The basic reproduction number of COVID-19 across Africa
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Abstract
The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by surprise. Following the first outbreak of COVID-19 in December 2019, several models have been developed to study and understand its transmission dynamics. Although the spread of COVID-19 is being slowed down by vaccination and other interventions, there is still a need to have a clear understanding of the evolution of the pandemic across countries, states and communities. To this end, there is a need to have a clearer picture of the initial spread of the disease in different regions. In this project, we used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa. Our estimates vary between 1.98 (Sudan) and 9.66 (Mauritius), with a median of 3.67 (90% CrI: 3.31–4.12). The estimates provided in this paper will help to inform COVID-19 modeling in the respective countries/regions.
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SciScore for 10.1101/2021.11.02.21265826: (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:Another limitation of this work includes not accounting for under-reporting. Due to the highly contagious nature of SARS-CoV-2, many countries advised individuals with COVID-19-like symptoms to self-isolate at home instead of going to the hospital, except they have a severe case of the disease. As a result, these individuals may not get a test to confirm if they had the disease, and therefore, they may not be captured in the reported …
SciScore for 10.1101/2021.11.02.21265826: (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:Another limitation of this work includes not accounting for under-reporting. Due to the highly contagious nature of SARS-CoV-2, many countries advised individuals with COVID-19-like symptoms to self-isolate at home instead of going to the hospital, except they have a severe case of the disease. As a result, these individuals may not get a test to confirm if they had the disease, and therefore, they may not be captured in the reported cases. This may lead to under-reporting. The availability and consistency of data is also another limitation of this work. Data collection during the COVID-19 pandemic has been very tedious worldwide, especially during the early stage of the disease when non-pharmaceutical interventions that impede movement and access to resources were imposed. Particularly, data collection in many developing countries across Africa is challenging due to the lack of adequate infrastructure, leading to inadequate data. The framework presented in this paper requires knowing the transition rates of infected individuals between the different compartments of the model. These parameters may not be immediately available for a novel disease like SARS-CoV-2 during the early stage of the disease. Another limitation of our model includes not explicitly modeling the dynamics of asymptomatic individuals. An interesting extension of the work presented in this paper includes incorporating a parameter for the ascertainment fraction of the reported cases of COVID-19 in each count...
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.
Results from scite Reference Check: We found no unreliable references.
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