An epidemic calculator for COVID infections

To a non-expert as most of us comprehending the numbers, the forecasts and the epidemiological parameters presented in the literature may be quite a challenge. I found online a very interesting calculator for COVID that addresses this gap in our understanding.

Figure 1. A calculator to be used to measure one’s risk of exposure to the disease for any given day of the epidemic

The variables for transmission dynamics that can be modified are:

• population inputs: size of population, number of initial infections
• basic reproduction number (measure of contagiousness) : the number of secondary infections each infected individual produces
• transmission times: length of incubation period, duration patient is infectious

The variables for clinical dynamics that can be modified are:

• mortality statistics: fatality rate, time from end of incubation to death
• recovery times : length of hospital stay, recovery time for mild cases
• case statistics: hospitalization rate, time to hospitalization

One may drag horizontally the line for the day of intervention in order to decrease the transmission and then the parameters for susceptible cases, exposed cases, infectious cases, population no longer infectious, fully recovered cases, number of active hospitalizations and fatality rate values will change accordingly.

The infectious disease is mathematically modelled using a compartmental model. The population is assigned to one of the four compartments: susceptible (S), exposed(E), infectious (I) and recovered(R). A mathematical set of equations is used to model the progress of people from one compartment to another. The model runs either on a set of ordinary differential equations (deterministic) or using a stochastic framework (more close to reality).

I attended many online meetings about various models for the clinical data available for COVID cases and I found this model as quite suitable. This epidemiologic calculator uses the SEIR model which assumes that S+E+I+R=N where N is constant as it is assumed that the birth and death rates are equal. I hope this calculator may be of assistance in better administrating the situation with this pandemic.

Happy Easter everyone!

The situation for COVID-19 cases in countries in Europe - 7 April 2020

COVID-19 affects everyone’s life and routine. The meetings started to become virtual meetings. The streets are empty, the offices are empty but the virtual world is very busy. I didn’t see an open communication with the public about the real situation in any of the countries that I have an eye on, The Netherlands where I live, UK and most importantly Romania, my home country.

Yesterday, randomly, I had a virtual meeting with the data science team from a company in Rotterdam that promotes a visualisation tool that can provide predictive insights to the government of any country. The tool can estimate the effects of non pharmaceutical interventions based on the understanding of the outbreak hotspots all over the world.

This is how I had a closer look at the resources that people have as reliable source of information on the number of confirmed cases and deaths in each country. This main source of reliable information represents the list of situation reports provided by the World Health Organisation. Yesterday, April 7, another situation report was released.

The number of confirmed cases and the number of deaths reported for each country are sureal. This is how I started to look at the data in Excel. I had problems to understand how much is too much, how can I interpret these values. One would not find as fair to say that the same value for confirmed cases for a small country has the same weight as for a country with a larger population. This is why I added another column, that of confirmed population for that country in 2020.

Maybe not all have time to do this research and this is the reason why I decided to share with you my Excel sheet with the raw data in the link above. I personally wanted to see which is the percentage of the population for each European country that represents the confirmed cases. I was surprised to see, in figure 1, that in fact we discuss here about less than 1% of the population for that country.

Figure 1. The total number of confirmed cases until April 7 versus the total population of the reported country

Later on I had a look at the total number of deaths until April 7 versus the total population of the reported country. Figure 2 presents the situation for these cases. The greatest value, with a small anomaly in San Marino at 0.1%, represents 0.03% of the total population for that country.

Figure 2. The total number of deaths until April 7 versus the total population of the reported country

Last but not least, one can have the “barometer” of the immune system per country, which is the percentage from the total number of confirmed cases until April 7 that represents the total number of deaths. Figure 3 shows that a maximum of 13% of the confirmed cases actually end up with the death of the patient.

Figure 3. The total number of deaths from the total number of confirmed cases until April 7

I know that people are not statistics but the fear that is in the air nowadays is a little bit pushed too far. People start to need a psychologist in order to handle the current lifestyle in isolation in the privacy of your own home. This doesn’t mean that we should not be cautious as before with the hygiene but I think that we also deserve to enjoy ourselves a little bit more now that Easter is coming.