key: cord-325001-5zd6fydo authors: Sinkala, M.; Nkhoma, P.; Zulu, M.; Kafita, D.; Tembo, R.; Daka, V. title: The COVID-19 Pandemic in Africa: Predictions using the SIR Model Indicate the Cases are Falling date: 2020-06-03 journal: nan DOI: 10.1101/2020.06.01.20118893 sha: doc_id: 325001 cord_uid: 5zd6fydo Since the earliest reports of the Coronavirus disease - 2019 (COVID-19) in Wuhan, China in December 2019, the disease has rapidly spread worldwide, attaining pandemic levels in early March 2020. However, the spread of COVID-19 has differed in the African setting compared to countries on other continents. To predict the spread of COVID-19 in Africa and within each country on the continent, we applied a Susceptible-Infectious-Recovered mathematical model. Here, our results show that, overall, Africa is currently (May 29, 2020) at the peak of the COVID-19 pandemic, after which we predict the number of cases would begin to fall in June 2020. Furthermore, we predict that the ending phase of the pandemic would be in Mid-August 2020 and that decreasing cases of COVID-19 infections would be detected until around December 2020 and January 2021. Our results also reveal that of the 51 countries with reported COVID-19 cases, only nine, including South Africa, Egypt and Ethiopia, are likely to report higher monthly COVID-19 cases in June 2020 than those reported in the previous months. Overall, at the end of this pandemic, we predict that approximately 279,000 (about 154,000 future cases) individuals in Africa would have been infected with the COVID-19 virus. Here, our predictions are data-driven and based on the previously observed trends in the spread of the COVID-19 pandemic. Shifts in the population dynamics and/or changes in the infectiousness of the COVID-19 virus may require new forecasts of the disease spread. The novel Coronavirus disease-2019 (COVID- 19) , which was first reported in China in December 2019, has quickly spread to become a global pandemic [1] [2] [3] . As of 29 th May 2020, over 6.1 million people have tested positive for COVID-19 [4] . So far, global infections of the virus have been unevenly distributed across continents and countries; Europe, North America and South America are among the most impacted. Despite more than 125,000 cases reported in Africa, the spread of COVID 19 has been surprisingly slow, and the disease has exhibited lower-case fatality rates in comparison to other continents [5] . It was expected that the continent, with fragile health systems, barriers to testing, and potentially vulnerable populations, would report high numbers of cases and deaths. Additionally, familiarity with infectious disease outbreaks and diseases leading to an educated immune system has been postulated as possible reasons for these observations [5, 6] . Recently, mathematical models have been applied to investigate the spread of COVID-19 pandemic in various countries, among others, China [7] , Italy [8] , and England [9] . The predictions gleaned from these models have offered a platform for decision making aimed at controlling and/or mitigating the spread of COVID-19 pandemic and the optimisation of lockdowns and treatment efforts [9] [10] [11] . However, currently, most of the COVID-19 modelling has been in high-income countries, and very few efforts have been made to model the spread of COVID-19 in many African countries. Mathematical models that have been employed to predict the spread of the pandemic include logistic models [12, 13] and Susceptible-Infected-Recovered (SIR) models [8, 14] . In modelling using the SIR approach, we assume that the population is a compartment of interacting individuals in which the disease spread from the infected to the susceptible, and the infected either recover and build an immunity toward the infectious agent or succumb to the infection [15, 16] . Here, we use the SIR model to predict the spread of the COVID-19 positive cases on the African continent as a whole and in 45 different countries on the continent. Overall, we provide valuable intuition regarding the expected trajectory of the disease in Africa. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint We obtained a dataset of the global COVID-19 cases from covid.ourworldindata.org. We found that out, as of May 27, 2020, 45 out of 56 African counties have reported the number of COVID-19 positive cases. We extracted information on COVID-19 cases in African countries to show that South Africa has reported the highest number of cases (25, 937) , followed by Egypt (19, 666) and Morocco (8,857; Figure 1 ). . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint to the steady growth phase around July 7 2020, and the ending phase will begin around August 11 2020. Overall, based on the current data and the trajectory of COVID-19 positive cases, we predict the COVID-19 virus will infect another 153,518 individuals to bring the total number of COVID-19 positive cases to about 279,000. Also, we predict that the pandemic would have ended on the dates between December 2020 and January 2021 (for more details, see Supplementary Table 1 ). . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint Start of steady growth 05-Jul-2020 Start of ending phase 08-Aug-2020 End of the epidemic (5 cases . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint We compared the reported COVID-19 positive cases in the most affected countries in Africa (South Africa and Egypt) to those in other countries that have been affected across the globe. Here, we showed that the scale of the COVID-19 cases was lower, even for the worst affected countries in Africa than that in the United States of America, Japan, China, Italy, United Kingdom and Brazil (Figure 4a ). This assertion remains valid even when we consider the number of reported COVID-19 cases as a per cent for each of the country's population size (Figure 4b) . . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint We have conducted a predictive analysis of the COVID-19 pandemic in Africa. Our results show that the scale of the pandemic is low across many countries in Africa. Many experts have debated the reason why fewer cases of COVID-19 are being reported in Africa. Some have pointed toward the lack of widespread testing of COVID-19 [17] [18] [19] [20] , whereas others point towards the African climate [21, 22] . We showed that, on average, most counties in Africa, including Zambia, Malawi, Togo and Chad, have reported fewer than 500 COVID-19 cases. Conversely, most European countries have reported, on average more than 5000 COVID-19 cases. May 2020 is unlikely to be surpassed by those in the next few months. Furthermore, whereas we predicted that the COVID-19 pandemic would disproportionately affect different countries in Africa, we expect that even the worst affected among these would report fewer COVID-19 positive cases compared to other regions of the World. Altogether, based on the current COVID-19 pandemic data and the spread of disease, our predictions show that the peak pandemic is now (May 29, 2020) for most African countries. Here, we caution that our results are only as good as the data and the previous trend observed in the spread of the COVID-19 pandemic. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint Hence, these predictions may not be indicative of future trends where certain parameters, such as the population dynamics and COVID-19 virus infectiousness, are shifted from those currently prevailing. Therefore, we encourage everyone (including individuals in African countries) to adhere to the guidelines that are aimed at reducing the spread of the COVID-19 virus as provided by the WHO and other relevant organisations. We analysed a COVID-19 dataset representing the reported virus-positive cases in the World as of May 28, 2020, obtained from https://covid.ourworldindata.org/data. We extracted the COVID-19 cases reported in 51 African countries and plotted these individually to show the trajectory of the COVID-19 pandemic for each country. Next, we aggregated all the reported COVID-19 cases in Africa since March 1, 2020. Then we used the Susceptible-Infected-Removed (SIR) mathematical model [15, 16] Briefly, we obtained the predicted number of COVID-19 using the SIR model. These predictions include multiple data points per day. Therefore, we aggregated the . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2020. . https://doi.org/10.1101/2020.06.01.20118893 doi: medRxiv preprint predictions made at irregular time intervals per day to yield a single prediction for each country per day by interpolation using the Cubic spline algorithm [26, 27] . Also, to predict the number of cases of COVID-19 infection of each country, we aggregated the predictions for each month (see Figure 3a ). The data that support the findings of this study are available at covid.ourworldindata.org. All the MATLAB source code used to process, analyse, and reproduce the major finding of this report is from the following websites: https://www.mathworks.com/matlabcentral/fileexchange/76435-covid-19predictions-in-africa-using-the-sir-model Supplementary File 1: Predict cases of COVID-19 using the SIR model for each day across each country in Africa. Why is it difficult to accurately predict the COVID-19 epidemic? COVID-19): A Perspective from China Estimation of the final size of the coronavirus epidemic by the logistic model Coronavirus Update (Live): 6,150,262 Cases and 370,500 Deaths from COVID-19 Virus Pandemic -Worldometer n COVID-19: protecting health-care workers Immunity, parasites, genetics and sex hormones: contributors to mild inflammatory responses in COVID-19? 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Access to lifesaving medical resources for African countries: COVID-19 testing and response, ethics, and politics COVID-19 on the African continent Managing COVID-19 in Low-and Middle-Income Countries Temperature and Latitude Analysis to Predict Potential Spread Extending the SIR epidemic model fitVirusCOVID19 -File Exchange -MATLAB Central A Practical Guide to Spline A New Method of Interpolation and Smooth Curve Fitting Based on Local Procedures The authors declare that they have no competing interests