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Background: The COVID-19 pandemic clock is ticking and the survival of manyof mankind's modern institutions and or survival of many individuals is atstake. There is a need for treatments to significantly reduce the morbidity andmortality of COVID-19. Hence, we delved deep into the SARS-CoV-2 genome, whichis the virus that has caused COVID-19. SARS-CoV-2 is from the same family asSARS-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 threesvRNAs in the SARS-CoV-2 genome. Instead of off-the-shelf search and alignmentalgorithms, which failed to discover the orthologs, we used a special alignmentscoring that does not penalize C/T and A/G mismatches as much as the othermutations. RNA bases C and U both can bind to G; similarly, A and G both canbind to U, hence, our scoring. We also validate this hypothesis using a novel,independent computational experiment. To validate our results, we confirmed thediscovered orthologs are fully conserved in all the tested publicly availablegenomes of various strains of SARS-CoV-2; the loci at which the SARS-CoV-2orthologs occur are close to the loci at which SARS-CoV svRNAs occur. We alsoreport potential targets for these svRNAs. We hypothesize that the discoveredorthologs play a role in pathogenesis of SARS-CoV-2, and therefore,antagomir-mediated inhibition of these SARS-CoV-2 svRNAs inhibits COVID-19.

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