Monthly Archives: February 2020

R0

from February 17, 2020

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It’s time to introduce another concept from epidemiology, the variable R0, also called R naught. It represents the reproduction rate of a virus spreading disease from one host to another. The simplest way to think of it is if R0=1, that means that each person infected spreads it to one other person. If the value is less than one, the disease is diminishing in the population, if it’s greater than one, it’s multiplying. At R0=2 or greater, we see exponential growth.

To put it in numbers, if a disease had a perfect R0=2 rate, we would see the numbers of cases like this increase at this rate over a set interval periods of time: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, etc.

If you look at the incidence of cases since about Feb 9 (with the exception of Feb 12 due to the change of diagnostic criteria in Hubei province), the number of new cases has remained relatively flat. Granted, it’s not a very long number of days to draw solid conclusions, but to me this is a pretty good indicator that R0 is pretty close to 1, which is a good sign. That could mean that the isolation, quarantine, and PPE measures that have been put in place are doing their job effectively.

On a broader sense, the longer we can delay the start of an outbreak, the better off we are. It provides time to get PPE measures in place, education of the public and healthcare providers, and time for vaccine development. For these reasons, I remain optimistic at present.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

CFR leveling?

from February 16, 2020

I am obviously getting concerned that the case fatality rate is beginning to level off at just above 2%. I’m still hoping that we see an increase in the number of survivors with minor illness that haven’t been captured in the data that would lower this number.

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There are also two other things that could mute the effect of this outbreak. First, Inovio Pharmaceuticals in San Diego has developed a vaccine against COVID-19. It obviously still has a lot of testing needed, but it is a hopeful development.

Second, there is also the possibility that the virus isn’t stable in hot, humid weather. As we get into summer in the northern hemisphere, that could be really good news in reducing transmission.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

COVID-19 Big Jump

from February 13, 2020

Don’t be alarmed at first glance.

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There appears to be a large jump in cases overnight. This is strictly due to the way that cases are being identified in Hubei province in China. Most testing has been through RNA tests, but results can take days. Hubei province decided to use CT scan to look for lung infections in order to start treatment earlier. This accounts for the large jump in cases. A similar thing occurred in the US in 1993 when the definition used for surveillance for AIDS changed, resulting in what looked like a massive jump that year.

A change in the testing methodology impacts two important variables: sensitivity and specificity. There are technical definitions for these but I’ll try to describe them in a way that makes them easier to understand.

In this case, switching to CT scan increased sensitivity. This essentially means that the test is more likely to capture cases. That’s why there is a large rise in the number of cases.

The other things that happens in this case is a decrease in specificity. A CT scan will identify any type of lung infection, not just from COVID-19. This is what is also known as a false positive test.

The takeaway is that this not something to get more concerned about. It makes sense to try to treat those at highest risk.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.