In mrc-ide/squire: SEIR transmission model of COVID-19

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The parameter table below summarises the current best estimates incorporated in squire as of v0.5. These will be updated when new information becomes available.

| Parameter | Value | Reference | | --- | --- | --- | | Basic reproductive number, R0 | 3.0 | Estimate from Europe, Flaxman et al | | Mean Incubation Period | 4.6 days | Estimated to be 5.1 days (Linton et al.; Li et al. The last 0.5 days are included in the I_MILD and I_CASE states to capture pre-symptomatic infectivity | | Generation Time | 6.75 days | Bi et al. | | Mean Duration in I_MILD | 2.1 days | Incorporates 0.5 days of infectiousness prior to symptoms; with parameters below ~95% of all infections are mild. In combination with mean duration in I_CASE this gives a mean generation time as above | | Mean Duration in I_CASE | 4.5 days | Mean onset-to-admission of 4 days. Values in the literature range from 1.2 to 12 days. Includes 0.5 days of infectiousness prior to symptom onset | | Mean Duration of Hospitalisation for non-critical Cases (I_HOSP) if survive | 9 days | Median value from five studies (Sreevalsan-Nair et al., Haw et al., Hawryluk et al., Oliveira et al., South African COVID-19 Modelling Consortium). Range from 8-15 days. | | Mean Duration of Hospitalisation for non-critical Cases (I_HOSP) if die | 9 days | As above | | Mean duration of Critical Care (I_ICU) if survive | 14.8 days | Mean duration in ICU of 13.3 days Pritchard et al.. Ratio of duration in critical care if die: duration in critical care if survive of 0.75 and 60.1% probability of survival in ICU (ICNARC report, from UK data, 16 October 2020) | | Mean duration of Critical Care (I_ICU) if die | 11.1 days | Mean duration in ICU of 13.3 days Pritchard et al.. Ratio of duration in critical care if die: duration in critical care if survive of 0.75 and 60.1% probability of survival in ICU (ICNARC report, from UK data, 16 October 2020) | | Mean duration of Stepdown post ICU (I_Rec) | 3 days | Working assumption based on unpublished UK data | | Mean duration of hospitalisation if require ICU but do not receive it and die | 1 day | Working assumption | | Mean duration of hospitalisation if require ICU but do not receive it and survive | 7.4 days | Working assumption (Half duration of ICU and survive) | | Mean duration of hospitalisation if require Oxygen but do not receive it and die | 4.5 days | Working assumption (Half duration of Oxygen and die) | | Mean duration of hospitalisation if require Oxygen but do not receive it and survive | 4.5 days | Working assumption (Half duration of ICU and survive) | | Probability of death if require critical care but do not receive it | 95% | Working assumption based on expert clinical opinion | | Probability of death if require hospitalisation but do not receive it | 60% | Working assumption based on expert clinical opinion |

Age-Specific Parameters

| Age-Group | Proportion of Infections Hospitalised | Proportion of hospitalised cases requiring critical care | Proportion of hospital deaths occurring in ICU | Proportion of non-critical care cases dying | Proportion of critical care cases dying | | --- | --- | --- | --- | --- | --- | | 0 to 4 | 0.001 | 0.181 | 0.8 | 0.013 | 0.227 | | 5 to 9 | 0.001 | 0.181 | 0.8 | 0.014 | 0.252 | | 10 to 14 | 0.002 | 0.181 | 0.8 | 0.016 | 0.281 | | 15 to 19 | 0.002 | 0.137 | 0.8 | 0.016 | 0.413 | | 20 to 24 | 0.003 | 0.122 | 0.8 | 0.018 | 0.518 | | 25 to 29 | 0.005 | 0.123 | 0.8 | 0.020 | 0.573 | | 30 to 34 | 0.007 | 0.136 | 0.8 | 0.023 | 0.576 | | 35 to 39 | 0.009 | 0.161 | 0.8 | 0.026 | 0.543 | | 40 to 44 | 0.013 | 0.197 | 0.8 | 0.030 | 0.494 | | 45 to 49 | 0.018 | 0.242 | 0.8 | 0.036 | 0.447 | | 50 to 54 | 0.025 | 0.289 | 0.8 | 0.042 | 0.417 | | 55 to 59 | 0.036 | 0.327 | 0.8 | 0.050 | 0.411 | | 60 to 64 | 0.050 | 0.337 | 0.8 | 0.056 | 0.443 | | 65 to 69 | 0.071 | 0.309 | 0.8 | 0.060 | 0.539 | | 70 to 74 | 0.100 | 0.244 | 0.8 | 0.123 | 0.570 | | 75 to 79 | 0.140 | 0.160 | 0.8 | 0.184 | 0.643 | | 80+ | 0.233 | 0.057 | 0.8 | 0.341 | 0.993 | | Source | Salje et al. | Salje et al. | Assumed | Calculated from IFR in Report 34 | Calculated from IFR in Report 34 |