Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates
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Abstract
We report the genome of a B.1.1.7+E484K severe acute respiratory syndrome coronavirus 2 from Southeastern Pennsylvania and compare it with all high-coverage B.1.1.7+E484K genomes (n = 235) available. Analyses showed the existence of at least 4 distinct clades of this variant circulating in the United States and the possibility of at least 59 independent acquisitions of the E484K mutation.
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SciScore for 10.1101/2021.04.21.440801: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: The sample was obtained by as part of routine clinical care, solely for non-research purposes, carrying minimal risk, and were therefore granted a waiver of informed consent as reviewed under protocol number under IRB 21-018478. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Briefly, WGS of extracted viral RNA was performed as previously described using Paragon Genomics CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel17,18. WGSsuggested: NoneAll the high coverage SARS-CoV-2 genomes (n=236) were assigned a clonal complex using the GNUVID v2.2 database … SciScore for 10.1101/2021.04.21.440801: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: The sample was obtained by as part of routine clinical care, solely for non-research purposes, carrying minimal risk, and were therefore granted a waiver of informed consent as reviewed under protocol number under IRB 21-018478. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Briefly, WGS of extracted viral RNA was performed as previously described using Paragon Genomics CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel17,18. WGSsuggested: NoneAll the high coverage SARS-CoV-2 genomes (n=236) were assigned a clonal complex using the GNUVID v2.2 database (version January 6th 2021)15. GNUVIDsuggested: NoneTemporal plots were plotted in GraphPad Prism v7.0a. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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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