Peak COVID: Part 1
Tags: Data Science, Data Visualisation, Covid 19

Recent COVID conversations have shifted from talk of exponential growth, flattening the curve and first waves to second waves, peaks and hotspots. The general view, as lockdowns continue to lift, seems to be that the worst of the pandemic is behind us – at the time of writing the US President has just declared that the US is now “post-COVID” – but does the data support this? In this article we will attempt to answer this question.

To do this we will develop a peak model, which, as the name suggests, is designed to model the growth of the outbreak to better understand the stage of the outbreak across the globe.

The Dataset

We will focus on the number of daily confirmed cases/fatalities for countries, using a dataset from Our World in Data, which provides daily case and fatality counts for more than 200 countries. Rather than use the are case/fatality counts we will make the following adjustments:

Because daily case counts can be erratic, we will smooth the raw data by using a 7-day rolling average; thus the number of cases on a particular day is actually the average of the previous 7 days’ cases.

To make it easier to compare countries of different sizes and with different scales of outbreaks, we will normalise these rolling averages by dividing each by the maximum/peak daily count for that country.

In this way, the smoothed daily counts are translated into numbers between 0 and 1, relative daily counts. A 1 corresponds to that country’s peak and a value of, for example, 0.5 means that the count fo that day is 50% of the peak .

The example opposite shows these relative daily case counts for Ireland. The outbreak began in early March and the 7-day rolling average peaked on April 16, with over 900 daily cases. After this the case counts began a steady fall to current levels, which are now <1% of this peak.

Peak COVID: Model & Examples

Understanding the course of the outbreak in a country or region involves more than simply identifying the peak. Each outbreak moves through a sequence of characteristic stages and how a particular country moves through these stages can be revealing. In our model we focus on four characteristic stages with particular threshold levels used to define the stage transitions, as follows:

The expansion stage refers to the period before the peak where cases/fatalities are steadily growing. It begins when the numbers exceed 15% of the peak. The peak stage begins when the daily cases/fatalities exceed 85% of the peak and concludes when daily cases/fatalities drop below this 15% threshold for the final time, before falling below the 15% threshold. The contraction stage begins when daily cases/fatalities drop below this 85% threshold for the final time and usually corresponds to a period of reducing daily case/fatality numbers, although these numbers sometimes plateau during this stage. A country is said to be stable if, after the contraction phase, the daily case/fatality numbers drop below 15% of the peak and remain below this threshold.

Obviously in the above we have chosen particular values for the peak thresholds — 15% and 85% for the lower and upper thresholds — but other reasonable values could also be used — e.g. 10%/90% or 20%/80% — which will impact the transitions between stages and stage durations.

When we apply this model to the daily cases for Ireland, we obtain the graph opposite. The start of each stage is indicated by the dashed vertical lines and labeled accordingly, and the graph is shaded in accordance with the relative case counts.The expansion phase lasted for 21 days and when cases peaked (at 903 daily cases) they remained above the 85% threshold for 6 days before contracting for 29 days during late April and May. Daily cases fell below the lower threshold in the second half of May and have remained stable since.

Contrast this with the very different experience in the US, (opposite). Daily cases expanded very quickly in late March/ early April to hit a peak in mid-April and remained above the peak threshold (85%) for approximately a month. As of a few days ago the US was technically contracting, in that until then its daily cases had been below the peak threshold since early May. The contraction stalled once states started to open up and then daily cases started to rise again. Recently passed the peak threshold again, and so now the US has technically been in in peak stage since April, having failed to sustain a contraction.

We can use this approach to generate peak models for regions or continents as well as individual countries, by aggregating daily cases/fatalities in a straightforward way.

For example, here we see the same model applied to the aggregate daily case numbers for the EU nations. The expansion stage lasted for 13 days and a peak of more than 28k daily cases was achieved in early April. The peak stage lasted for 14 days, before a steady decline in cases from early April to June (52 days) when daily cases dipped below 15% of peak values. Currently, the EU is stable and the contrast between the EU and the US is striking.

Continents, Regions, Countries

In this section we provide a number of summary charts to facilitate a more direct comparison between continents, regions within continents, and countries within regions.

Continental Analysis

To begin, below we aggregate daily cases by continent. At this level of abstraction, it is clear that the current COVID situation is far from behind us. Europe and the much smaller Oceania are the only continents that have passed their peak, and while Oceania is now stable, Europe as a whole has some way to go, given that current daily cases remain at approximately 50% of their peak; daily cases remain high for Europe due mainly to the outbreak in Russia and some other Eastern European countries, as we shall see. Unfortunately, for Asia, Africa, and the Americas the situation is even more challenging: cases are still expanding and it may be some time before they peak, let alone contract; the absolute numbers are low in Africa, suggesting that it may be at a very early stage in its outbreak.

Regional Analysis

The situation improves somewhat when we look at the regions that make up the continents, at least in the sense that some regions are doing well. The graph below shows the peak models for 22 different regions (comprising 167 countries with populations >500k) across 6 continents. The continents are arranged from left to right in ascending order of their peak dates (averaged across their regions) and the regions are stacked from bottom to top in descending order of total case count (averaged across their countries).