Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Setting and Data Sources
2.2. Assumptions
2.3. Statistical Model
- Y = dependent variable
- X = the matrix of independent variable
- β = vector of regression model parameters
- σ2 = Standard deviation
- μ = prior mean μ
- Λ = prior precision matrix
- k = number of regression coefficients
- V = prior hyperparameter values
2.4. Spatial Analysis
3. Results
3.1. Descriptive Analysis
3.1.1. Bayesian Regression Model
3.1.2. Bayesian Prediction Model
3.1.3. Estimated Infection Fatality Rate by Country
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Appendix A.1. Sensitivity Analysis of the Infection Fatality Rates of the Posterior Summary Statistics, 30 May 2020
Posterior Summary Statistics | Mean | Maximum | ||||
---|---|---|---|---|---|---|
75% Cred. Interval | 90% Cred. Interval | 95% Cred. Interval | 75% Cred. Interval | 90% Cred. Interval | 95% Cred. Interval | |
Cumulative COVID-19 Infections Estimated (as of 30 May 2020) | 47,366 [44,565, 50,167] | 56,839 [54,038, 59,640] | 63,154 [60,353, 65,955] | 1,265,159 [1,262,358, 1,267,960] | 1,518,191 [1,515,390, 1,520,992] | 1,686,879 [1,684,078, 1,689,680] |
Calculated IFR (as of 30 May 2020) | 8.28% | 6.90% | 6.21% | 0.31% | 0.26% | 0.23% |
Total Number of Infections Per confirmed Case (as of 30 May 2020) | 0.35 | 0.42 | 0.47 | 9.36 | 11.24 | 12.48 |
Appendix A.2. Posterior Predictive Checks for Convergence Across All Model Parameters
Appendix A.3. Posterior Predictive Summary for Test Statistics
Posterior Predictive Summary | MCMC Sample Size = 1000 | |||||
---|---|---|---|---|---|---|
T | Mean | Std. Dev. | E(T_Obs) | P(T ≥ T_Obs) | ||
Mean | 6.749488 | 0.3085233 | 6.775585 | 0.462 | ||
Min | 2.818528 | 1.005077 | 3.218876 | 0.389 | ||
Max | 10.89979 | 1.062004 | 10.28329 | 0.694 |
Appendix A.4. WHO COVID-19 Transmission Classification Type
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Mean | Std.Dev | MCSE | Median | Equal-Tailed 95% Cred. Interval | ||
---|---|---|---|---|---|---|
Confirmed_Cases | ||||||
Population Density | −0.0052613 | 0.0021246 | 0.000067 | −0.0051941 | −0.009677 | −0.0011185 |
Aged 65 Older | 0.1831922 | 0.1896953 | 0.005703 | 0.1855481 | −0.174675 | 0.550733 |
Cvd Death Rate | −0.0011224 | 0.0036282 | 0.000113 | −0.0011888 | −0.008117 | 0.0061924 |
Diabetes Prevalence | 0.062837 | 0.0799469 | 0.002528 | 0.0618234 | −0.093096 | 0.2195652 |
Handwashing Facilities | 0.0200225 | 0.0102218 | 0.000319 | 0.0200439 | 0.0006078 | 0.0405081 |
Extreme Poverty | −0.0028848 | 0.010585 | 0.000335 | −0.0029234 | −0.024479 | 0.017851 |
_Cons | 6.22023 | 1.139261 | 0.036027 | 6.19992 | 3.77586 | 8.390462 |
Var | 2.209552 | 0.5010807 | 0.018107 | 2.147209 | 1.413217 | 3.442549 |
Country | Total Cases Reported | Total Deaths Reported | Cumulative Infections Estimated | Estimated IFR | Crude CFR | COVID-19 Transmission Classification Type |
---|---|---|---|---|---|---|
Algeria | 9134 | 638 | 272,017 | 0.24% | 7.00% | Community transmission |
Angola | 77 | 4 | 19,187 | 0.02% | 5.20% | Clusters of cases |
Benin | 224 | 3 | 8884 | 0.03% | 1.30% | Community transmission |
Botswana | 35 | 1 | 22,819 | 0.00% | 2.90% | Clusters of cases |
Burkina Faso | 847 | 53 | 10,257 | 0.52% | 6.30% | Community transmission |
Burundi | 42 | 1 | 1959 | 0.05% | 2.40% | Clusters of cases |
Cameroon | 5436 | 177 | 17,603 | 1.01% | 3.30% | Clusters of cases |
Cape Verde | 405 | 4 | 12,464 | 0.03% | 1.00% | Community transmission |
Central African Republic | 874 | 1 | 23,043 | 0.00% | 0.10% | Clusters of cases |
Chad | 759 | 65 | 17,517 | 0.37% | 8.60% | Community transmission |
Comoros | 87 | 2 | 4894 | 0.04% | 2.30% | Community transmission |
Congo | 587 | 19 | 40,170 | 0.05% | 3.20% | Community transmission |
Cote d’Ivoire | 2750 | 32 | 10,386 | 0.31% | 1.20% | Community transmission |
Democratic Republic of Congo | 2833 | 69 | 14,499 | 0.48% | 2.40% | Community transmission |
Djibouti | 2914 | 20 | 23,332 | 0.09% | 0.70% | Clusters of cases |
Egypt | 22,082 | 879 | 205,083 | 0.43% | 4.00% | Clusters of cases |
Equatorial Guinea | 1043 | 12 | 39,917 | 0.03% | 1.20% | Community transmission |
Ethiopia | 968 | 8 | 19,147 | 0.04% | 0.80% | Clusters of cases |
Gabon | 2613 | 15 | 27,858 | 0.05% | 0.60% | Clusters of cases |
Gambia | 25 | 1 | 5357 | 0.02% | 4.00% | Community transmission |
Ghana | 7616 | 34 | 21,248 | 0.16% | 0.40% | Sporadic cases |
Guinea | 3656 | 22 | 16,782 | 0.13% | 0.60% | Community transmission |
Guinea-Bissau | 1256 | 8 | 8235 | 0.10% | 0.60% | Community transmission |
Kenya | 1745 | 62 | 15,440 | 0.40% | 3.60% | Community transmission |
Liberia | 273 | 27 | 11,455 | 0.24% | 9.90% | Community transmission |
Libya | 118 | 5 | 25,774 | 0.02% | 4.20% | Community transmission |
Madagascar | 698 | 5 | 30,097 | 0.02% | 0.70% | Clusters of cases |
Malawi | 273 | 4 | 5695 | 0.07% | 1.50% | Clusters of cases |
Mali | 1226 | 73 | 42,636 | 0.17% | 6.00% | Clusters of cases |
Mauritania | 423 | 20 | 18,496 | 0.11% | 4.70% | Community transmission |
Mauritius | 335 | 10 | 19,972 | 0.05% | 3.00% | Clusters of cases |
Morocco | 7714 | 202 | 25,380 | 0.80% | 2.60% | Clusters of cases |
Mozambique | 234 | 2 | 11,812 | 0.02% | 0.90% | Clusters of cases |
Niger | 955 | 64 | 12,248 | 0.52% | 6.70% | Clusters of cases |
Nigeria | 9302 | 261 | 17,052 | 1.53% | 2.80% | Community transmission |
Sao Tome and Principe | 463 | 12 | 10,292 | 0.12% | 2.60% | Community transmission |
Senegal | 3429 | 41 | 13,239 | 0.31% | 1.20% | Clusters of cases |
Sierra Leone | 829 | 45 | 8729 | 0.52% | 5.40% | Community transmission |
Somalia | 1828 | 72 | 19,366 | 0.37% | 3.90% | Community transmission |
South Africa | 29,240 | 611 | 47,859 | 1.28% | 2.10% | Sporadic cases |
South Sudan | 994 | 10 | 26,287 | 0.04% | 1.00% | Community transmission |
Sudan | 4521 | 233 | 71,606 | 0.33% | 5.20% | Clusters of cases |
Swaziland | 279 | 2 | 22,122 | 0.01% | 0.70% | Community transmission |
Tanzania | 509 | 21 | 41,536 | 0.05% | 4.10% | Community transmission |
Togo | 428 | 13 | 9720 | 0.13% | 3.00% | Community transmission |
Tunisia | 1071 | 48 | 302,601 | 0.02% | 4.50% | Community transmission |
Zambia | 1057 | 7 | 14,677 | 0.05% | 0.70% | Community transmission |
Zimbabwe | 160 | 4 | 20,130 | 0.02% | 2.50% | Sporadic cases |
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Onovo, A.A.; Kalaiwo, A.; Obanubi, C.; Odezugo, G.; Estill, J.; Keiser, O. Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis. BioMed 2021, 1, 63-79. https://doi.org/10.3390/biomed1010005
Onovo AA, Kalaiwo A, Obanubi C, Odezugo G, Estill J, Keiser O. Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis. BioMed. 2021; 1(1):63-79. https://doi.org/10.3390/biomed1010005
Chicago/Turabian StyleOnovo, Amobi Andrew, Abiye Kalaiwo, Christopher Obanubi, Gertrude Odezugo, Janne Estill, and Olivia Keiser. 2021. "Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis" BioMed 1, no. 1: 63-79. https://doi.org/10.3390/biomed1010005