Speaker
Description
Viral phosphodiesterases (PDEs) are a striking example of how the acquisition of new genes through mechanisms such as horizontal transfer and duplication can shape the interactions between RNA viruses and their hosts. These PDEs, which recurrently arose via horizontal transfer of cellular AKAP7 mRNA into multiple coronavirus subgenera, including MERS-related coronaviruses, inhibit activation of the OAS-RNase L pathway by degrading the 2’-5’ oligoadenylate second messenger with exquisite specificity. Given the energetic and fidelity challenges posed by expanding genome size, newly acquired genes should provide a rapid fitness advantage to escape destruction. We used experimental evolution of a model coronavirus, mouse hepatitis virus (MHV), to study retention and/or loss of a cellular PDE, AKAP7, under different selective conditions when expressed from a viral genome. AKAP7, when expressed from the MHV genome, functionally replaces the native MHV PDE, NS2. Viruses without a PDE are restricted by OAS-RNase L in macrophages, allowing us to use macrophage infection as a strong selective environment. We serial passaged MHVAKAP7 under conditions of strong (macrophages) or relaxed (fibroblasts) selection and tracked the evolution of AKAP7 over time. In macrophages AKAP7 was retained through ten passages whereas deletions in the AKAP7 gene quickly appeared in fibroblasts by passage 3. In striking contrast, the gene encoding the inactive native PDE, ORF2 was not deleted through fifteen passages in either cell type and did not revert, indicating AKAP7 fully absorbed the OAS-RNase L selective pressure in macrophages. An analysis of embecoviruses (the betacoronavirus subgenus inclusive of MHV) diversity revealed viruses that viruses have either no ORF2 (HKU1) or retain the complete gene even if the gene product is destroyed by premature stop codons (Rabbit coronavirus-HKU14) suggesting that, at least partial, deletions in this region of the genome are selected against. These experimental studies proved directly informative to the evolution of SARS-CoV-2. The SARS-CoV-2 ORF8 gene arose via duplication and in several globally significant lineages has recurrently acquired mutations that eliminate the protein product. We analyzed the ORF8 evolutionary trajectory in six SARS-CoV-2 lineages, finding clear evidence that despite the loss of its protein product, deletion of the ORF8 gene is selected against. These results demonstrate the power of experimental evolution of model viruses to inform our understanding of emerging and pandemic viruses in the wild. Experimental evolution may allow us to make specific evolutionary predictions that can be tested in viruses of public health concern.
