordions to rapidly adapt against host antiviral defenses

Despite low mutation rates, poxviruses and other large DNA viruses are highly adaptable and often undergo cross-species transmission. To determine mechanisms of adaptation we subjected vaccinia, the model poxvirus, to serial infections in human cells, where the anti-host viral factor K3L is maladapted against anti-viral Protein kinase R (PKR). Viruses rapidly acquired higher fitness via recurrent K3L gene amplifications to defeat PKR, despite incurring up to 7-10% increases in genome size. Gene expansions counteracted human PKR and facilitated the gain of an adaptive amino acid substitution in K3L to defeat PKR. These genomic expansions appear transient, with subsequent reductions in gene amplifications offsetting costs associated with larger genomes while still retaining adaptive substitutions. Our discovery of viral 'gene- accordions' explains how poxviruses can rapidly adapt to defeat different host defenses despite low mutation rates and reveals how classical Red Queen conflicts progress through unrecognized intermediates.