Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States
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Abstract
Genomic surveillance can lead to early identification of novel viral variants and inform pandemic response. Using this approach, we identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.). The earliest sequenced genomes of this variant, referred to as 20C-US, can be traced to Texas in late May of 2020. This variant circulated in the U.S. uncharacterized for months and rose to recent prevalence during the third pandemic wave. It initially acquired five novel, relatively unique non-synonymous mutations. 20C-US is continuing to acquire multiple new mutations, including three independently occurring spike protein mutations. Monitoring the ongoing evolution of 20C-US, as well as other novel emerging variants, will be essential for understanding SARS-CoV-2 host adaptation and predicting pandemic outcomes.
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SciScore for 10.1101/2021.01.11.426287: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization From each of these subsets, Nextstrain attempts to randomly pick an equal number of samples. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequencing was performed with Oxford Nanopore Technology’s MinION platform using ARTIC Network protocol (https://artic.network/ncov-2019) with slight modifications to the protocol. Oxford Nanoporesuggested: (Oxford Nanopore Technologies, RRID:SCR_003756)MinIONsuggested: (MinION, RRID:SCR_017985)Briefly, the Augur pipeline utilized by Nextstrain filters sequences for metadata values and N content before … SciScore for 10.1101/2021.01.11.426287: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization From each of these subsets, Nextstrain attempts to randomly pick an equal number of samples. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequencing was performed with Oxford Nanopore Technology’s MinION platform using ARTIC Network protocol (https://artic.network/ncov-2019) with slight modifications to the protocol. Oxford Nanoporesuggested: (Oxford Nanopore Technologies, RRID:SCR_003756)MinIONsuggested: (MinION, RRID:SCR_017985)Briefly, the Augur pipeline utilized by Nextstrain filters sequences for metadata values and N content before aligning them using MAFFT (30). Augursuggested: NoneMAFFTsuggested: (MAFFT, RRID:SCR_011811)The pipeline conducts a maximum likelihood phylogenetic analysis using the general time reversible model allowing for invariant sites and a gamma distribution (GTR+I+G) in IQ-TREE (31). IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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.
- 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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