Assumptions for R and Coronavirus User Journey
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Day
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% of casesSeverity0123456789101112131415161718192021222324252627
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30%Asymptomatic / Very MildProgressionNo symptoms
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# Daily Contacts
20202020202020202020202020202020202020202020202020202020
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Transmission rate
0.50%0.50%0.50%0.50%0.50%1.00%1.00%0.50%0.50%0.50%0.50%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%
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Relative contagiousness
1111122111100000000000000000
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56%Mild/ModerateProgressionNo symptomsSymptoms (mild/moderate)Recovery
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# Daily Contacts
20202020202010101010102020202020202020202020202020202020
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Transmission rate
0.50%1.00%1.50%1.50%2.00%2.50%3.00%2.50%2.00%1.50%1.00%0.50%0.50%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%
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Relative contagiousness
1233456543211000000000000000
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10%SevereProgressionNo symptomsSymptoms (severe) pre-hospitalizationHospitalizationRecovery
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# Daily Contacts
2020202020205555533333333202020202020202020
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Transmission rate
0.50%1.00%1.50%2.00%2.50%3.00%3.00%3.00%3.00%3.00%3.00%2.50%2.50%2.00%1.50%1.00%0.50%0.50%0.50%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%0.00%
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Relative contagiousness
1234566666655432111000000000
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4%CriticalProgressionNo symptomsSymptoms (severe) pre-hospitalizationHospitalizationVentilation / ICU
Death / Recovery
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# Daily Contacts
2020202020205555533333322222222200
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Transmission rate
0.50%1.00%2.00%2.50%3.00%3.50%3.50%3.50%3.50%3.50%3.50%3.00%3.00%2.50%2.00%1.50%1.50%1.50%1.50%1.00%0.50%0.50%0.50%0.50%0.50%0.50%0.00%0.00%
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Relative contagiousness
1245677777766543333211111100
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0.10.170.2440.2580.3280.4280.250.1920.1640.1360.1080.0670.0670.0090.0070.0050.0030.0030.0030.00100000000
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Cross-checking validity of above estimates
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CHECK For Overall R0 - this should be ~2.52.55
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CHECK For Doubling Rate (# new cases every ~6 days) - this should be a bit under ~21.78
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Assumptions
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Transmission Rate0.50%<----This has been adjusted to achieve an R0 of ~2.5
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Daily Contacts w/o symptoms20<----Based on a model created by researchers estimating daily contacts in Portland Oregon. Daily contact rate of ~20 is what was most common for age groups, but is likely high for children (under 18 yrs) or seniors (over 60 yrs). It also will vary based on population density of the region and other factors, but this is probably a reasonable initial estimate
https://www.researchgate.net/publication/228649013_Mixing_patterns_between_age_groups_in_social_networks
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Daily Contacts w/ Mild Symptoms10<----Assuming people cut contact by ~50% when they start feeling symptoms
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Daily Contacts w/ Mod/Severe Symptoms5<----Assuming people cut contact by ~75% when they feel more serious symptoms
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Daily Contacts in Hospital3<----Assuming limited contact once in a hospital, and even less in the ICU. Patiens come into contact with more than 2 or 3 people per day,
but I am assuming the baseline precautions put in place at a hospital reduce the likelihood of transmission.
So really, the daily contacts number should be higher but the transmission rate should be much lower. Could definitely use better research to inform this.
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Daily Contacts in ICU2<----
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SourcesConfidence LevelSource URL
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Proportion of Mild/Moderate vs. Severe vs. Critical cases
Med
https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf
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Proportion of asymptomatic cases
Low-Med
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.10.2000180
https://www.medrxiv.org/content/10.1101/2020.02.03.20020248v2
https://www.ecdc.europa.eu/sites/default/files/documents/RRA-sixth-update-Outbreak-of-novel-coronavirus-disease-2019-COVID-19.pdf
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Daily ContactsMed
https://www.researchgate.net/publication/228649013_Mixing_patterns_between_age_groups_in_social_networks
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Incubation period (days until onset of symptoms)
High
https://annals.org/aim/fullarticle/2762808/incubation-period-coronavirus-disease-2019-covid-19-from-publicly-reported
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Progression of illness - once hospitalized
Med-High
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30566-3/fulltext
https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf
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Contagiousness as illness progresses
Low
https://www.medrxiv.org/content/10.1101/2020.03.05.20030502v1.full.pdf
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30113-4/fulltext
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A note on the "Relative Contagiousness" assumptions:
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We looked at the various studies that swabbed and tested for virus levels at different periods of time (usually days after onset of symptoms) and turned what was a logrithmic scale for viral load in the test (e.g., x copies x 10^y) and turned it into a linear scale (1 unit per 10x). So if there were 5x10^8 copies detected on day 5 and 5x10^7 on day 6, we put in relative contagiousness of 8 and 7, respectively. A better modeling approach would be welcome, although our goal here is to be representative rather than perfect.

Then, to figure out what the relative contagiousness was before symptoms appeared, we estimated based on the trendlines and research suggested, which is that tranmission prior to having symptoms is relatively common for COVID19 compared to others (e.g., SARS) and when the peak levels of virus are detected (usually a few days after symptoms appear). But we wasn't able to find data on # of virus copies present in infected individuals before they get symptoms and how contagious they are. So this is an area of the model that would require further research.

Finally, we dropped contagiousness to 0 even while copies of the virus were still present based on the German and JHU studies that suggested that by day 10 of onset of symptoms for most patients, they were no longer contagious even though there was still detectable virus in their tests
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Assumptions Imperial College
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-baseline R=2.4 (test values between 2 and 2.6)
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-Symptomatic individuals 50% more infectous
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-individual infectiousness gamma distribution mean 1 and alpha=0,25
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-Early January seeded in each country with doubling time of 5 days (rate of seeding calibrated to current available cumulative number of deaths data of local epidemics in each country)
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-2/3 of cases self-isolate within 1day of symptoms, mean delay from symptoms to hospitalization of 5 days (rest of 1/3 are asymptomatic)
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-Apply estimates of IFR per age to each country based on data from China with non-uniform attack rate
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-In GB this means 0,9% IFR and 4,4% hospitalized (on average) but this has to be done per country
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-30% of hospitalized require critical care
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-50% of those in critical care will die
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-An age dependent proportion of those that don't require critical care die (calculated to match overall IFR)
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-8 days in hospital if critical care not required
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-16 days (10 days in ICU) if critical care is required
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-Both of those metrics assume that they don't have to wait longer for negative testing results (slower testing => more time in hospital)
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