SARS-CoV-2 genome surveillance in Mainz, Germany, reveals convergent origin of the N501Y spike mutation in a hospital setting
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Abstract
While establishing a regional SARS-Cov-2 variant surveillance by genome sequencing, we have identified three infected individuals in a clinical setting (two long-term hospitalized patients and a nurse) that shared the spike N501Y mutation within a genotype background distinct from the current viral variants of concern. We suggest that the adaptive N501Y mutation, known to increase SARS-CoV-2 transmissibility, arose by convergent evolution around December in Mainz, Germany. Hospitalized patients with a compromised immune system may be a potential source of novel viral variants, which calls for monitoring viral evolution by genome sequencing in clinical settings.
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SciScore for 10.1101/2021.02.11.21251324: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources For phylogenetic tree reconstruction, individual FASTA genome files were combined into a single multi-sequence FASTA file and aligned by MAFFT v7.450 (Katoh and Standley 2013, Katoh et al. 2002) using default criteria. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood trees were calculated using RAxML (Stamatakis 2014) under the GTR substitution model and gamma distribution with 1000 bootstraps. RAxMLsuggested: (RAxML, RRID:SCR_006086)Mapping and visualization of individual amino acid replacements in the SARS-CoV-2 spike protein (data not shown) were produced using the CoVsurver … SciScore for 10.1101/2021.02.11.21251324: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources For phylogenetic tree reconstruction, individual FASTA genome files were combined into a single multi-sequence FASTA file and aligned by MAFFT v7.450 (Katoh and Standley 2013, Katoh et al. 2002) using default criteria. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood trees were calculated using RAxML (Stamatakis 2014) under the GTR substitution model and gamma distribution with 1000 bootstraps. RAxMLsuggested: (RAxML, RRID:SCR_006086)Mapping and visualization of individual amino acid replacements in the SARS-CoV-2 spike protein (data not shown) were produced using the CoVsurver online tool (https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/). CoVsurversuggested: NoneResults 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.
Results from scite Reference Check: We found no unreliable references.
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