  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.
