Targeting evolutionary conserved sequences circumvents the evolution of resistance in a viral gene drive against human cytomegalovirus

M. Walter, R. Perrone and E. Verdin,  bioRxiv,  2021.01.08.425902. 2021.

Gene drives are genetic systems designed to efficiently spread a modification through a population. Most engineered gene drives rely on CRISPR-Cas9 and were designed in insects or other eukaryotic species. We recently developed a viral gene drive in herpesviruses that efficiently spread into a population of wildtype viruses. A common consequence of gene drives is the appearance and selection of drive-resistant sequences that are no longer recognized by CRISPR-Cas9. Here, we analyze in cell culture experiments the evolution of resistance in a gene drive against human cytomegalovirus. We report that after an initial invasion of the wildtype population, a drive-resistant population is positively selected over time and outcompetes gene drive viruses. However, we show that targeting evolutionary conserved regions ensures that drive-resistant viruses have a replication defect, leading to a long-term reduction of viral levels. This marks an important step toward developing effective gene drives in viruses, especially for therapeutic applications.Competing Interest StatementA patent application describing the use of a gene drive in DNA viruses has been filed by the Buck Institute for Research on Aging (Application number PCT/US2019/034205, pending, inventor: M.W.). E.V. and R.P. declare no competing interests.

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