SARS-CoV-2 orthologs of pathogenesis-involved small viral RNAs of SARS-CoV

Background: The COVID-19 pandemic clock is ticking and the survival of many of mankind's modern institutions and or survival of many individuals is at stake. There is a need for treatments to significantly reduce the morbidity and mortality of COVID-19. Hence, we delved deep into the SARS-CoV-2 genome, which is the virus that has caused COVID-19. SARS-CoV-2 is from the same family as SARS-CoV in which three small viral RNAs (svRNA) were recently identified; those svRNAs play a significant role in the virus pathogenesis in mice. Contribution: In this paper, we report potential orthologs of those three svRNAs in the SARS-CoV-2 genome. Instead of off-the-shelf search and alignment algorithms, which failed to discover the orthologs, we used a special alignment scoring that does not penalize C/T and A/G mismatches as much as the other mutations. RNA bases C and U both can bind to G; similarly, A and G both can bind to U, hence, our scoring. We also validate this hypothesis using a novel, independent computational experiment. To validate our results, we confirmed the discovered orthologs are fully conserved in all the tested publicly available genomes of various strains of SARS-CoV-2; the loci at which the SARS-CoV-2 orthologs occur are close to the loci at which SARS-CoV svRNAs occur. We also report potential targets for these svRNAs. We hypothesize that the discovered orthologs play a role in pathogenesis of SARS-CoV-2, and therefore, antagomir-mediated inhibition of these SARS-CoV-2 svRNAs inhibits COVID-19.