RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.
RNA. 2020 May 12;:
Authors: Rangan R, Zheludev IN, Das R
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. Here we present a first look at RNA sequence conservation and structural propensities in the SARS-CoV-2 genome. 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 subsequently reported from the 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 extended 5' UTR,...

Source: RNA - May 11, 2020 Category: Genetics & Stem Cells Authors: Rangan R, Zheludev IN, Das R Tags: RNA Source Type: research