Thread by @Fatima_AlSayah

1/ TESTING TESTING & MORE TESTING! 🇱🇧
Why the confirmed # of COVID-19 cases in Lebanon highly underestimates the actual # of cases?
@mophleb @WHOLebanon @thehealthnerds
#Lebanon #COVID19 #FlattenTheCurve #RaiseTheLine #healthNERDS

2/ Keep in mind, we can never know the actual # of cases because we cannot test the whole population. However, we should do as many tests as possible – especially during this stage of the outbreak – to gage the scale of the problem, isolate/ treat +ve cases & plan next steps.

3/ If we can’t test the whole population, how can we know the actual # of cases? We try to estimate; one way of doing so is by using the case fatality rate (CFR). CFR reflects the severity of the disease in a particular context, at a particular time, in a particular population.

4/ CFR (%) = (# of deaths/# of confirmed cases) * 100
Remember CFR is not constant and keeps changing over time; the only stable CFR estimate is calculated when the outbreak ends. In Lebanon, CFR on March 31 was reported to be 2.6% 👇

5/Calculating CFR from “current” total # of confirmed cases underestimates the risk of death because there’s a lag (15-20 days) from the time of diagnosis to death. So, patients who got diagnosed on March 31 may die within the next 15-20 days & won’t be counted in the current CFR

6/ To calculate CFR on Mar 31, we can go back 17 days (Mar 14) & use the total # of cases on that day (93).

A CFR of 12.9% seems very high compared to published rates ranging from 1% - 5%!
So what is it? Are the 93 cases on March 14 an under-estimate of the # of cases?

7/ Let’s ask the question in a slightly different way: Given that published CFRs range from 1-5% & total # of deaths on March 31 was 12, how many cases should have been on March 14 to lead to 12 deaths as of March 31?

Here are 3 scenarios:

8/ Now we have estimates of the possible # of cases on March 14. So, what is the potential # of cases on March 31?

Here are two scenarios projecting total # of cases based on doubling time of 5 & 7 days & % of cases captured out of the total potential estimate

9/ If we go with the scenario of 2.5% CFR & doubling time of 7 days, we would have 2880 cases by March 31. Based on the # of confirmed cases on March 31 (463), we are missing ~ 84% of potential cases (range 64% - 87%).

10/ Sensitivity analysis: Let’s estimate the total # of cases at CFR of 2.5% & doubling time of 7 days with the duration from diagnosis to death set of 10, 15 or 20 days:

11/ This exercise is not to estimate an exact # of cases; this is to demonstrate that we are missing a large # of potential positive cases who continue to spread the infection, and why we need to TEST MORE, a LOT MORE.

12/ Without increasing testing capacity, we won’t be able to evaluate whether the relatively small numbers we’ve been seeing the last few days are due to the effectiveness of containment measures or due to low rates of testing.

References:
Li et al. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia. N Engl J Med 2020; 382:1199-1207.

Dorigatti I et al. Report 4: Severity of 2019-novel coronavirus (nCoV). Available from: imperial.ac.uk/media/imperial…

References:
Pueyo T. Coronavirus: why you must act now. Available from: medium.com/@tomaspueyo/co…

Jung S et al. Real time estimation of the risk of death from novel coronavirus (2019-nCoV) infection: Inference using exported cases. Available from: medrxiv.org/content/10.110…

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@Rattibha please organize this thread. Thanks