Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold
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SciScore for 10.1101/2020.04.27.20081893: (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:A crucial caveat in exporting these calculations to immunization by natural infection is that natural infection does not occur at random. Individuals who are more susceptible or more exposed are more prone to be infected and …
SciScore for 10.1101/2020.04.27.20081893: (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:A crucial caveat in exporting these calculations to immunization by natural infection is that natural infection does not occur at random. Individuals who are more susceptible or more exposed are more prone to be infected and become immune, which lowers the threshold (14). In our model, the herd immunity threshold declines sharply when coefficients of variation increase from 0 to 2 and remains below 20% for more variable populations. The amplitude of the decline depends on what property is heterogeneous and how it is distributed but the downwards trend is robust (Figures 3 and S22). Heterogeneity in the transmission of respiratory infections has traditionally focused on variation in exposure summarized into age-structured contact matrices. Besides overlooking differences in susceptibility given exposure, the aggregation of individuals into age groups curtails coefficients of variation with important downstream implications. We calculated CV for the landmark POLYMOD matrices (15,16) and obtained values between 0.3 and 0.5. Recent studies of COVID-19 integrated contact matrices with age-specific susceptibility to infection (structured in three levels) (17) or with social activity (three levels also) (18) which, again, resulted in coefficients of variation less than 1. We show that models with coefficients of variation of this magnitude would appear to differ only moderately from homogeneous approximations when compared with those that incorporate CVs between 2 and 3, as estimate...
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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SciScore for 10.1101/2020.04.27.20081893: (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 We show that models with coefficients of variation of this magnitude would appear to differ only moderately from homogeneous approximations when compared with those that incorporate CVs between 2 and 3, as estimated for a variety of infectious diseases (Figure 3) and supported by detailed mobility data in the city of Portland, Oregon, USA (19) (we obtained an estimate rounding = 2 based on data extracted with WebPlotDigitizer). WebPlotDigitizersuggested: (WebPlotDigitizer, SCR_013996)Nature 438 , 355-359 ( 2005) . 10 . … SciScore for 10.1101/2020.04.27.20081893: (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 We show that models with coefficients of variation of this magnitude would appear to differ only moderately from homogeneous approximations when compared with those that incorporate CVs between 2 and 3, as estimated for a variety of infectious diseases (Figure 3) and supported by detailed mobility data in the city of Portland, Oregon, USA (19) (we obtained an estimate rounding = 2 based on data extracted with WebPlotDigitizer). WebPlotDigitizersuggested: (WebPlotDigitizer, SCR_013996)Nature 438 , 355-359 ( 2005) . 10 . A . Endo , Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group , S. Abbott , A . J . Kucharski , S. Funk , Estimating the overdispersion in COVID-19 transmission using outbreak sizes outsize China [ version 1; peer review: awaiting peer review] . Abbottsuggested: (Abbott, SCR_010477)Results from OddPub: Thank you for sharing your code.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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