Identifying RNA secondary structures in the SARS-CoV-2 viral genome




Ziesel, Alison

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Motivation: SARS-CoV-2 is the virus responsible for the COVID-19 pandemic that currently impacts our world. SARS-CoV-2 is an enveloped, positive sense single stranded RNA virus and like other RNA viruses is known to form RNA secondary structure in its genome. In related viruses the secondary structures are responsible for fulfilling roles including proper expression of viral gene products and possibly regulation of viral genome replication. I hypothesize that SARS-CoV-2 may be capable of forming additional secondary structures beyond what is already known and that those secondary structures are identifiable on the basis of sequence conservation with related RNA viruses. Results: By repurposing and expanding an existing computational pipeline de- signed for the detection of structural RNAs in vertebrates, I identified 40 regions of the SARS-CoV-2 genome highly likely to form secondary structure. Partial re- identification of known secondary structures in the SARS-CoV-2 genome was achieved. To further explore the role these structures may fill, the 9 most conservatively pre- dicted structures were analyzed in wild viral samples collected from three Canadian provinces, and distinct patterns of mutation were observed. The 40 regions identi- fied by my modified pipeline were compared against three contemporary works and the differences between findings were quantified. Lastly, Variants of Concern for SARS-CoV-2 were analyzed for prevalent but poorly reported mutations that may influence RNA secondary structure. Code developed for this work is available at



computational biology, RNA biology, RNA secondary structure, viral biology, bioinformatics