Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reproduction number has become an essential parameter for monitoring disease transmission across settings and guiding interventions. The UK published weekly estimates of the reproduction number in the UK starting in May 2020 which are formed from multiple independent estimates. In this paper, we describe methods used to estimate the time-varying SARS-CoV-2 reproduction number for the UK. We used multiple data sources and estimated a serial interval distribution from published studies. We describe regional variability and how estimates evolved during the early phases of the outbreak, until the relaxing of social distancing measures began to be introduced in early July. Our analysis is able to guide localized control and provides a longitudinal example of applying these methods over long timescales.
This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK'.
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SciScore for 10.1101/2020.04.13.20062760: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Other factors that may influence the timing are delays in case identification and reporting and limitations in the estimation methods. Subsequent to mid-April we estimate Rt largely remained below one until the end of the lock-down period. The multiple data sources we considered each have their advantages and drawbacks. Counts of test-positive cases and telephone triage calls provide a rapid indication of infection risk and capture a …
SciScore for 10.1101/2020.04.13.20062760: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Other factors that may influence the timing are delays in case identification and reporting and limitations in the estimation methods. Subsequent to mid-April we estimate Rt largely remained below one until the end of the lock-down period. The multiple data sources we considered each have their advantages and drawbacks. Counts of test-positive cases and telephone triage calls provide a rapid indication of infection risk and capture a broad representation of age groups, but may be influenced by changes in behaviour and testing policy. In the UK, initial attempts at community tracing were abandoned when case numbers started to outstrip test availability and afterwards testing was only performed on hospital admissions for suspected COVID-19 [6]. Later, test capacity was increased and the policy reversed to include more community cases, again altering the nature of the population being tested. Although a regional breakdown of testing capacity was not available at the time of this analysis, we do know that capacity was exceeded in the early phase of the epidemic, and this is one reason why case based Rt estimates must be interpreted with caution until the middle of April. Hospital admissions and death data are less subject to changes in sampling strategy, although are subject to reporting delays and biases in ascertainment. As COVID-19 mortality is overwhelmingly in the elderly, statistics based on deaths mainly represent older groups. Due to reduced contact in the elderly we prop...
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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