A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic
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Abstract
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SciScore for 10.1101/2020.04.21.054221: (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
No key resources detected.
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: We detected the following sentences addressing limitations in the study:An important caveat of the present study is that the current sampling of available public genomes does likely not represent the extant genetic diversity of virus populations in circulation due to biases of genome data deposits …
SciScore for 10.1101/2020.04.21.054221: (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
No key resources detected.
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: We detected the following sentences addressing limitations in the study:An important caveat of the present study is that the current sampling of available public genomes does likely not represent the extant genetic diversity of virus populations in circulation due to biases of genome data deposits from the sequencing laboratories based mainly in the northern hemisphere and new datasets may define new clades in the near future from regions, including Africa, the Indian subcontinent and Latin America with comparably few genomes available at present. In this case, additional identifiers within an evolving barcode scheme can be added to track and monitor future emerging clades with higher resolution. On the other hand, the genetic stability of SARS-CoV-218 may result in the continuing circulation of a limited number of clades until such time as mitigation measures including the isolation of vulnerable populations and the availability of efficacious antivirals and vaccines reduces the genetic diversity in circulation. This molecular genotyping approach has been demonstrated for other viruses (e.g. measles, poliovirus, rotavirus and human papillomaviruses) with herd-immunity vaccination programmes working to eliminate pathogens from endemic circulation in humans19,20,21,22. The availability of a barcoding scheme that rapidly generates a SNP allowing clade assignment will be critical in this elimination phase when widespread availability of vaccines permits eradication of SARS-CoV-2 from endemicity in humans. Our work provides a baseline global genomic ...
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 32. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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