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RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
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 ge...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217285/ https://www.ncbi.nlm.nih.gov/pubmed/32511306 http://dx.doi.org/10.1101/2020.03.27.012906 |
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author | Rangan, Ramya Zheludev, Ivan N. Das, Rhiju |
author_facet | Rangan, Ramya Zheludev, Ivan N. Das, Rhiju |
author_sort | Rangan, Ramya |
collection | PubMed |
description | 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-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 ‘SARS-CoV-2-conserved-unstructured’ genomic regions may be most easily targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies. |
format | Online Article Text |
id | pubmed-7217285 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-72172852020-06-07 RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses Rangan, Ramya Zheludev, Ivan N. Das, Rhiju bioRxiv Article 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-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 ‘SARS-CoV-2-conserved-unstructured’ genomic regions may be most easily targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies. Cold Spring Harbor Laboratory 2020-04-06 /pmc/articles/PMC7217285/ /pubmed/32511306 http://dx.doi.org/10.1101/2020.03.27.012906 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. |
spellingShingle | Article Rangan, Ramya Zheludev, Ivan N. Das, Rhiju RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title | RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title_full | RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title_fullStr | RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title_full_unstemmed | RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title_short | RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses |
title_sort | rna genome conservation and secondary structure in sars-cov-2 and sars-related viruses |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217285/ https://www.ncbi.nlm.nih.gov/pubmed/32511306 http://dx.doi.org/10.1101/2020.03.27.012906 |
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