The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look
Open accessAbstract
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 nt 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, frameshifting stimulation element, and 3′ UTR. Lastly, we predict regions of the SARS-CoV-2 viral genome that 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 accessible by hybridization in primer-based diagnostic strategies.
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Cites
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Cited by
Haniff, H. S., Tong, Y., Liu, X., Chen, J. L., Suresh, B. M., Andrews, R. J., Peterson, J. M., O’Leary, C. A., Benhamou, R. I., Moss, W. N., et al. (2020) · ACS Central Science · doi:10.1021/acscentsci.0c00984 · Cited by 205
Zhang, K., Zheludev, I. N., Hagey, R. J., Haslecker, R., Hou, Y. J., Kretsch, R., Pintilie, G. D., Rangan, R., Kladwang, W., Li, S., et al. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00653-y · Cited by 189
Self-citationSecondary structure of the SARS-CoV-2 5’-UTR
Miao, Z., Tidu, A., Eriani, G., & Martin, F. (2021) · RNA Biology · doi:10.1080/15476286.2020.1814556 · Cited by 156
Zhang, D., Qiao, L., Lei, X., Dong, X., Tong, Y., Wang, J., Wang, Z., & Zhou, R. (2023) · Nature Communications · doi:10.1038/s41467-023-39410-8 · Cited by 21
Metadata
- Authors
- Rangan, R., Zheludev, I. N., Hagey, R. J., Pham, E. A., Wayment-Steele, H. K., Glenn, J. S., & Das, R.
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2020-05-12
- Volume
- 26
- Issue
- 8
- Pages
- 937-959
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- OpenAlex
- W3024057275
- Cited by
- 281
- References
- 46
- FWCI
- 6.43
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Rangan, R., Zheludev, I. N., Hagey, R. J., Pham, E. A., Wayment-Steele, H. K., Glenn, J. S., & Das, R. (2020). RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look. RNA. https://doi.org/10.1261/rna.076141.120
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