South Africa is not experiencing a second wave of COVID-19 (yet)


Since the national lockdown was relaxed in South Africa there have been numerous reports (here and here) of a spike in the number of new COVID-19 infections, and the Minister of Health, Dr Zweli Mkhize, and his wife, have tested positive for COVID-19. There have also been reports of super-spreader events in Cape Town and the Eastern Cape. This has led to an increasing concern that South Africa is now entering a second wave of the pandemic. This is happening in the context of a very real and dramatic second wave of this disease currently occurring in many countries in Europe and elsewhere, leading to another wave of lockdowns with various degrees of severity.

To understand whether we are indeed entering a second wave, it is useful to examine some key indicators. There are: the trend in new cases and deaths, the doubling rate of infections and the Rt, or reproductive rate.

What does the data tell us?

At present we are averaging about 1600 new cases of COVID-19 per day, which has been largely stable since the beginning of September. This equates to about 3 cases per 100 000 of the population

You can see this, shown another way, in the graph below, which shows the trend in new cases per 100 000, by province. All the provinces have stabilised at quite low levels. The Free State and the Northern Cape had epidemics which started later, and stabilised at higher levels, although these are also starting to decrease. The Eastern Cape is showing an uptick in infections, which, although concerning, requires more time to determine whether this is the start of a major outbreak in that province. As long as South Africa continues to keep new infections below 5 per 100 000, we will avoid a 2nd wave of high community transmission of COVID-19.

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Figure 1: Average number of new infections per 100,000 people. (Genesis Analytics)

At the height of out peak we were averaging about 2000 deaths per week. This has decreased to about 630 deaths per week since the start of September, although this number does fluctuate. While this is still an unacceptably high number of people dying from this infection, there is no indication that the number of deaths is increasing significantly, and this would not be expected in the absence of a large increase in cases.

The doubling rate is another indicator of how fast the virus is spreading. Doubling time, in the context of COVID-19, is defined as the amount of days it takes for the number of infected people to double. So, it effectively captures the rate of spread of COVID-19. The lower the doubling time, the faster the virus is spreading and vice versa.

The doubling rate, as shown below, remains high in all the provinces at the moment. In many European countries it is between 10 and 20 days, and even below 10 days. In South Africa the doubling rate is well over 100 days in all provinces.

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Figure 2: Latest doubling rate as an average of the past five days (Genesis Analytics)

The reproductive number, Rt, is defined as the average number of people who become infected by an infectious person. It is also used as an indicator of how fast the virus is spreading through a population. When the Rt number is less than 1.0, that indicates that the virus will stop spreading because most people who are infected are not passing that infection on to anyone else. The higher the Rt, the more people are becoming infected, and the faster virus is spreading.

Both of these indicators can be used to identify whether we are entering the second wave and we can do this by identifying what the Rt and doubling rate were at the beginning of the first wave, and use that to understand what these indicators should be now if we are in fact entering the second wave.

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Figure 3: Change in Rt, or reproductive number, since the beginning of the epidemic until now (Mediahack)

We can see from Figure 3, that at the beginning of the First Wave, the Reproductive Estimate was around 1.5, reaching a peak of 1.55 on the 13th of April 2020. This is also roughly when the first wave of COVID-19 started taking off in South Africa.

At the moment, the Rt estimate is only 0.93 for the whole of South Africa. If we analyse the data at a provincial level, the Eastern Cape is the only province who’s Rt is currently similar to what it was at the beginning of the first wave at 1.51. All other provinces seem to be holding steady with an Rt estimate slightly above 1.0 (Western Cape: Rt = 1.06 and KwaZulu-Natal: Rt = 1.01) or less than 1.0 (Mpumalanga, Northern Cape, North West, Free State, Gauteng, Limpopo). .

Based on all of these indicators, South Africa is not experiencing a 2nd wave of COVID-19. We are seeing an increase in the Rt in the Eastern Cape, but it is too soon to know whether this is a limited outbreak or whether this is an early sign of more widespread viral transmission.

What do we need to look for?

Given what we are seeing in other countries, it seems unlikely that we will escape another wave of COVID-19 infections, especially as we enter the holiday season in South Africa. However, we can only start saying that we are in a second wave when the Rt estimate is similar to that experienced during the first wave, above 1.5 nationally, and in different locations around the country. We need to continue to monitor the Rt, new cases and the doubling rate for any indication that the epidemic is flaring up again.

We can prevent a second wave by continuing to communicate the importance of mask-use and physical distancing, and by implementing an aggressive test and trace programme, especially in areas which seem to have spikes of COVID-19 infections. Hopefully there is currently a strong public health response in the Eastern Cape, to ensure that the outbreak there does not spread further.

First published on LinkedIn on 2 November 2020