Synthetic Rational Design of Attenuated RNA Viruses Based on Computational Model

Synthetic virology is an important multidisciplinary scientific field, with emerging applications in biotechnology and medicine, aiming at developing methods to generate and engineer synthetic viruses. Many viruses of the Flaviviridae family, including the hepatitis C virus (HCV) and Zika virus (ZIKV), are widespread pathogens of significant importance to human health. Yet, and despite extensive research, there are currently no approved vaccines available for these viruses. Therefore, designing attenuated synthetic versions of these viruses and controlling their virulence and replication rate is a fundamental milestone in the continuing efforts in fighting the diseases they cause. Specifically, this approach should help improve our understanding of the genomes of these viruses and may promote developing potential vaccines and virus based therapies. Using a computational based pipeline model for the rational design of attenuated synthetic RNA viruses, we generated dozens of HCV and ZIKV variants, based on procedures that preserve viral amino acid content, but affect various functional silent aspects of their genome. Results in Huh7 human liver cells show a gradient of attenuations of the examined HCV strains, as well as mRNA levels, which correlate with our model predictions. In addition, foci size comparison and replication kinetic results in ZIKV show significant variant attenuation in Vero cells. Finally, results in mouse model demonstrated prolonged time and higher survival ratio for mice vaccinated with the synthetic attenuated ZIKV variants. Hence, our tested model based abilities in design and synthesis of such viruses could contribute to the development of vaccines and virus based therapies.