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disease_covid19.yml
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disease_covid19.yml
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name: Covid-19
infection_rate: 0.07
# Summary of evidence:
# 1: 11.2% secondary attack rate in house holds: 1.112^(1/8.5)=1.012568 -> 1.2568% infection chance per day.
# We assume that 20% of the time is spent within 2 meters in the household -> 1.2568% / 20% = 6.284% or 0.06284
# Qifang Bhi et al., Lancet, 2020. DOI: https://doi.org/10.1016/S1473-3099(20)30287-5
# 2: Source paper: https://www.sciencedirect.com/science/article/pii/S2468042720300063
# This paper reports a peak value of R ~ 8 among the crew of the Diamond Princess (who are probably subject to similar confinement levels).
# Deriving from that: 8**(1 / 8.5)= 1.277 -> infection rate of 0.277 in a heavily confined cruiseship setting with little precautions and awareness.
# 13.8% secondary attack rate in house holds: 1.138^(1/8.5)= 1.015325 -> 1.5325% infections chance per day.
# We assume that 20% of the time is spent within 2 meters in the household -> 1.5325% / 20% = 7.6625% or 0.076625
# Wei Li et al., clinical Infectious Diseases 2020. Source paper: https://doi.org/10.1093/cid/ciaa450
# Verity et al., Lancet, 2020. Median age, (probability)
mortality:
- [4.5,0.000026]
- [14.5,0.000148]
- [24.5,0.000600]
- [34.5,0.00146]
- [44.5,0.00295]
- [54.5,0.0125]
- [64.5,0.0399]
- [74.5,0.0861]
- [84.5,0.134]
hospitalised:
- [4.5,0.0000]
- [14.5,0.000408]
- [24.5,0.0104]
- [34.5,0.0343]
- [44.5,0.0425]
- [54.5,0.0816]
- [64.5,0.118]
- [74.5,0.166]
- [84.5,0.184]
mortality_period: 12.0 # from day of hospitalisation (ICU)
# https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-06371-6/tables/2 (subtracted admission to ICU (2.0) from admission to outcome (~14.0))
recovery_period: 12.0 # from day of hospitalisation (ICU)
# https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-06371-6/tables/2 (subtracted admission to ICU (2.0) from admission to outcome (~14.0))
mild_recovery_period: 9.0 # (7-10 days) https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
incubation_period: 4 # https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
# 5 days of incubation, infectiousness starts 36 hours before the end of incubation.
# Clinical course and risk factors for mortality of adult inpatients with Covid-19 in Wuhan, China: a retrospective cohort study
# Fei Zhou et al. The Lancet vol. 395.
period_to_hospitalisation: 14.0 #this is period to ICU.
immunity_duration: 273.0
immunity_fraction: 0.0
mutations:
alpha:
infection_rate: 0.112
delta:
infection_rate: 0.165