Re: [stem-dev] Operon Ebola Models Available

Dear all,

It is nice to see progress in the STEM modeling community. Thanks for sharing. It is a bit difficult for me to attend the weekly telephone conferences, so I thought I share a few comments through this mailing list.

In my opinion, it is not very sensible to simulate a hypothetical outbreak of Ebola in the US, assuming that all parameters are the same as in West Africa. The R0 of Ebola in the US and other western countries would clearly be lower, most likely below 1. That means, that any import of cases could only cause a small outbreak as seen in Nigeria for example.

The doubling time of a simulated epidemic is determined by your assumed values of R0 and the average generation time. So it's no surprise that the doubling time you observe is similar to the one in West Africa. You could easily calculate the doubling time from your formulas.

I don't think that the infectivity period is the same as the interval from symptom onset to hospital discharge. People who are discharged will not have been infectious for at least a few days. From the WHO paper, I think it is better to look at the interval from symptom onset to hospitalization (5 days) or death (7.5 days). Alternatively, you can calculate the infectious duration as the difference between the serial interval (generation time) and the incubation period, i.e., 15.3 days - 11.4 days = 3.9 days. Remember that in your model you want to know the time during which people do transmit, and not the time during which they could transmit. If people are hospitalized quickly and there is not much transmission in the hospital, that means that the infectious duration can become shorter.

I don't really follow how you describe the rate at which infected individuals recover and die. If the infectious duration is given by 1/gamma and the case fatality rate is f, you can say that infected individuals recover at rate (1-f)*gamma and die at a rate f*gamma. In your model, the total rate at which infected individuals recover or die is 4*gamma, that means that their infectious duration is also only 1/(4*gamma). Based on your parameters, that will be a duration of 4.1 days that actually is a good value for the infectious duration. But I don't think this is really what you wanted to model, is it?

Best,
Christian
_________________________________________
University of Bern
Institute of Social and Preventive Medicine (ISPM)

Dr. Christian L. Althaus
SNF Ambizione Research Fellow

Finkenhubelweg 11
3012 Bern
Switzerland
Tel +41 31 631 56 40
Fax +41 31 631 35 20

calthaus@xxxxxxxxxxxxx
www.ispm.ch
www.immuno-epidemiology.ch

On Fri, Oct 17, 2014 at 2:22 AM, wrote:
I updated the STEM Wiki documentation and uploaded the Operon "B2" Ebola model project for the United States.  I will upload the West Africa project as well shortly.  My model predicts a 'time to peak infected' of 375 days post-introduction into the U.S.

http://wiki.eclipse.org/Ebola_Models

My results agree VERY CLOSELY with the observed multi-country outbreak doubling time.  (14.79 days in model, vs 15.74 days in reality).

The latest Operon Labs 'B2' Ebola Outbreak Model SEIR parameters are as follows (derived from the NEJM/WHO data):

1/σ (Incubation Period) : 11.4 days (Multi-day Exposures, All Countries, Observed)

1/γ (Infectivity Period): 16.4 days (Interval from Symptom onset to Hospital Discharge, All Countries)

σ (Incubation Rate/Day)  : 1 / 11.4 days = 0.08771930

γ (Infectivity Rate/Day)  : 1 / 16.4 days = 0.06097561

δ (Fatality Rate/Day) : 3 * γ = 0.1829268 (Try for ~71% Case Fatality Rate)

R0 (Reproduction Num#) : 1.84 ( Weighted Avg, All Countries)

βstem(Transmission Rate) = R0 * (γ + δ)

βstem(Transmission Rate) = 1.84 * (γ + δ)

βstem(Transmission Rate): = 0.4487805

Experimental testing of the above parameters in the United States with standard SEIR+D resulted in the following results:

Td_model (Model Doubling Time) = 14.79 days

Td_actual (Actual Doubling Time) = 15.74 days (Weighted Average, Liberia+SL+Guinea)

Serial Interval (Model Serial Interval) = 19.6 days

Serial Interval (Actual Serial Interval) = 17.6 days
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