Pan-African evolution of within- and between-country COVID-19 dynamics
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Abstract
We created a strategy for understanding the evolution of the COVID-19 pandemic throughout the African continent. Because high-quality mobility data are challenging to obtain across Africa, the approach provides the ability to distinguish cases arising from within a country or from its neighbors. The results further show how testing capacity and social and health policy contribute to the dynamics of cases, and generate short-term prediction of the evolution of the pandemic on a country-by-country basis. This framework improves the ability to interpret and act upon real-time complex COVID-19 data from the African continent. These findings emphasize that regional efforts to coordinate country-specific strategies in transmission suppression should be a continental priority to control the COVID-19 pandemic in Africa.
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SciScore for 10.1101/2020.11.13.20231241: (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:3.1 Limitations: A number of assumptions were made in our analysis. Contact patterns across countries were assumed to be constant over time. Current patterns, such as inter-country air travel and border crossing by land might not follow the weights we have assumed, and actual population contact probabilities might not be constant over time. Nevertheless, the use of higher order neighborhood (beyond sharing a border) contact patterns …
SciScore for 10.1101/2020.11.13.20231241: (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:3.1 Limitations: A number of assumptions were made in our analysis. Contact patterns across countries were assumed to be constant over time. Current patterns, such as inter-country air travel and border crossing by land might not follow the weights we have assumed, and actual population contact probabilities might not be constant over time. Nevertheless, the use of higher order neighborhood (beyond sharing a border) contact patterns led to improved model fit compared to an assumption of first order neighbors (bordering countries) only. Other assumptions related to the testing and stringency policies. These are coarse approximations of governmental response to the surveillance and control disease transmission. The absence of quantifiable tests per capita is a limitation of this approach. We are aware that SARS-COV-2 is often carried by apparently healthy individuals who might unknowingly transmit the pathogen. In the present analysis, we could not disentangle asymptomatic and symptomatic disease. Under-reporting can introduce artifacts in the autocorrelation structure and may confound the estimation of lag weights of the underlying serial interval distribution (52). Additionally, we assumed that model coefficients were constant over time. This is not the optimal fit for SARS-COV-2 transmission if there is seasonal variation, and implies that the interaction with weather is the same in summer and winter. We avoided adding sinusoidal (smooth, repetitive oscillation) functions in...
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 35. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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