Impact of reduction of susceptibility to SARS-CoV-2 on epidemic dynamics in four early-seeded metropolitan regions
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Abstract
As we enter a chronic phase of the SARS-CoV-2 pandemic, with uncontrolled infection rates in many places, relative regional susceptibilities are a critical unknown for policy planning. Tests for SARS-CoV-2 infection or antibodies are indicative but unreliable measures of exposure. Here instead, for four highly-affected countries, we determine population susceptibilities by directly comparing country-wide observed epidemic dynamics data with that of their main metropolitan regions. We find significant susceptibility reductions in the metropolitan regions as a result of earlier seeding, with a relatively longer phase of exponential growth before the introduction of public health interventions. During the post-growth phase, the lower susceptibility of these regions contributed to the decline in cases, independent of intervention effects. Forward projections indicate that non-metropolitan regions will be more affected during recurrent epidemic waves compared with the initially heavier-hit metropolitan regions. Our findings have consequences for disease forecasts and resource utilisation.
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SciScore for 10.1101/2020.07.28.20163154: (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
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:The use of sub-standard finger-prick blood samples, as well as testing bias introduced through inhomogeneous test responsiveness in the selected test population, are further limitations of the REACT study. Our modelling also assumes lasting immunity following acute infection, in keeping with normal immunological responses to viral …
SciScore for 10.1101/2020.07.28.20163154: (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
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:The use of sub-standard finger-prick blood samples, as well as testing bias introduced through inhomogeneous test responsiveness in the selected test population, are further limitations of the REACT study. Our modelling also assumes lasting immunity following acute infection, in keeping with normal immunological responses to viral infections [29]. Yet, for the purposes of our projections, immunity need only be preserved for as long as infection rates are uncontrollable. The level used for ‘controllable disease’ was chosen in accordance with data from countries achieving containment, and assumes a goal of elimination utilising, among other measures, tracking and tracing. It is possible that technological improvements will allow a successful track-and-trace strategy at higher infection levels. Forward-projecting continuations of modest relaxations of restrictions appears to make containment achievable, but observed slow down in the decline of death rates indicates that this will be reached later than would have occurred under more stringent restrictions.
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 10.1101/2020.07.28.20163154: (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 note that Discussion 5 Threshold chosen in accordance with infection levels in countries with well-developed public health infrastructure (e.g. New Zealand, South Korea, Cuba, and Fiji) with proactive testing and ‘track and trace’ interventions resulting in lasting containment approaching elimination of locallyacquired cases. Fijisuggested: (Fiji, SCR_002285)ProMED PRO/AH/EDR, Undiagnosed pneumonia - China (HU): request for information, (2019-12-30) Archive Number: 20191230.6864153, available at: https : / / … SciScore for 10.1101/2020.07.28.20163154: (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 note that Discussion 5 Threshold chosen in accordance with infection levels in countries with well-developed public health infrastructure (e.g. New Zealand, South Korea, Cuba, and Fiji) with proactive testing and ‘track and trace’ interventions resulting in lasting containment approaching elimination of locallyacquired cases. Fijisuggested: (Fiji, SCR_002285)ProMED PRO/AH/EDR, Undiagnosed pneumonia - China (HU): request for information, (2019-12-30) Archive Number: 20191230.6864153, available at: https : / / promedmail . org / promed post/?id=6864153, visited on 07/12/2020. 11.Zhu, N. et al., Numbersuggested: (BioNumbers, SCR_002782)Coronavirus disease 2019 (COVID-19): situation report, 51, (2020) available at: https : / / www . who . int / emergencies / diseases / novel - coronavirus - 2019 / situation - reports, visited on 06/11/2020. 13.Sekine, T. et al., “Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19”, bioRxiv (2020). 14.Seow, J. et al., “Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection”, medRxiv (2020). 15.Checchi, F. and Roberts, L., “Interpreting and using mortality data in humanitarian emergencies” bioRxivsuggested: (bioRxiv, SCR_003933), Humanitarian Practice Network 52 (2005). 17.Nogueira, P. et al., “Excess mortality estimation during the COVID-19 pandemic: preliminary data from Portugal”, Acta Médica Portuguesa 33, 376–383 (2020). 18.Aron, J. et al., A pandemic primer on excess mortality statistics and their comparability across countries, Our World in Data (June 29, 2020), available at: https://ourworldindata.org/covid-excess-mortality, visited on 07/12/2020. 19.Financial Times, Excess mortality during the Covid-19 pandemic, available at: https://github.com/Financial- Times/coronavirus- excessmortality-data, visited on 07/01/2020. 1.Wahltinez, O. et al., Covid-open-data: curating a fine-grained, globalscale COVID-19 data repository, (2020) available at: https://github. com/open-covid-19/data, visited on 06/05/2020. 20.Ciufolini, I. and Paolozzi, A., “An improved mathematical prediction of the time evolution of the Covid-19 pandemic in Italy, with monte carlo simulations and error analyses”, The European Physical Journal Plus 135, 495 (2020). 2.New York City Department of Health, COVID-19 Data, available at: https://www1.nyc.gov/site/doh/covid/covid- 19- data.page, visited on 06/02/2020. 21. Portugal”suggested: NoneData from additional tools added to each annotation on a weekly basis.
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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