Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context
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Abstract
In October 2020, an outbreak of at least 50 COVID-19 cases was reported surrounding individuals employed at or visiting the White House. Here, we applied genomic epidemiology to investigate the origins of this outbreak. We enrolled two individuals with exposures linked to the White House COVID-19 outbreak into an IRB-approved research study and sequenced their SARS-CoV-2 infections. We find these viral sequences are identical to each other, but are distinct from over 190,000 publicly available SARS-CoV-2 genomes. These genomes fall as part of a lineage circulating in the USA since April or May 2020 and detected in Virginia and Michigan. Looking forwards, sequencing of additional community SARS-CoV-2 infections collected in the USA prior to October 2020 may shed further light on its geographic ancestry. In sequencing of SARS-CoV-2 infections collected after October 2020, it may be possible to identify infections that likely descend from the White House COVID-19 outbreak.
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SciScore for 10.1101/2020.10.31.20223925: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All participants completed informed consent. 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 Consensus genome sequences for both WH1 and WH2 are also available from github.com/blab/ncov-wh. Analysis: Consensus genome sequences of WH1 and WH2 were combined with SARS-CoV-2 genomes downloaded from GISAID [16,17] and processed using the Nextstrain [13] bioinformatics pipeline Augur to align genomes via MAFFT v7.4 [19], build maximum likelihood phylogeny via IQ-TREE v1.6 [20] and reconstruct nucleotide and amino acid changes on the … SciScore for 10.1101/2020.10.31.20223925: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All participants completed informed consent. 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 Consensus genome sequences for both WH1 and WH2 are also available from github.com/blab/ncov-wh. Analysis: Consensus genome sequences of WH1 and WH2 were combined with SARS-CoV-2 genomes downloaded from GISAID [16,17] and processed using the Nextstrain [13] bioinformatics pipeline Augur to align genomes via MAFFT v7.4 [19], build maximum likelihood phylogeny via IQ-TREE v1.6 [20] and reconstruct nucleotide and amino acid changes on the ML tree. MAFFTsuggested: (MAFFT, RRID:SCR_011811)IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: Thank you for sharing your code.
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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