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Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
Published on: December 23, 2020
Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and
Amber R Paulson1,2, Vincent Montoya1, Jeffrey B Joy1,2,3
1BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
Abstract:
Small viral RNAs (svRNAs) have emerged as key factors in host adaptation and virulence, with evidence of their presence in both SARS-CoV-2 and SARS-CoV-1. Here, using functional genomics, we identify 6 candidate svRNA-triplex-forming oligonucleotides (svRNA-TFOs) in SARS-CoV-2 and, through comparative analyses with SARS-CoV-1, delineate evolutionary pathways for svRNA-TFOs in Sarbecoviruses. In addition to the significant enrichment of candidate svRNA-TFO enhancer-gene targets among differentially expressed genes during SARS-CoV-2 infection, these svRNA-TFOs also show nonrandom associations with over 25% of the recombination breakpoints and hotspots in the Wuhan-Hu-1 genome. Small RNA-sequencing reveals highly abundant svRNA-TFO-N derived from the nucleocapsid of SARS-CoV-2. Using synonymous-site conservation analysis, we show that svRNA-TFO-N and other svRNA-TFOs are conserved among both SARS-CoV-2- and SARS-CoV-1-related lineages. Furthermore, BLASTn reveals that svRNA-TFO-N and svRNA-TFO-S.1 share sequence homology against various mammalian genomes, which supports a proposed mechanism of host adaptation. Finally, based on RNA structural modeling, we identify variant of concern-associated S:D614G and N:D377Y mutations, which may alter precursor structures predicted for svRNA-TFO-S.1 and svRNA-TFO-N, respectively. Collectively, these findings provide support for the hypothesis that svRNA-mediated epigenetic interference contributes to virulence in SARS-CoV-2 and SARS-CoV-1.
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