The COVID-19 landscape (03/2022)

Introduction

COVID-19 is the disease caused by the most recently discovered coronavirus, SARS-CoV-2. The main symptoms of this disease are fever, dry cough and tiredness, although the loss of taste and smell are some distinguishing symptoms of this infection. The pandemic hit really heavy all around the world, impacting both the health and economy of everyone. Education also suffered a heavy blow, with impacts on the learning of children that are outside of the school.

Although the situation seem to have improved worldwide, it is still critical that we do everything in our disposition to prevent the circulation and spreading of the virus. For this reason, we all have to protect ourselves, following the safety protocols and vaccinating as soon as possible to diminish the impact of this disease.

With the goal to reassess the situation regarding the number of cases and deaths occurring in Brazil and also worldwide, in this notebook I will analyse recent data from Our World in Data regarding COVID-19 infections/vaccination globally. Later on, I will analyse data specific to Brazil.

COVID virus (www.paho.org)

Getting the data

Fouded by Max Roser, Our World In Data (OWID) is a scientific online publication whose mission is to publish the “research and data to make progress against the world’s largest problems”. Providing data from COVID-19 to nuclear weapons, these problems include poverty, war, disease and hunger, among others.

OWID has been collecting and maintaining COVID-19 data from various sources since de pandemic started. This data includes information on testing, vaccinations, hospitalizations, number of confirmed cases and deaths. This data has been updated daily during the COVID-19 pandemic.

COVID-19 worldwide

The COVID-19 pandemic certainly changed everyone’s lives. Here, after carefully preparing the dataset, we will take a look at the evolution of the disease in the world. We will observe the pandemic in a few aspects: how it evolved around the world, in different continents and countries. We also take a special look at data regarding the infections in Brazil (which is where I am currently).

First, let’s see the data regarding the situation worldwide:

Evolution of cases and deaths by COVID-19 worldwide (linear scale)

It is easy to see how much the number of cases and death have increase since the beginning of the pandemic. However, none of the peaks of new cases come close to the beginning of 2022, that is when the Omicron variant started spreading, which is known to spread more easily than the other variants. We can also see that there are peaks in new cases that preceed the Omicron variant. As one can expect, these peaks also happen concurrently with the peaks in new deaths (Jan-Feb/2021, May-Jun/2021, Aug-Sep/2021).

Following the analysis, when we look at the location and iso_code variables, it is possible to see that there are entries in the dataset that do not correspond to countries. Instead, these entries refer to other ways in which the data is stored in the dataset: values grouped by continent and country income (Classifications made by The World Bank. The details about each category are available here).

Let’s narrow it down.

COVID-19 by continent

Overall, the total number of deaths and cases was higher in Europe, followed by North America (deaths) and Asia (cases). This, however, could be partially explained by the higher availability of testing in these continents, especially in countries with higher income. This is likely to also be true for data regarding new cases:

Cases and deaths per continent (in the top 5 continents with most deaths)
New cases in top 5 continents with most deaths

When we look at the new cases confirmed, using the smoothed values, a sharp increase in the number of new reported cases in January 2022 is noticed. This is consistent with the Omicron variant, which spread with alarming rates when it emerged.

COVID-19 by income

What happens if we take into account the countries’ income?

Cases and deaths per income
New cases per income (smoothed)

From these plots, we can see that High income countries dominate in total and new cases, while the total deaths is higher in Upper middle income countries.

COVID-19 by Country

Now, let’s see which 5 countries dominate the dataset regarding most deaths and most cases.

Cases and deaths per country (in the top 5 countries with most deaths)
New casesper country (in the top 5 countries with most deaths)

Unsurprisingly, we see that the United States, Brazil and India are the top 3 countries with most cases and deaths up until 20th of March, 2022. In terms of cases, France and the UK are the 4th and 5th countries, while for deaths the top 3 is followed by Russia and Mexico. Let’s see how new cases and new deaths have been reported in the countries with most deaths:

Here we can see that, even though India and Brazil are the second and third countries with most cases, the number of new cases reported for these countries is very far behind those reported in the United States. Still, Brazil is 2nd in terms of deaths caused by COVID-19, even with less than half the total number of cases in the US. When comparing the peaks in new deaths reported, one can identify a decrease in new deaths reported in the most recent peak of new cases.

However, looking at absolute numbers is not always the best way to visualize data. Sometimes, a great number of cases will occur because of the population sizes or other undiscovered factors. An example of this is the fact that the 4th and 5th countries with most cases are not the ones with most deaths at the same ranking. Also, seeing the data in a logarithmic scale allows us to perceive rapid, exponential growth. Let’s see how these changes will affect our perception of the data.

Log scales

Let us see how the log scale affects our plotting.

Worldwide

Evolution of cases and deaths by COVID-19 worldwide (log scale)

Continent

New cases smoothed (log scale)

Country

Looking at these plots in the log scale, we can see that, overall, the number of total cases, new cases, total deaths and new deaths seem to have been stabilising, until the appearance of the new variant, Omicron, which caused new peaks to arise.

Data per-millionLooking at these plots in the log scale, we can see that, overall, the number of total cases, new cases, total deaths and new deaths seem to have been stabilising, until the appearance of the new variant, Omicron, which caused new peaks to arise.

Data per million

Another way to look at this data is to do it per million. This ensures that we are looking proportionally to the population of each country.

Per million cases and deaths by country (top 5 in each category)

Looking at the proportional number of total cases and deaths (per million), we can see that they are very different from the absolute numbers. This indicates a greater burden of the disease in these countries, in relation to their population sizes.

Analysing data from Brazil

In November of 2020, Brazil had the second highest death toll by COVID-19 in the world. This is largely reflective of the inadequate way that the pandemic was dealt with by government authorities.

“We have to stop being a country of sissies.” — Jair Bolsonaro

In Brazil, the first case was reported on 2020–02–26 and the first death on 2020–03–17, according to this dataset. From these, we can see that the first death was reported almost one month after the first case was registered in Brazil, and over three months after the first case was reported worldwide.

Evolution of cases and deaths in Brazil (linear scale)
Evolution of cases and deaths in Brazil (log scale)

“Stop whining. How long are you going to keep crying about it?” — Jair Bolsonaro

When we look at the linear scale lineplots, we can identify peaks of increase in total and new cases/deaths that are consistent with the appearance of the new variants. We also see, in the log scale, that overall the rate at which total cases and deaths increased has diminished. The number of new cases/deaths started decreasing, until the arrival of the Omicron variant earlier this year (2022).

Even with such high numbers of cases and deaths, the president still regarded and dismissed the disease, repeatedly, as just a “little flu”.

COVID-19 vaccination

Vaccination is a successful global health strategy that saves millions of lives every year. Because of years of previous research on viruses and infections, cientists were able to develop the COVID-19 vaccine in record time, surpassing the development of the vaccine for the mumps, which took four years.

Vaccinating can save your life from COVID-19. In addition to provide strong protection against the infections, it also decreases the possibility that you pass the infection on to other people. This makes vaccination not an individual choice, but a collective obligation to people around you and all over the world. However, even after vaccination, one should still take all the available precautions to protect themselves and others.

Let’s try to see, in our analysis, the impacts of vaccination on the pandemic. Below, we look at how it made an impact in new cases and new deaths in Brazil and also worldwide.

Brazil

New cases and new vaccinations, smoothed (Brazil)
New cases and new deaths, smoothed (Brazil)

Looking at these plots it becomes very clear the effect of the vaccination to the Brazilian population. First of all, when vaccinations started there was a massive decrease in the number of new daily cases. This, of course, changed when the new variant started circulating in Brazil.

However, despite the sharp increase in new cases, even with the increased number of vaccinated individuals, there was a sharp decrease in the number of new deaths. This fact cleary demonstrates the protective effect of the vaccine in the entire population.

Let’s also see how this happened worldwide.

Worldwide

New cases and new vaccinations, smoothed (worldwide)
New cases and new deaths, smoothed (worldwide)

Although we don’t see a sharp decrease in new cases, this could be explained by the peak caused by the Omicron variant which was far superior than the others. Still, after vaccinations started worldwide, there were some moments when the number of new cases decreased. For the new deaths reported, the effect of the vaccination is also present, with decreases in the number of new cases reported.

Looking at data from the entire world, however, is complicated by the fact that different countries started vaccinating the population at different time points and at different speeds that depended on the availability of the vaccine. Thus, this data should be look at with caution.

Conclusion

Overall, we can see that the number of new cases was far superior in countries classified as High Income. This was also true for Europe when we looked at data per continents. This could be partially explained by the increased testing in these places due to economical reasons.

We can also see that the number of total cases/deaths seem to be attaining stability worldwide and in Brazil. A greater increase in new cases and deaths, however, happened when the new variant appeared by the end of 2021 and its subsequent spread in early 2022.

The fact that vaccination is the most efficient way to reduce the impact of the pandemic, regarding new cases and deaths, is made clear when we see that an increase in vaccination is couple with reduction of cases and deaths compared to early stages of the COVID-19 pandemic.

Nonetheless, we should take these results with a grain of salt as no statistical comparisons were done to justify the observed effects in the data.

Detailed analysis: Jupyter Notebook
Where to find me: GitHub | LinkedIn

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Carlos Henrique Fantecelle

Carlos Henrique Fantecelle

Transcriptomics researcher working with infectious diseases and aging of the immune system, but also working on developing other Data Science skills.