| Literature DB >> 35633775 |
Joyce Kiarie1, Samuel Mwalili1,2, Rachel Mbogo1.
Abstract
COVID-19, a coronavirus disease 2019, is an ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first case in Kenya was identified on March 13, 2020, with the pandemic increasing to about 237,000 confirmed cases and 4,746 deaths by August 2021. We developed an SEIR model forecasting the COVID-19 pandemic in Kenya using an Autoregressive Integrated moving averages (ARIMA) model. The average time difference between the peaks of wave 1 to wave 4 was observed to be about 130 days. The 4th wave was observed to have had the least number of daily cases at the peak. According to the forecasts made for the next 60 days, the pandemic is expected to continue for a while. The 4th wave peaked on August 26, 2021 (498th day). By October 26, 2021 (60th day), the average number of daily infections will be 454 new cases and 40 severe cases, which would require hospitalization, and 16 critically ill cases requiring intensive care unit services. The findings of this study are key in developing informed mitigation strategies to ensure that the pandemic is contained and inform the preparedness of policymakers and health care workers.Entities:
Keywords: ARIMA; COVID-19; Forecasting; Infectious disease model; Kenya pandemic; SEIR
Year: 2022 PMID: 35633775 PMCID: PMC9125995 DOI: 10.1016/j.idm.2022.05.001
Source DB: PubMed Journal: Infect Dis Model ISSN: 2468-0427
Fig. 1A schematic illustration of the underlying model.
List of the parameters used in the SEIR model; a description of both the literature values, their sources, and the OLS values.
| Parameter description | Symbol | Literature Value | Source | OLS Value (calculated) |
|---|---|---|---|---|
| Rate of transmission from S to E due to contact with IA | 0.15 | 0.151 | ||
| Rate of transmission from S to E due to contact with IM | 0.08 | 0.436 | ||
| Proportion of symptomatic infectious people | 0.85 | 0.803 | ||
| Progression rate from E to either IA or IS | 0.196 | 0.15 | ||
| The recovery rate of the asymptomatic infected individuals | 1 | 0.9495 | ||
| Recovery rate of the symptomatic infected individuals | 0.9815 | 0.4996 | ||
| Recovery rate of the hospitalized individuals | 0.1 | 0.5003 | ||
| The recovery rate of the critically ill individuals | 0.5 | 0.55 | ||
| Rate of movement from hospitalization to critical illness condition | 0.3 | 0.4994 | ||
| The hospitalization rate of the symptomatic infected individuals | 0.044 | 0.02598 | ||
| The death rate of the critically ill due to the virus | 0.25 | 0.4999 |
COVID-19 peak days, daily and cumulative cases in Kenya.
| Pandemic Peak days and number of Daily cases by Wave in Kenya | |||||
|---|---|---|---|---|---|
| 1st Wave | 2nd Wave | 3rd Wave | 4th Wave | 60th day Forecast | |
| 13-07-2020 | 19-10-2020 | 9/3/2021 | 26-08-2021 | 26-10-2021 | |
| 122 | 221 | 358 | 498 | 566 | |
| 1163 | 1464 | 1443 | 849 | 470 | |
| 89 | 119 | 104 | 64 | 41 | |
| 34 | 46 | 40 | 25 | 16 | |
| 30,697 | 83,194 | 144,745 | 204,275 | 241,145 | |
| 398 | 1,459 | 2,774 | 4,094 | 4,764 | |
Fig. 2This chart presents a scatter plot (orange dots) of the measured/observed number of COVID-19 cases. The predicted cases are presented in a line chart (blue line) and the forecasted daily cases in Kenya (in red) for the next 60 days.
Fig. 3This chart presents the forecast of the severe daily cases of COVID-19 for the next 60 days in Kenya. It also contains a scatter plot of the observed cases (orange dots) and the predictions (blue line)., predicted, and forecasted daily severe cases in Kenya (red line).
Fig. 4The scatter plot of the measured (orange dots), predicted (blue line), and forecasted (red line); daily critical cases (those that require ICU admissions intervention) in Kenya.
Fig. 5The chart presents the cumulative plot of the observed cases (orange line), predicted (blue line), and the 60 days forecast (red line) of the daily new cases in Kenya.
Fig. 6Cumulative plot of the measured, predicted and the forecasted deaths in Kenya; the orange line represents the observed, blue line the predicted and the red is the forecasted COVID-19 cases for the next 60 days.
Accuracy measures for selecting the best order of the ARIMA model. ∗
| ME | RMSE | MAE | MPE | MAPE | MASE | ACF1 | loglikelihood | AIC | p | q | d | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Training set | 0.00000 | 0.228 | 0.194 | −4.971 | 19.574 | 12.675 | 0.994 | 29.503 | −55.005 | 0 | 0 | 0 |
| Training set1 | 0.00040 | 0.020 | 0.015 | 0.026 | 1.438 | 0.998 | 0.782 | 1250.254 | −2498.509 | 0 | 0 | 1 |
| Training set2 | −0.00004 | 0.013 | 0.010 | 0.024 | 0.933 | 0.643 | −0.165 | 1457.594 | −2913.187 | 0 | 0 | 2 |
| Training set3 | 0.00010 | 0.117 | 0.099 | −2.499 | 9.955 | 6.452 | 0.940 | 367.451 | −728.902 | 0 | 1 | 0 |
| Training set4 | 0.00024 | 0.016 | 0.012 | 0.022 | 1.151 | 0.795 | 0.295 | 1384.887 | −2765.774 | 0 | 1 | 1 |
| Training set5 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.939 | 0.649 | −0.003 | 1464.242 | −2924.485 | 0 | 1 | 2 |
| Training set6 | 0.00020 | 0.067 | 0.056 | −1.363 | 5.639 | 3.664 | 0.794 | 646.417 | −1284.833 | 0 | 2 | 0 |
| Training set7 | 0.00018 | 0.014 | 0.011 | 0.022 | 1.031 | 0.712 | 0.191 | 1446.981 | −2887.962 | 0 | 2 | 1 |
| Training set8 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.938 | 0.648 | −0.003 | 1464.440 | −2922.879 | 0 | 2 | 2 |
| Training set9 | 0.00065 | 0.020 | 0.016 | 0.027 | 1.464 | 1.014 | 0.780 | 1251.076 | −2496.153 | 1 | 0 | 0 |
| Training set10 | 0.00007 | 0.013 | 0.010 | 0.025 | 0.934 | 0.644 | −0.049 | 1489.515 | −2975.030 | 1 | 0 | 1 |
| Training set11 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.936 | 0.648 | 0.005 | 1464.607 | −2925.213 | 1 | 0 | 2 |
| Training set12 | 0.00044 | 0.016 | 0.012 | 0.021 | 1.151 | 0.794 | 0.294 | 1385.906 | −2763.812 | 1 | 1 | 0 |
| Training set13 | 0.00006 | 0.013 | 0.010 | 0.026 | 0.929 | 0.642 | −0.006 | 1490.299 | −2974.598 | 1 | 1 | 1 |
| Training set14 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.940 | 0.650 | 0.001 | 1464.871 | −2923.742 | 1 | 1 | 2 |
| Training set15 | 0.00037 | 0.014 | 0.011 | 0.020 | 1.031 | 0.712 | 0.190 | 1448.245 | −2886.491 | 1 | 2 | 0 |
| Training set16 | 0.00007 | 0.013 | 0.010 | 0.024 | 0.925 | 0.638 | 0.001 | 1494.855 | −2981.709 | 1 | 2 | 1 |
| Training set17 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.940 | 0.650 | 0.001 | 1464.871 | −2921.742 | 1 | 2 | 2 |
| Training set18 | 0.00006 | 0.013 | 0.010 | 0.021 | 0.935 | 0.645 | −0.051 | 1489.578 | −2971.156 | 2 | 0 | 0 |
| Training set19 | 0.00006 | 0.013 | 0.010 | 0.027 | 0.927 | 0.640 | 0.009 | 1490.558 | −2975.115 | 2 | 0 | 1 |
| Training set20 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.939 | 0.650 | 0.002 | 1464.788 | −2923.575 | 2 | 0 | 2 |
| Training set21 | −0.00004 | 0.013 | 0.010 | −0.022 | 0.951 | 0.652 | −0.115 | 1489.952 | −2969.903 | 2 | 1 | 0 |
| Training set22 | 0.00006 | 0.013 | 0.010 | 0.027 | 0.923 | 0.638 | 0.022 | 1491.764 | −2975.528 | 2 | 1 | 1 |
| Training set23 | −0.00004 | 0.013 | 0.010 | 0.027 | 0.940 | 0.650 | 0.001 | 1464.871 | −2921.742 | 2 | 1 | 2 |
| Training set24 | 0.00017 | 0.013 | 0.010 | 0.000 | 0.922 | 0.635 | −0.002 | 1498.813 | −2985.626 | 2 | 2 | 0 |
| Training set25 | 0.00007 | 0.013 | 0.010 | 0.024 | 0.925 | 0.638 | 0.001 | 1494.859 | −2979.717 | 2 | 2 | 1 |
| Training set26 | −0.00051 | 0.013 | 0.010 | −0.020 | 0.922 | 0.638 | 0.019 | 1486.797 | −2963.593 | 2 | 2 | 2 |
∗ME = Mean Error, RMSE = Root Mean Square Error, MAE = Mean Absolute Error, MPE = Mean Percentage Error, MAPE = Mean Absolute Percentage Error, ACF = Autocorrelation Function, AIC = Akaike Information Criterion, and (p, d, q) represent the ARIMA order.