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  . RNA bases C and U both can bind to G; similarly, A and G both can bind to U, hence, our scoring.  To validate our results, we confirmed the discovered orthologs are fully conserved in all the  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.
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.
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as much as the other mutations
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We also validate this hypothesis using a novel, independent computational experiment.
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tested