Tools
Tools
Bidula, Stefan 
ORCID: https://orcid.org/0000-0002-3790-7138 and Brázda, Václav
(2023)
Genomic analysis of non-B nucleic acids structures in SARS-CoV-2: Potential key roles for these structures in mutability, translation, and replication?
Genes, 14 (1).
ISSN 2073-4425
Preview |
PDF (genes-14-00157)
- Published Version
Available under License Creative Commons Attribution. Download (1MB) | Preview |
Abstract
Non-B nucleic acids structures have arisen as key contributors to genetic variation in SARS-CoV-2. Herein, we investigated the presence of defining spike protein mutations falling within inverted repeats (IRs) for 18 SARS-CoV-2 variants, discussed the potential roles of G-quadruplexes (G4s) in SARS-CoV-2 biology, and identified potential pseudoknots within the SARS-CoV-2 genome. Surprisingly, there was a large variation in the number of defining spike protein mutations arising within IRs between variants and these were more likely to occur in the stem region of the predicted hairpin stem-loop secondary structure. Notably, mutations implicated in ACE2 binding and propagation (e.g., ΔH69/V70, N501Y, and D614G) were likely to occur within IRs, whilst mutations involved in antibody neutralization and reduced vaccine efficacy (e.g., T19R, ΔE156, ΔF157, R158G, and G446S) were rarely found within IRs. We also predicted that RNA pseudoknots could predominantly be found within, or next to, 29 mutations found in the SARS-CoV-2 spike protein. Finally, the Omicron variants BA.2, BA.4, BA.5, BA.2.12.1, and BA.2.75 appear to have lost two of the predicted G4-forming sequences found in other variants. These were found in nsp2 and the sequence complementary to the conserved stem-loop II-like motif (S2M) in the 3′ untranslated region (UTR). Taken together, non-B nucleic acids structures likely play an integral role in SARS-CoV-2 evolution and genetic diversity.
| Item Type: | Article |
|---|---|
| Additional Information: | Publisher Copyright: © 2023 by the authors. |
| Uncontrolled Keywords: | adaptation,g-quadruplex,inverted repeats,mutation,pseudoknot,sars-cov-2,spike protein,genetics,genetics(clinical),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1311 |
| Faculty \ School: | Faculty of Science > School of Pharmacy |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 13 Feb 2023 15:30 |
| Last Modified: | 29 Jun 2023 15:31 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/91120 |
| DOI: | 10.3390/genes14010157 |
Downloads
Downloads per month over past year
Actions (login required)
 |
View Item |