SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions
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Abstract
Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.
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SciScore for 10.1101/2020.08.24.20180927: (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:There are other limitations to our study, including its retrospective design. Similar to previous work6, we did not consider targeted non-pharmaceutical interventions that are difficult to date and quantify, such as contact tracing or case isolation policies. Data were analyzed at the national level, although much virus transmission was often concentrated in specific areas and some non-pharmaceutical interventions were implemented at …
SciScore for 10.1101/2020.08.24.20180927: (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:There are other limitations to our study, including its retrospective design. Similar to previous work6, we did not consider targeted non-pharmaceutical interventions that are difficult to date and quantify, such as contact tracing or case isolation policies. Data were analyzed at the national level, although much virus transmission was often concentrated in specific areas and some non-pharmaceutical interventions were implemented at the sub-national level38. Our phylogeographic inferences did not consider the travel history of patients, whose inclusion in Bayesian models was recently shown to alleviate sampling bias39. From a statistical standpoint, the interval lengths in the dated phylogeny were treated as fixed quantities in the survival models. Ignoring the uncertainty of the estimated lengths might underestimate the width of confidence intervals, although this is unlikely to have biased the pointwise estimates and the ranking of interventions’ effects. The number of genomes included by country did not necessarily reflect the true number of cases, which might have influenced country comparison results in Fig. 2, but not intervention effectiveness models in Fig. 3 which were adjusted for between-country variations of Rt. Finally, our estimates represent averages over many countries with different epidemiological contexts, healthcare systems, cultural behaviors and nuances in intervention implementation details and population compliance. This global approach, similar to pr...
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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