A cytosine-to-uracil change within the programmed -1 ribosomal frameshift signal of SARS-CoV-2 results in structural similarities with the MERS-CoV signal
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the ongoing COVID-19 pandemic, like many other viruses, uses programmed ribosomal frameshifting (PRF) to enable synthesis of multiple proteins from its compact genome. In independent analyses, we evaluated the PRF regions of all SARS-CoV-2 sequences available in GenBank and from the Global Initiative on Sharing All Influenza Data for variations. Of the 5,156 and 27,153 sequences analyzed, respectively, the PRF regions were identical in 95.7% and 97.2% of isolates. The most common change from the reference sequence was from C to U at position 13,536, which lies in the three-stemmed pseudoknot known to stimulate frameshifting. With the conversion of the G 13493 -C 13536 Watson-Crick pair to G-U, the SARS-CoV-2 PRF closely resembles its counterpart in the Middle East respiratory syndrome coronavirus. The occurrence of this change increased from 0.5 to 3% during the period of March to May 2020.
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SciScore for 10.1101/2020.06.26.174193: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources From the selected sequences, a 2,500-base region (11,500 to 14,000 bases from the 5’ end) containing the 85 nucleotides of the -1 PRF region of ORF1a/b were extracted and aligned using ClustalX software57. ClustalXsuggested: (Clustal X , RRID:SCR_017055)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the …SciScore for 10.1101/2020.06.26.174193: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources From the selected sequences, a 2,500-base region (11,500 to 14,000 bases from the 5’ end) containing the 85 nucleotides of the -1 PRF region of ORF1a/b were extracted and aligned using ClustalX software57. ClustalXsuggested: (Clustal X , RRID:SCR_017055)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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