Apr 6, 2020

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

BioRxiv : the Preprint Server for Biology
Benjamin M SkinnerNabeel A Affara

Abstract

As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of antivirals and diagnostics. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nucleotides as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences reported to date from the current COVID-19 outbreak, and we present a curated list of 30 'SARS-related-conserved' regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 'SARS-CoV-2-conserved-structured' regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the 5' UTR, frame-shifting element, and 3' UTR. Last, we predict regions of the SARS-Co...Continue Reading

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Mentioned in this Paper

Fertility
Phacochoerus africanus
Short Interspersed Nucleotide Elements
HSFY2
Benign Neoplasm of Testis
Y Chromosome
PIGS
Mutation, Nonsense
Babyrousa babyrussa
Genes

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