Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
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SciScore for 10.1101/2020.07.31.20166082: (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 Phylogenetics and calculation of maximum parsimony clusters: Maximum likelihood (ML) phylogenetic trees were estimated separately using IQTree v1.6.12 for major global lineages (Minh et al., 2020; Rambaut et al.). IQTreesuggested: NoneThe model was implemented in BEAST v1.10.5(Suchard et al., 2018). BEASTsuggested: (BEAST, RRID:SCR_010228)This model was implemented in the BEAST2 PhyDyn package(Bouckaert et al.; Volz and Siveroni, 2018) and is available here: https://ait.io/JJUZv. BEAST2suggested: (BEAST2, RRID:SCR_017307)PhyDynsuggested: (PhyDyn, RRID:SCR_018544)Results from OddPub: We did …
SciScore for 10.1101/2020.07.31.20166082: (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 Phylogenetics and calculation of maximum parsimony clusters: Maximum likelihood (ML) phylogenetic trees were estimated separately using IQTree v1.6.12 for major global lineages (Minh et al., 2020; Rambaut et al.). IQTreesuggested: NoneThe model was implemented in BEAST v1.10.5(Suchard et al., 2018). BEASTsuggested: (BEAST, RRID:SCR_010228)This model was implemented in the BEAST2 PhyDyn package(Bouckaert et al.; Volz and Siveroni, 2018) and is available here: https://ait.io/JJUZv. BEAST2suggested: (BEAST2, RRID:SCR_017307)PhyDynsuggested: (PhyDyn, RRID:SCR_018544)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:Several limitations of the data and analysis should be considered when interpreting our finding that the sampling frequency of variant 614G increased. We have applied classic population genetic models premised on contrasting the exponential growth rates of the 614G and 614D populations while controlling for founder effects, but in reality the SARS-CoV-2 epidemic is noisy and structured in ways not accounted for by this model. The frequency of 614G and 614D variants can change rapidly due to stochastic fluctuations, especially early in the epidemic. The sampling process is also inhomogeneous through time and sometimes reactive to short-term public health situations (e.g. nosocomial outbreaks) rather than being fully randomised and systematic. Most of the SARS-CoV-2 genome sequencing performed by centres in the UK is focused on symptomatic cases, often using diagnostic residual samples. As testing priorities change, and as cases in different segments of the population fluctuate, signals may emerge that are due to operational changes rather than shifts in virus biology. Phylodynamic estimates of reproduction numbers are sensitive to the context of early spread of epidemic clusters which may have involved superspreading events (Endo et al., 2020). These events are highly variable and phylodynamic methods are inherently imprecise with poorly resolved phylogenies. The Spike 614 polymorphism explains little variance in the rate of spread of individual clusters, but incorporating add...
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.
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- No protocol registration statement was detected.
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