From acb037e489fb809e1e434a08c6a62f336ae71f91 Mon Sep 17 00:00:00 2001 From: Marc Bevand Date: Wed, 7 Oct 2020 22:03:33 -0700 Subject: [PATCH] apply_ifr.py: add seasonal flu to comparison table --- README.md | 452 ++++++++++++++++++++++++++------------------------- apply_ifr.py | 56 ++----- 2 files changed, 247 insertions(+), 261 deletions(-) diff --git a/README.md b/README.md index 4d1b6cc..90de9b5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -*Updated: 01 Oct 2020* +*Updated: 07 Oct 2020* Author: Marc Bevand @@ -75,11 +75,14 @@ total_illnesses = symptomatic_illnesses / .575 # Age-stratified IFR applied to countries' population pyramids The script [apply_ifr.py](apply_ifr.py) uses a handful of age-stratified -IFR estimates (from the chart above) and applies them to countries' population pyramids, to -find their expected overall IFR assuming equal prevalence of the disease among all -age groups. +IFR estimates for COVID-19 and the seasonal flu and +applies them to countries' population pyramids, to find their expected average +IFR. The calculation assumes equal prevalence of the disease among all age groups. -Of course, the real-world overall IFR will dependent on many factors: varying +IFR estimates are a subset of the same sources as in `covid_vs_flu.py`. The flu +IFR is from the last flu season, 2019-2020. + +The real-world overall IFR will, of course, dependent on many factors: varying prevalence among age groups, underlying health conditions, access to healthcare, socioeconomic status, ethnicity, etc. @@ -90,234 +93,237 @@ specifically the first sheet of [Population by Age Groups - Both Sexes](https:// ## Results -The overall expected IFR percentages are summarized in this table (sorted by -IFR according to ENE-COV column): +The overall expected IFR percentages are summarized in this table (sorted on the +ENE-COVID column): -| ENE-COV | US_CDC | Verity | Levin | Gudbj | O'Drisc | Region | -| ------- | ------- | ------- | ------- | ------- | ------- | ------ | -| 1.274 | 1.311 | 1.605 | 2.247 | 1.283 | 0.961 | Japan | -| 1.065 | 1.092 | 1.382 | 1.847 | 1.068 | 0.811 | Italy | -| 1.041 | 1.043 | 1.339 | 1.806 | 1.057 | 0.796 | Greece | -| 0.993 | 1.012 | 1.305 | 1.702 | 0.994 | 0.764 | Germany | -| 0.984 | 1.045 | 1.320 | 1.726 | 0.986 | 0.753 | Portugal | -| 0.931 | 0.985 | 1.270 | 1.648 | 0.918 | 0.704 | Martinique | -| 0.919 | 0.933 | 1.221 | 1.658 | 0.918 | 0.706 | Lithuania | -| 0.916 | 0.942 | 1.207 | 1.648 | 0.921 | 0.694 | Spain | -| 0.914 | 0.941 | 1.201 | 1.606 | 0.913 | 0.682 | France | -| 0.899 | 1.008 | 1.248 | 1.556 | 0.883 | 0.671 | Finland | -| 0.881 | 0.919 | 1.192 | 1.624 | 0.870 | 0.672 | Latvia | -| 0.875 | 0.957 | 1.205 | 1.528 | 0.857 | 0.655 | Puerto Rico | -| 0.868 | 0.892 | 1.171 | 1.516 | 0.870 | 0.672 | Estonia | -| 0.865 | 0.932 | 1.209 | 1.487 | 0.855 | 0.665 | Croatia | -| 0.855 | 0.965 | 1.205 | 1.471 | 0.835 | 0.637 | Malta | -| 0.846 | 0.881 | 1.137 | 1.478 | 0.847 | 0.639 | Belgium | -| 0.843 | 0.905 | 1.181 | 1.489 | 0.829 | 0.645 | Slovenia | -| 0.840 | 0.943 | 1.154 | 1.471 | 0.838 | 0.632 | Sweden | -| 0.836 | 0.910 | 1.149 | 1.462 | 0.830 | 0.638 | Austria | -| 0.825 | 0.897 | 1.132 | 1.447 | 0.819 | 0.624 | Switzerland | -| 0.810 | 0.861 | 1.117 | 1.396 | 0.802 | 0.615 | Europe | -| 0.802 | 0.909 | 1.141 | 1.394 | 0.785 | 0.603 | Netherlands | -| 0.801 | 0.949 | 1.181 | 1.377 | 0.779 | 0.608 | Bulgaria | -| 0.798 | 0.864 | 1.113 | 1.399 | 0.779 | 0.600 | Guadeloupe | -| 0.797 | 0.935 | 1.136 | 1.370 | 0.782 | 0.595 | Denmark | -| 0.794 | 0.868 | 1.089 | 1.384 | 0.794 | 0.598 | United Kingdom | -| 0.791 | 0.811 | 1.102 | 1.367 | 0.761 | 0.588 | China, Hong Kong SAR | -| 0.759 | 0.830 | 1.090 | 1.285 | 0.745 | 0.578 | Romania | -| 0.753 | 0.854 | 1.101 | 1.323 | 0.732 | 0.573 | Hungary | -| 0.745 | 0.800 | 1.064 | 1.285 | 0.724 | 0.557 | Poland | -| 0.739 | 0.828 | 1.059 | 1.315 | 0.737 | 0.565 | Channel Islands | -| 0.738 | 0.878 | 1.092 | 1.302 | 0.717 | 0.555 | Czechia | -| 0.734 | 0.810 | 1.047 | 1.288 | 0.714 | 0.548 | Canada | -| 0.719 | 0.756 | 0.998 | 1.259 | 0.705 | 0.534 | Barbados | -| 0.713 | 0.808 | 1.038 | 1.210 | 0.694 | 0.538 | Curaçao | -| 0.709 | 0.802 | 1.007 | 1.239 | 0.699 | 0.528 | Norway | -| 0.680 | 0.800 | 1.029 | 1.160 | 0.659 | 0.515 | Serbia | -| 0.676 | 0.694 | 0.904 | 1.193 | 0.686 | 0.505 | Uruguay | -| 0.675 | 0.745 | 0.967 | 1.181 | 0.660 | 0.503 | Northern America | -| 0.671 | 0.736 | 0.944 | 1.174 | 0.670 | 0.503 | Australia | -| 0.671 | 0.733 | 0.983 | 1.103 | 0.651 | 0.513 | Ukraine | -| 0.669 | 0.738 | 0.958 | 1.169 | 0.654 | 0.497 | United States of America | -| 0.659 | 0.757 | 1.011 | 1.088 | 0.620 | 0.503 | Bosnia and Herzegovina | -| 0.654 | 0.742 | 0.945 | 1.137 | 0.645 | 0.490 | New Zealand | -| 0.644 | 0.735 | 0.941 | 1.131 | 0.630 | 0.489 | Cuba | -| 0.641 | 0.877 | 1.059 | 1.152 | 0.608 | 0.491 | United States Virgin Islands | -| 0.633 | 0.725 | 0.963 | 1.090 | 0.606 | 0.483 | Republic of Korea | -| 0.628 | 0.686 | 0.938 | 1.100 | 0.599 | 0.472 | China, Taiwan Province of China | -| 0.624 | 0.663 | 0.916 | 1.030 | 0.606 | 0.473 | Russian Federation | -| 0.624 | 0.657 | 0.921 | 1.082 | 0.606 | 0.483 | Belarus | -| 0.615 | 0.668 | 0.881 | 1.078 | 0.616 | 0.467 | Luxembourg | -| 0.607 | 0.670 | 0.896 | 1.002 | 0.598 | 0.464 | Georgia | -| 0.605 | 0.683 | 0.888 | 1.061 | 0.599 | 0.453 | Iceland | -| 0.604 | 0.709 | 0.935 | 1.059 | 0.580 | 0.457 | Slovakia | -| 0.582 | 0.667 | 0.891 | 0.989 | 0.567 | 0.444 | Montenegro | -| 0.563 | 0.653 | 0.838 | 0.972 | 0.559 | 0.424 | Ireland | -| 0.561 | 0.649 | 0.839 | 0.957 | 0.559 | 0.426 | Cyprus | -| 0.548 | 0.659 | 0.857 | 0.941 | 0.533 | 0.418 | Albania | -| 0.531 | 0.652 | 0.874 | 0.920 | 0.508 | 0.412 | Aruba | -| 0.518 | 0.580 | 0.754 | 0.902 | 0.526 | 0.388 | Oceania | -| 0.510 | 0.588 | 0.795 | 0.881 | 0.491 | 0.385 | Thailand | -| 0.500 | 0.569 | 0.763 | 0.880 | 0.493 | 0.377 | Réunion | -| 0.499 | 0.545 | 0.710 | 0.872 | 0.516 | 0.371 | Israel | -| 0.497 | 0.522 | 0.748 | 0.794 | 0.491 | 0.377 | Armenia | -| 0.497 | 0.616 | 0.816 | 0.851 | 0.474 | 0.378 | North Macedonia | -| 0.493 | 0.550 | 0.736 | 0.861 | 0.492 | 0.370 | Chile | -| 0.479 | 0.550 | 0.796 | 0.829 | 0.433 | 0.356 | Singapore | -| 0.454 | 0.515 | 0.671 | 0.790 | 0.471 | 0.343 | Argentina | -| 0.449 | 0.514 | 0.738 | 0.770 | 0.412 | 0.328 | China, Macao SAR | -| 0.447 | 0.544 | 0.732 | 0.772 | 0.425 | 0.331 | Mauritius | -| 0.435 | 0.501 | 0.721 | 0.766 | 0.413 | 0.332 | Republic of Moldova | -| 0.415 | 0.511 | 0.681 | 0.717 | 0.402 | 0.310 | Trinidad and Tobago | -| 0.413 | 0.475 | 0.638 | 0.712 | 0.417 | 0.309 | Costa Rica | -| 0.413 | 0.468 | 0.626 | 0.704 | 0.413 | 0.304 | Saint Lucia | -| 0.409 | 0.507 | 0.695 | 0.707 | 0.385 | 0.308 | China | -| 0.394 | 0.497 | 0.648 | 0.712 | 0.409 | 0.303 | Antigua and Barbuda | -| 0.387 | 0.495 | 0.651 | 0.668 | 0.377 | 0.286 | Sri Lanka | -| 0.377 | 0.487 | 0.635 | 0.622 | 0.373 | 0.284 | Dem. People's Republic of Korea | -| 0.376 | 0.437 | 0.594 | 0.645 | 0.382 | 0.282 | Brazil | -| 0.365 | 0.464 | 0.611 | 0.618 | 0.373 | 0.279 | Guam | -| 0.364 | 0.425 | 0.569 | 0.627 | 0.381 | 0.275 | Jamaica | -| 0.361 | 0.454 | 0.605 | 0.663 | 0.375 | 0.279 | Saint Vincent and the Grenadines | -| 0.359 | 0.399 | 0.540 | 0.623 | 0.380 | 0.269 | Panama | -| 0.358 | 0.418 | 0.566 | 0.615 | 0.370 | 0.269 | WORLD | -| 0.356 | 0.410 | 0.555 | 0.614 | 0.371 | 0.267 | Latin America and the Caribbean | -| 0.355 | 0.412 | 0.560 | 0.613 | 0.367 | 0.267 | Colombia | -| 0.354 | 0.438 | 0.595 | 0.642 | 0.368 | 0.271 | Grenada | -| 0.347 | 0.399 | 0.528 | 0.595 | 0.377 | 0.265 | El Salvador | -| 0.343 | 0.363 | 0.528 | 0.602 | 0.355 | 0.257 | Viet Nam | -| 0.342 | 0.408 | 0.552 | 0.588 | 0.356 | 0.260 | Turkey | -| 0.339 | 0.397 | 0.537 | 0.583 | 0.358 | 0.258 | Peru | -| 0.336 | 0.394 | 0.553 | 0.579 | 0.344 | 0.256 | Tunisia | -| 0.327 | 0.432 | 0.573 | 0.547 | 0.328 | 0.249 | New Caledonia | -| 0.325 | 0.394 | 0.541 | 0.559 | 0.331 | 0.245 | Asia | -| 0.310 | 0.350 | 0.463 | 0.535 | 0.346 | 0.233 | Bolivia (Plurinational State of) | -| 0.309 | 0.348 | 0.480 | 0.532 | 0.333 | 0.232 | Dominican Republic | -| 0.307 | 0.348 | 0.503 | 0.505 | 0.319 | 0.236 | Kazakhstan | -| 0.306 | 0.352 | 0.485 | 0.532 | 0.327 | 0.230 | Mexico | -| 0.305 | 0.365 | 0.502 | 0.526 | 0.317 | 0.228 | Venezuela (Bolivarian Republic of) | -| 0.303 | 0.347 | 0.474 | 0.525 | 0.329 | 0.228 | Ecuador | -| 0.295 | 0.346 | 0.482 | 0.501 | 0.317 | 0.225 | Lebanon | -| 0.293 | 0.400 | 0.542 | 0.477 | 0.284 | 0.225 | Seychelles | -| 0.287 | 0.384 | 0.527 | 0.513 | 0.286 | 0.220 | French Polynesia | -| 0.282 | 0.326 | 0.456 | 0.456 | 0.298 | 0.208 | Guyana | -| 0.280 | 0.335 | 0.463 | 0.469 | 0.298 | 0.211 | Suriname | -| 0.273 | 0.313 | 0.474 | 0.452 | 0.279 | 0.208 | Azerbaijan | -| 0.272 | 0.337 | 0.474 | 0.462 | 0.284 | 0.207 | Morocco | -| 0.269 | 0.358 | 0.495 | 0.460 | 0.272 | 0.206 | Bahamas | -| 0.263 | 0.325 | 0.453 | 0.442 | 0.279 | 0.196 | Malaysia | -| 0.260 | 0.305 | 0.426 | 0.446 | 0.289 | 0.198 | Algeria | -| 0.257 | 0.307 | 0.418 | 0.436 | 0.287 | 0.193 | Paraguay | -| 0.251 | 0.297 | 0.403 | 0.423 | 0.288 | 0.190 | Bhutan | -| 0.246 | 0.301 | 0.431 | 0.418 | 0.263 | 0.186 | Iran (Islamic Republic of) | -| 0.234 | 0.293 | 0.414 | 0.398 | 0.253 | 0.176 | India | -| 0.229 | 0.293 | 0.416 | 0.387 | 0.244 | 0.172 | Indonesia | -| 0.228 | 0.259 | 0.373 | 0.393 | 0.262 | 0.173 | Nicaragua | -| 0.221 | 0.269 | 0.368 | 0.374 | 0.255 | 0.167 | Bangladesh | -| 0.221 | 0.232 | 0.349 | 0.374 | 0.260 | 0.170 | Cabo Verde | -| 0.217 | 0.284 | 0.375 | 0.310 | 0.247 | 0.163 | Tonga | -| 0.215 | 0.277 | 0.401 | 0.366 | 0.228 | 0.161 | Myanmar | -| 0.208 | 0.235 | 0.334 | 0.351 | 0.244 | 0.153 | Belize | -| 0.206 | 0.235 | 0.331 | 0.353 | 0.249 | 0.155 | Honduras | -| 0.204 | 0.233 | 0.323 | 0.349 | 0.253 | 0.155 | Guatemala | -| 0.204 | 0.255 | 0.360 | 0.342 | 0.232 | 0.152 | Philippines | -| 0.202 | 0.267 | 0.360 | 0.344 | 0.232 | 0.151 | Nepal | -| 0.197 | 0.249 | 0.381 | 0.331 | 0.210 | 0.149 | Brunei Darussalam | -| 0.194 | 0.237 | 0.331 | 0.330 | 0.233 | 0.146 | Haiti | -| 0.193 | 0.251 | 0.355 | 0.325 | 0.220 | 0.145 | South Africa | -| 0.193 | 0.222 | 0.339 | 0.316 | 0.220 | 0.145 | Turkmenistan | -| 0.192 | 0.247 | 0.343 | 0.321 | 0.224 | 0.142 | Egypt | -| 0.192 | 0.262 | 0.376 | 0.318 | 0.206 | 0.142 | Fiji | -| 0.188 | 0.220 | 0.335 | 0.310 | 0.217 | 0.141 | Kyrgyzstan | -| 0.188 | 0.245 | 0.353 | 0.344 | 0.216 | 0.143 | French Guiana | -| 0.187 | 0.219 | 0.340 | 0.317 | 0.212 | 0.142 | Uzbekistan | -| 0.185 | 0.224 | 0.323 | 0.317 | 0.222 | 0.140 | Syrian Arab Republic | -| 0.182 | 0.226 | 0.324 | 0.307 | 0.216 | 0.140 | Libya | -| 0.181 | 0.229 | 0.319 | 0.308 | 0.221 | 0.136 | Lesotho | -| 0.173 | 0.216 | 0.320 | 0.294 | 0.201 | 0.130 | Mongolia | -| 0.170 | 0.225 | 0.317 | 0.287 | 0.205 | 0.128 | Djibouti | -| 0.170 | 0.238 | 0.325 | 0.271 | 0.197 | 0.126 | Samoa | -| 0.168 | 0.221 | 0.314 | 0.288 | 0.199 | 0.126 | Cambodia | -| 0.164 | 0.210 | 0.292 | 0.274 | 0.206 | 0.123 | Pakistan | -| 0.158 | 0.204 | 0.273 | 0.268 | 0.208 | 0.118 | Eritrea | -| 0.157 | 0.183 | 0.277 | 0.252 | 0.203 | 0.123 | Maldives | -| 0.157 | 0.194 | 0.268 | 0.281 | 0.212 | 0.120 | Mayotte | -| 0.156 | 0.199 | 0.279 | 0.260 | 0.199 | 0.118 | Jordan | -| 0.155 | 0.203 | 0.289 | 0.263 | 0.193 | 0.115 | Botswana | -| 0.154 | 0.199 | 0.287 | 0.257 | 0.191 | 0.115 | Lao People's Democratic Republic | -| 0.152 | 0.209 | 0.279 | 0.253 | 0.197 | 0.113 | Timor-Leste | -| 0.146 | 0.180 | 0.282 | 0.248 | 0.177 | 0.112 | Saudi Arabia | -| 0.145 | 0.187 | 0.254 | 0.239 | 0.199 | 0.109 | Eswatini | -| 0.139 | 0.173 | 0.248 | 0.234 | 0.188 | 0.104 | Namibia | -| 0.135 | 0.176 | 0.302 | 0.222 | 0.145 | 0.103 | Kuwait | -| 0.134 | 0.173 | 0.244 | 0.224 | 0.183 | 0.100 | Sudan | -| 0.133 | 0.173 | 0.245 | 0.221 | 0.182 | 0.101 | Gabon | -| 0.130 | 0.167 | 0.231 | 0.216 | 0.183 | 0.096 | Ethiopia | -| 0.130 | 0.174 | 0.242 | 0.224 | 0.179 | 0.098 | Solomon Islands | -| 0.128 | 0.158 | 0.245 | 0.207 | 0.169 | 0.095 | Tajikistan | -| 0.127 | 0.165 | 0.236 | 0.212 | 0.176 | 0.094 | Africa | -| 0.125 | 0.157 | 0.229 | 0.212 | 0.176 | 0.095 | Iraq | -| 0.125 | 0.150 | 0.253 | 0.199 | 0.156 | 0.093 | Bahrain | -| 0.124 | 0.163 | 0.225 | 0.204 | 0.176 | 0.092 | South Sudan | -| 0.123 | 0.168 | 0.244 | 0.196 | 0.163 | 0.091 | Vanuatu | -| 0.122 | 0.165 | 0.247 | 0.204 | 0.160 | 0.090 | Papua New Guinea | -| 0.121 | 0.157 | 0.226 | 0.203 | 0.171 | 0.091 | Liberia | -| 0.121 | 0.157 | 0.222 | 0.203 | 0.173 | 0.090 | Benin | -| 0.120 | 0.155 | 0.224 | 0.199 | 0.170 | 0.089 | Mauritania | -| 0.120 | 0.157 | 0.222 | 0.196 | 0.171 | 0.089 | State of Palestine | -| 0.119 | 0.150 | 0.219 | 0.173 | 0.170 | 0.089 | Sao Tome and Principe | -| 0.118 | 0.178 | 0.278 | 0.228 | 0.136 | 0.087 | Micronesia (Fed. States of) | -| 0.118 | 0.138 | 0.222 | 0.195 | 0.165 | 0.090 | Oman | -| 0.118 | 0.160 | 0.260 | 0.195 | 0.143 | 0.087 | Western Sahara | -| 0.116 | 0.157 | 0.230 | 0.190 | 0.159 | 0.085 | Ghana | -| 0.116 | 0.146 | 0.216 | 0.193 | 0.166 | 0.086 | Madagascar | -| 0.113 | 0.149 | 0.220 | 0.193 | 0.162 | 0.085 | Comoros | -| 0.112 | 0.142 | 0.205 | 0.188 | 0.169 | 0.085 | Zimbabwe | -| 0.112 | 0.146 | 0.216 | 0.193 | 0.161 | 0.083 | Rwanda | -| 0.111 | 0.146 | 0.208 | 0.184 | 0.165 | 0.083 | Senegal | -| 0.110 | 0.144 | 0.203 | 0.182 | 0.166 | 0.081 | Democratic Republic of the Congo | -| 0.107 | 0.139 | 0.202 | 0.175 | 0.160 | 0.078 | Yemen | -| 0.106 | 0.141 | 0.203 | 0.174 | 0.159 | 0.079 | Sierra Leone | -| 0.103 | 0.165 | 0.239 | 0.197 | 0.135 | 0.076 | Kiribati | -| 0.103 | 0.136 | 0.192 | 0.168 | 0.160 | 0.076 | Mozambique | -| 0.102 | 0.135 | 0.192 | 0.168 | 0.158 | 0.075 | Somalia | -| 0.102 | 0.139 | 0.202 | 0.168 | 0.152 | 0.075 | Togo | -| 0.101 | 0.137 | 0.201 | 0.166 | 0.152 | 0.075 | Congo | -| 0.101 | 0.133 | 0.191 | 0.166 | 0.156 | 0.074 | Central African Republic | -| 0.100 | 0.134 | 0.194 | 0.166 | 0.154 | 0.074 | Guinea | -| 0.100 | 0.135 | 0.197 | 0.165 | 0.152 | 0.074 | Côte d'Ivoire | -| 0.098 | 0.130 | 0.189 | 0.160 | 0.153 | 0.072 | Cameroon | -| 0.097 | 0.130 | 0.192 | 0.160 | 0.150 | 0.071 | Guinea-Bissau | -| 0.097 | 0.129 | 0.183 | 0.157 | 0.155 | 0.071 | Malawi | -| 0.096 | 0.129 | 0.186 | 0.157 | 0.152 | 0.071 | United Republic of Tanzania | -| 0.096 | 0.128 | 0.184 | 0.156 | 0.151 | 0.070 | Afghanistan | -| 0.094 | 0.122 | 0.186 | 0.153 | 0.148 | 0.070 | Kenya | -| 0.094 | 0.130 | 0.190 | 0.154 | 0.145 | 0.068 | Nigeria | -| 0.092 | 0.118 | 0.179 | 0.149 | 0.149 | 0.069 | Equatorial Guinea | -| 0.091 | 0.126 | 0.177 | 0.146 | 0.149 | 0.067 | Gambia | -| 0.091 | 0.116 | 0.170 | 0.150 | 0.152 | 0.067 | Chad | -| 0.090 | 0.112 | 0.203 | 0.141 | 0.126 | 0.067 | Qatar | -| 0.088 | 0.121 | 0.172 | 0.146 | 0.147 | 0.064 | Niger | -| 0.088 | 0.118 | 0.173 | 0.144 | 0.145 | 0.064 | Burkina Faso | -| 0.088 | 0.109 | 0.169 | 0.144 | 0.146 | 0.064 | Burundi | -| 0.087 | 0.117 | 0.169 | 0.145 | 0.147 | 0.064 | Mali | -| 0.085 | 0.111 | 0.164 | 0.139 | 0.145 | 0.063 | Angola | -| 0.083 | 0.104 | 0.190 | 0.130 | 0.124 | 0.063 | United Arab Emirates | -| 0.083 | 0.107 | 0.158 | 0.134 | 0.144 | 0.061 | Zambia | -| 0.074 | 0.099 | 0.147 | 0.121 | 0.137 | 0.054 | Uganda | -| ENE-COV | US_CDC | Verity | Levin | Gudbj | O'Drisc | Region | +| ENE-COVID | COVID: US CDC | COVID: Verity | COVID: Levin | Flu: US CDC | Region | +| ------------- | ------------- | ------------- | ------------- | ------------- | ------ | +| 1.274 | 1.311 | 1.605 | 2.247 | 0.125 | Japan | +| 1.065 | 1.092 | 1.382 | 1.847 | 0.106 | Italy | +| 1.041 | 1.043 | 1.339 | 1.806 | 0.102 | Greece | +| 0.993 | 1.012 | 1.305 | 1.702 | 0.100 | Germany | +| 0.984 | 1.045 | 1.320 | 1.726 | 0.104 | Portugal | +| 0.931 | 0.985 | 1.270 | 1.648 | 0.100 | Martinique | +| 0.919 | 0.933 | 1.221 | 1.658 | 0.095 | Lithuania | +| 0.916 | 0.942 | 1.207 | 1.648 | 0.093 | Spain | +| 0.914 | 0.941 | 1.201 | 1.606 | 0.095 | France | +| 0.899 | 1.008 | 1.248 | 1.556 | 0.102 | Finland | +| 0.881 | 0.919 | 1.192 | 1.624 | 0.095 | Latvia | +| 0.875 | 0.957 | 1.205 | 1.528 | 0.096 | Puerto Rico | +| 0.868 | 0.892 | 1.171 | 1.516 | 0.093 | Estonia | +| 0.865 | 0.932 | 1.209 | 1.487 | 0.098 | Croatia | +| 0.855 | 0.965 | 1.205 | 1.471 | 0.099 | Malta | +| 0.846 | 0.881 | 1.137 | 1.478 | 0.089 | Belgium | +| 0.843 | 0.905 | 1.181 | 1.489 | 0.095 | Slovenia | +| 0.840 | 0.943 | 1.154 | 1.471 | 0.093 | Sweden | +| 0.836 | 0.910 | 1.149 | 1.462 | 0.090 | Austria | +| 0.825 | 0.897 | 1.132 | 1.447 | 0.089 | Switzerland | +| 0.810 | 0.861 | 1.117 | 1.396 | 0.089 | Europe | +| 0.802 | 0.909 | 1.141 | 1.394 | 0.093 | Netherlands | +| 0.801 | 0.949 | 1.181 | 1.377 | 0.098 | Bulgaria | +| 0.798 | 0.864 | 1.113 | 1.399 | 0.090 | Guadeloupe | +| 0.797 | 0.935 | 1.136 | 1.370 | 0.093 | Denmark | +| 0.794 | 0.868 | 1.089 | 1.384 | 0.087 | United Kingdom | +| 0.791 | 0.811 | 1.102 | 1.367 | 0.087 | China, Hong Kong SAR | +| 0.759 | 0.830 | 1.090 | 1.285 | 0.089 | Romania | +| 0.753 | 0.854 | 1.101 | 1.323 | 0.093 | Hungary | +| 0.745 | 0.800 | 1.064 | 1.285 | 0.087 | Poland | +| 0.739 | 0.828 | 1.059 | 1.315 | 0.084 | Channel Islands | +| 0.738 | 0.878 | 1.092 | 1.302 | 0.092 | Czechia | +| 0.734 | 0.810 | 1.047 | 1.288 | 0.085 | Canada | +| 0.719 | 0.756 | 0.998 | 1.259 | 0.079 | Barbados | +| 0.713 | 0.808 | 1.038 | 1.210 | 0.084 | Curaçao | +| 0.709 | 0.802 | 1.007 | 1.239 | 0.082 | Norway | +| 0.680 | 0.800 | 1.029 | 1.160 | 0.088 | Serbia | +| 0.676 | 0.694 | 0.904 | 1.193 | 0.071 | Uruguay | +| 0.675 | 0.745 | 0.967 | 1.181 | 0.079 | Northern America | +| 0.671 | 0.736 | 0.944 | 1.174 | 0.076 | Australia | +| 0.671 | 0.733 | 0.983 | 1.103 | 0.080 | Ukraine | +| 0.669 | 0.738 | 0.958 | 1.169 | 0.078 | United States of America | +| 0.659 | 0.757 | 1.011 | 1.088 | 0.085 | Bosnia and Herzegovina | +| 0.654 | 0.742 | 0.945 | 1.137 | 0.077 | New Zealand | +| 0.644 | 0.735 | 0.941 | 1.131 | 0.077 | Cuba | +| 0.641 | 0.877 | 1.059 | 1.152 | 0.094 | United States Virgin Islands | +| 0.633 | 0.725 | 0.963 | 1.090 | 0.077 | Republic of Korea | +| 0.628 | 0.686 | 0.938 | 1.100 | 0.077 | China, Taiwan Province of China | +| 0.624 | 0.663 | 0.916 | 1.030 | 0.074 | Russian Federation | +| 0.624 | 0.657 | 0.921 | 1.082 | 0.075 | Belarus | +| 0.615 | 0.668 | 0.881 | 1.078 | 0.070 | Luxembourg | +| 0.607 | 0.670 | 0.896 | 1.002 | 0.073 | Georgia | +| 0.605 | 0.683 | 0.888 | 1.061 | 0.073 | Iceland | +| 0.604 | 0.709 | 0.935 | 1.059 | 0.079 | Slovakia | +| 0.582 | 0.667 | 0.891 | 0.989 | 0.075 | Montenegro | +| 0.563 | 0.653 | 0.838 | 0.972 | 0.070 | Ireland | +| 0.561 | 0.649 | 0.839 | 0.957 | 0.069 | Cyprus | +| 0.548 | 0.659 | 0.857 | 0.941 | 0.071 | Albania | +| 0.531 | 0.652 | 0.874 | 0.920 | 0.072 | Aruba | +| 0.518 | 0.580 | 0.754 | 0.902 | 0.062 | Oceania | +| 0.510 | 0.588 | 0.795 | 0.881 | 0.065 | Thailand | +| 0.500 | 0.569 | 0.763 | 0.880 | 0.063 | Réunion | +| 0.499 | 0.545 | 0.710 | 0.872 | 0.060 | Israel | +| 0.497 | 0.522 | 0.748 | 0.794 | 0.059 | Armenia | +| 0.497 | 0.616 | 0.816 | 0.851 | 0.070 | North Macedonia | +| 0.493 | 0.550 | 0.736 | 0.861 | 0.061 | Chile | +| 0.479 | 0.550 | 0.796 | 0.829 | 0.067 | Singapore | +| 0.454 | 0.515 | 0.671 | 0.790 | 0.056 | Argentina | +| 0.449 | 0.514 | 0.738 | 0.770 | 0.062 | China, Macao SAR | +| 0.447 | 0.544 | 0.732 | 0.772 | 0.063 | Mauritius | +| 0.435 | 0.501 | 0.721 | 0.766 | 0.062 | Republic of Moldova | +| 0.415 | 0.511 | 0.681 | 0.717 | 0.058 | Trinidad and Tobago | +| 0.413 | 0.475 | 0.638 | 0.712 | 0.053 | Costa Rica | +| 0.413 | 0.468 | 0.626 | 0.704 | 0.051 | Saint Lucia | +| 0.409 | 0.507 | 0.695 | 0.707 | 0.061 | China | +| 0.394 | 0.497 | 0.648 | 0.712 | 0.052 | Antigua and Barbuda | +| 0.387 | 0.495 | 0.651 | 0.668 | 0.056 | Sri Lanka | +| 0.377 | 0.487 | 0.635 | 0.622 | 0.050 | Dem. People's Republic of Korea | +| 0.376 | 0.437 | 0.594 | 0.645 | 0.050 | Brazil | +| 0.365 | 0.464 | 0.611 | 0.618 | 0.052 | Guam | +| 0.364 | 0.425 | 0.569 | 0.627 | 0.047 | Jamaica | +| 0.361 | 0.454 | 0.605 | 0.663 | 0.051 | Saint Vincent and the Grenadines | +| 0.359 | 0.399 | 0.540 | 0.623 | 0.045 | Panama | +| 0.358 | 0.418 | 0.566 | 0.615 | 0.048 | WORLD | +| 0.356 | 0.410 | 0.555 | 0.614 | 0.047 | Latin America and the Caribbean | +| 0.355 | 0.412 | 0.560 | 0.613 | 0.047 | Colombia | +| 0.354 | 0.438 | 0.595 | 0.642 | 0.050 | Grenada | +| 0.347 | 0.399 | 0.528 | 0.595 | 0.045 | El Salvador | +| 0.343 | 0.363 | 0.528 | 0.602 | 0.043 | Viet Nam | +| 0.342 | 0.408 | 0.552 | 0.588 | 0.047 | Turkey | +| 0.339 | 0.397 | 0.537 | 0.583 | 0.045 | Peru | +| 0.336 | 0.394 | 0.553 | 0.579 | 0.047 | Tunisia | +| 0.327 | 0.432 | 0.573 | 0.547 | 0.049 | New Caledonia | +| 0.325 | 0.394 | 0.541 | 0.559 | 0.047 | Asia | +| 0.310 | 0.350 | 0.463 | 0.535 | 0.039 | Bolivia (Plurinational State of) | +| 0.309 | 0.348 | 0.480 | 0.532 | 0.040 | Dominican Republic | +| 0.307 | 0.348 | 0.503 | 0.505 | 0.042 | Kazakhstan | +| 0.306 | 0.352 | 0.485 | 0.532 | 0.041 | Mexico | +| 0.305 | 0.365 | 0.502 | 0.526 | 0.042 | Venezuela (Bolivarian Republic of) | +| 0.303 | 0.347 | 0.474 | 0.525 | 0.040 | Ecuador | +| 0.295 | 0.346 | 0.482 | 0.501 | 0.041 | Lebanon | +| 0.293 | 0.400 | 0.542 | 0.477 | 0.045 | Seychelles | +| 0.287 | 0.384 | 0.527 | 0.513 | 0.046 | French Polynesia | +| 0.282 | 0.326 | 0.456 | 0.456 | 0.038 | Guyana | +| 0.280 | 0.335 | 0.463 | 0.469 | 0.039 | Suriname | +| 0.273 | 0.313 | 0.474 | 0.452 | 0.039 | Azerbaijan | +| 0.272 | 0.337 | 0.474 | 0.462 | 0.041 | Morocco | +| 0.269 | 0.358 | 0.495 | 0.460 | 0.042 | Bahamas | +| 0.263 | 0.325 | 0.453 | 0.442 | 0.039 | Malaysia | +| 0.260 | 0.305 | 0.426 | 0.446 | 0.037 | Algeria | +| 0.257 | 0.307 | 0.418 | 0.436 | 0.037 | Paraguay | +| 0.251 | 0.297 | 0.403 | 0.423 | 0.035 | Bhutan | +| 0.246 | 0.301 | 0.431 | 0.418 | 0.037 | Iran (Islamic Republic of) | +| 0.234 | 0.293 | 0.414 | 0.398 | 0.037 | India | +| 0.229 | 0.293 | 0.416 | 0.387 | 0.036 | Indonesia | +| 0.228 | 0.259 | 0.373 | 0.393 | 0.032 | Nicaragua | +| 0.221 | 0.269 | 0.368 | 0.374 | 0.031 | Bangladesh | +| 0.221 | 0.232 | 0.349 | 0.374 | 0.029 | Cabo Verde | +| 0.217 | 0.284 | 0.375 | 0.310 | 0.032 | Tonga | +| 0.215 | 0.277 | 0.401 | 0.366 | 0.036 | Myanmar | +| 0.208 | 0.235 | 0.334 | 0.351 | 0.029 | Belize | +| 0.206 | 0.235 | 0.331 | 0.353 | 0.029 | Honduras | +| 0.204 | 0.233 | 0.323 | 0.349 | 0.029 | Guatemala | +| 0.204 | 0.255 | 0.360 | 0.342 | 0.032 | Philippines | +| 0.202 | 0.267 | 0.360 | 0.344 | 0.033 | Nepal | +| 0.197 | 0.249 | 0.381 | 0.331 | 0.032 | Brunei Darussalam | +| 0.194 | 0.237 | 0.331 | 0.330 | 0.030 | Haiti | +| 0.193 | 0.251 | 0.355 | 0.325 | 0.032 | South Africa | +| 0.193 | 0.222 | 0.339 | 0.316 | 0.029 | Turkmenistan | +| 0.192 | 0.247 | 0.343 | 0.321 | 0.031 | Egypt | +| 0.192 | 0.262 | 0.376 | 0.318 | 0.033 | Fiji | +| 0.188 | 0.220 | 0.335 | 0.310 | 0.029 | Kyrgyzstan | +| 0.188 | 0.245 | 0.353 | 0.344 | 0.031 | French Guiana | +| 0.187 | 0.219 | 0.340 | 0.317 | 0.029 | Uzbekistan | +| 0.185 | 0.224 | 0.323 | 0.317 | 0.029 | Syrian Arab Republic | +| 0.182 | 0.226 | 0.324 | 0.307 | 0.028 | Libya | +| 0.181 | 0.229 | 0.319 | 0.308 | 0.029 | Lesotho | +| 0.173 | 0.216 | 0.320 | 0.294 | 0.027 | Mongolia | +| 0.170 | 0.225 | 0.317 | 0.287 | 0.028 | Djibouti | +| 0.170 | 0.238 | 0.325 | 0.271 | 0.029 | Samoa | +| 0.168 | 0.221 | 0.314 | 0.288 | 0.029 | Cambodia | +| 0.164 | 0.210 | 0.292 | 0.274 | 0.026 | Pakistan | +| 0.158 | 0.204 | 0.273 | 0.268 | 0.026 | Eritrea | +| 0.157 | 0.183 | 0.277 | 0.252 | 0.024 | Maldives | +| 0.157 | 0.194 | 0.268 | 0.281 | 0.024 | Mayotte | +| 0.156 | 0.199 | 0.279 | 0.260 | 0.025 | Jordan | +| 0.155 | 0.203 | 0.289 | 0.263 | 0.027 | Botswana | +| 0.154 | 0.199 | 0.287 | 0.257 | 0.026 | Lao People's Democratic Republic | +| 0.152 | 0.209 | 0.279 | 0.253 | 0.025 | Timor-Leste | +| 0.146 | 0.180 | 0.282 | 0.248 | 0.024 | Saudi Arabia | +| 0.145 | 0.187 | 0.254 | 0.239 | 0.024 | Eswatini | +| 0.139 | 0.173 | 0.248 | 0.234 | 0.023 | Namibia | +| 0.135 | 0.176 | 0.302 | 0.222 | 0.024 | Kuwait | +| 0.134 | 0.173 | 0.244 | 0.224 | 0.023 | Sudan | +| 0.133 | 0.173 | 0.245 | 0.221 | 0.023 | Gabon | +| 0.130 | 0.167 | 0.231 | 0.216 | 0.022 | Ethiopia | +| 0.130 | 0.174 | 0.242 | 0.224 | 0.023 | Solomon Islands | +| 0.128 | 0.158 | 0.245 | 0.207 | 0.022 | Tajikistan | +| 0.127 | 0.165 | 0.236 | 0.212 | 0.022 | Africa | +| 0.125 | 0.157 | 0.229 | 0.212 | 0.022 | Iraq | +| 0.125 | 0.150 | 0.253 | 0.199 | 0.021 | Bahrain | +| 0.124 | 0.163 | 0.225 | 0.204 | 0.021 | South Sudan | +| 0.123 | 0.168 | 0.244 | 0.196 | 0.023 | Vanuatu | +| 0.122 | 0.165 | 0.247 | 0.204 | 0.023 | Papua New Guinea | +| 0.121 | 0.157 | 0.226 | 0.203 | 0.021 | Liberia | +| 0.121 | 0.157 | 0.222 | 0.203 | 0.021 | Benin | +| 0.120 | 0.155 | 0.224 | 0.199 | 0.021 | Mauritania | +| 0.120 | 0.157 | 0.222 | 0.196 | 0.021 | State of Palestine | +| 0.119 | 0.150 | 0.219 | 0.173 | 0.020 | Sao Tome and Principe | +| 0.118 | 0.178 | 0.278 | 0.228 | 0.027 | Micronesia (Fed. States of) | +| 0.118 | 0.138 | 0.222 | 0.195 | 0.020 | Oman | +| 0.118 | 0.160 | 0.260 | 0.195 | 0.024 | Western Sahara | +| 0.116 | 0.157 | 0.230 | 0.190 | 0.021 | Ghana | +| 0.116 | 0.146 | 0.216 | 0.193 | 0.020 | Madagascar | +| 0.113 | 0.149 | 0.220 | 0.193 | 0.021 | Comoros | +| 0.112 | 0.142 | 0.205 | 0.188 | 0.020 | Zimbabwe | +| 0.112 | 0.146 | 0.216 | 0.193 | 0.021 | Rwanda | +| 0.111 | 0.146 | 0.208 | 0.184 | 0.020 | Senegal | +| 0.110 | 0.144 | 0.203 | 0.182 | 0.019 | Democratic Republic of the Congo | +| 0.107 | 0.139 | 0.202 | 0.175 | 0.020 | Yemen | +| 0.106 | 0.141 | 0.203 | 0.174 | 0.019 | Sierra Leone | +| 0.103 | 0.165 | 0.239 | 0.197 | 0.023 | Kiribati | +| 0.103 | 0.136 | 0.192 | 0.168 | 0.019 | Mozambique | +| 0.102 | 0.135 | 0.192 | 0.168 | 0.019 | Somalia | +| 0.102 | 0.139 | 0.202 | 0.168 | 0.019 | Togo | +| 0.101 | 0.137 | 0.201 | 0.166 | 0.019 | Congo | +| 0.101 | 0.133 | 0.191 | 0.166 | 0.019 | Central African Republic | +| 0.100 | 0.134 | 0.194 | 0.166 | 0.019 | Guinea | +| 0.100 | 0.135 | 0.197 | 0.165 | 0.019 | Côte d'Ivoire | +| 0.098 | 0.130 | 0.189 | 0.160 | 0.018 | Cameroon | +| 0.097 | 0.130 | 0.192 | 0.160 | 0.019 | Guinea-Bissau | +| 0.097 | 0.129 | 0.183 | 0.157 | 0.018 | Malawi | +| 0.096 | 0.129 | 0.186 | 0.157 | 0.018 | United Republic of Tanzania | +| 0.096 | 0.128 | 0.184 | 0.156 | 0.018 | Afghanistan | +| 0.094 | 0.122 | 0.186 | 0.153 | 0.018 | Kenya | +| 0.094 | 0.130 | 0.190 | 0.154 | 0.019 | Nigeria | +| 0.092 | 0.118 | 0.179 | 0.149 | 0.018 | Equatorial Guinea | +| 0.091 | 0.126 | 0.177 | 0.146 | 0.017 | Gambia | +| 0.091 | 0.116 | 0.170 | 0.150 | 0.017 | Chad | +| 0.090 | 0.112 | 0.203 | 0.141 | 0.018 | Qatar | +| 0.088 | 0.121 | 0.172 | 0.146 | 0.017 | Niger | +| 0.088 | 0.118 | 0.173 | 0.144 | 0.017 | Burkina Faso | +| 0.088 | 0.109 | 0.169 | 0.144 | 0.017 | Burundi | +| 0.087 | 0.117 | 0.169 | 0.145 | 0.017 | Mali | +| 0.085 | 0.111 | 0.164 | 0.139 | 0.016 | Angola | +| 0.083 | 0.104 | 0.190 | 0.130 | 0.016 | United Arab Emirates | +| 0.083 | 0.107 | 0.158 | 0.134 | 0.016 | Zambia | +| 0.074 | 0.099 | 0.147 | 0.121 | 0.015 | Uganda | Note that in addition to countries, there are rows for each continent and for the world. ## Findings -The overall IFR estimates, with the exception of Levin et al. and O’Driscoll et al., are relatively -consistent with each other, usually within 30-40%. Levin et al. is up to +The overall IFR estimates of COVID-19, with the exception of Levin et al., are relatively +consistent with each other, usually within 30-40%. Levin et al. is often up to 2-fold higher than the others, depending on the country. The country with the oldest population is expected to have the highest overall -IFR: Japan at 1.3-1.6% (excluding Levin et al. and O’Driscoll et al.) +IFR: Japan at 1.274-1.605% (excluding Levin et al.) The country with the youngest population is expected to have the lowest overall -IFR: Uganda at 0.074-0.147% +IFR: Uganda at 0.074-0.147%. + +The **IFR of COVID-19 is one order of magnitude (10×) higher than the seasonal flu** +for all regions. For example, in the US the average flu IFR is 0.078%, compared to +0.669-1.169% for COVID-19. The **overall IFR varies dramatically by more than 10-fold** between countries with a young population and those with an old population. @@ -326,7 +332,7 @@ In fact, **the young age of the population in Africa is a major factor explainin relatively small number of deaths** on this continent. We find (ENE-COVID) IFR=0.127% for Africa, and IFR=0.810% in Europe, a 6-fold difference. -The overall IFR is, for each world region and the world: +The overall IFR of COVID-19 is, for each world region and the world: * 0.810% Europe * 0.675% Northern America diff --git a/apply_ifr.py b/apply_ifr.py index f43af34..8b321fd 100755 --- a/apply_ifr.py +++ b/apply_ifr.py @@ -22,12 +22,15 @@ age_groups = [(0,4), (5,9), (10,14), (15,19), (20,24), (25,29), (30,34), (35,39) # age group 20-24 in France: pyramid['France'][(20,24)] pyramid = {} +# For a description of cdc_sympt, see the same variable name defined in covid_vs_flu.py +cdc_sympt = .575 + # Various age-stratified IFR estimates ifrs = [ # Calculated from Spanish ENE-COVID study # (see calc_ifr.py) - ('ENE-COV', { + ('ENE-COVID', { (0,9): 0.003, (10,19): 0.004, (20,29): 0.015, @@ -43,7 +46,7 @@ ifrs = [ # US CDC estimate as of 10 Sep 2020 # https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html # (table 1) - ('US_CDC', { + ('COVID: US CDC', { (0,19): 0.003, (20,49): 0.02, (50,69): 0.5, @@ -53,7 +56,7 @@ ifrs = [ # Verity et al. # https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30243-7/fulltext # (table 1) - ('Verity', { + ('COVID: Verity', { (0,9): 0.00161, (10,19): 0.00695, (20,29): 0.0309, @@ -68,7 +71,7 @@ ifrs = [ # Levin et al. # https://www.medrxiv.org/content/10.1101/2020.07.23.20160895v5 # (table 3) - ('Levin', { + ('COVID: Levin', { (0,34): 0.004, (35,44): 0.06, (45,54): 0.2, @@ -78,38 +81,15 @@ ifrs = [ (85,maxage): 22.3, }), - # Gudbjartsson et al., Humoral Immune Response to SARS-CoV-2 in Iceland - # https://www.nejm.org/doi/full/10.1056/NEJMoa2026116 - # Supplementary Appendix 1 - # https://www.nejm.org/doi/suppl/10.1056/NEJMoa2026116/suppl_file/nejmoa2026116_appendix_1.pdf - # (table S7) - ('Gudbj', { - (0,70): 0.1, - (71,80): 2.4, - (81,maxage): 11.2, - }), - - # O’Driscoll et al., Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries - # https://www.medrxiv.org/content/10.1101/2020.08.24.20180851v1 - # (table S4) - ("O'Drisc", { - (0,4): 0.002, - (5,9): 0.000, - (10,14): 0.000, - (15,19): 0.002, - (20,24): 0.004, - (25,29): 0.009, - (30,34): 0.017, - (35,39): 0.029, - (40,44): 0.053, - (45,49): 0.086, - (50,54): 0.154, - (55,59): 0.241, - (60,64): 0.359, - (65,69): 0.642, - (70,74): 1.076, - (75,79): 2.276, - (80,maxage): 7.274, + # IFR for seasonal influenza + # US CDC 2019-2020 influenza burden + # https://www.cdc.gov/flu/about/burden/2019-2020.html + ('Flu: US CDC', { + (0,4): 254/4_291_677 * 100 * cdc_sympt, + (5,17): 180/8_214_257 * 100 * cdc_sympt, + (18,49): 2_669/15_325_708 * 100 * cdc_sympt, + (50,64): 5_133/8_416_702 * 100 * cdc_sympt, + (65,maxage): 13_673/1_946_161 * 100 * cdc_sympt, }), ] @@ -171,7 +151,7 @@ def calc_overall_ifrs(): def show_overall_ifrs(oifrs): def header(): for i in ifrs: - print(f'| {i[0]:>7} ', end='') + print(f'| {i[0]:>13} ', end='') print('| Region |') # Each entry in the oifrs array is a tuple: # (, , , ...) @@ -181,7 +161,7 @@ def show_overall_ifrs(oifrs): header() for region in oifrs: for i in region[1:]: - print(f'| {i:7.3f} ', end='') + print(f'| {i:13.3f} ', end='') print(f'| {region[0]} |') header()