South Africa is on the cusp of a third Covid wave with some provinces already there. The country hasn’t vaccinated nearly enough people for its vaccination roll-out to make a difference to the potential severity of this wave, experts have warned. By 6 June 2021, only 479,768 (0.96%) of South Africa’s population of about 60-million people had been fully vaccinated, and 870,477 had received one of two shots of Pfizer’s Covid vaccine. 

According to the former chair of the Covid ministerial advisory committee, Salim Abdool Karim, a country would need to vaccinate well over 70% of people of 60 and older in order to reduce deaths and hospitalisations significantly.  

South Africa therefore only has the natural immunity of those who have had Covid caused by the Beta variant, which is the main form of the virus circulating in South Africa, as well as adherence to mask-wearing, social distancing and hand-washing, to rely on. 

But how does South Africa decide whether a new Covid wave has emerged? Well, there’s a  formula, which was developed by our modelling consortium and adopted by the ministerial advisory committee (MAC), that we use.  

Bhekisisa and Media Hack explain how the formula works and apply it to each province to make it easy to understand where we’re at. 

We also spoke to Abdool Karim to break down the factors that will influence how South Africa’s third wave plays out, how long it will last and whether — and when — we’ll see a fourth wave. 

Are we in a third wave? 

South African Covid-19 Modelling Consortium (SACMC) developed a formula that the health department uses, at the recommendation of the MAC, to calculate whether the country or a province has entered a new Covid wave.  

The formula says a Covid wave starts when the seven-day moving average of new cases exceeds 30% of the peak of the previous wave. A moving average means that you’ve taken numbers for each of the seven days selected (in this case new Covid cases), added them up and divided them by seven to get the average of those days. You would then plot them on a graph, so that it helps you to see what new cases look like over time (instead of plotting daily numbers, which may sometimes vary widely and be confusing to interpret). 

Let’s apply this formula to the current seven-day moving average of both national and provincial cases and see where we’re at. 

The seven-day average of daily cases in South Africa, from the first wave to the current period. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

On 6 June the national seven-day rolling average of daily cases was 4,820. At the peak of the second wave (blue line) it was 19,042, which was reached on 11 January. The average daily cases on 6 June is 25% of the peak of the second wave. So, technically, by the criteria being used, South Africa isn’t yet in the third wave.

But, at the peak of the first wave (red line), which was on 19 July 2020, the seven-day rolling average was 12,584 cases. The 4,820 cases on 6 June are 38% of the peak reached in the first wave, so by that measure, we are now in the third wave.

In other words, whether the country is in the third wave depends on which of the first two waves is used as the baseline.

So what about the provinces? 

The third Covid wave has begun in four provinces, according to the MAC’s formula: the Northern Cape, Free State, North West and Gauteng.

Daily confirmed Covid-19 cases in Northern Cape. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

The Northern Cape has been the worst hit. Its third wave began around the middle of April and the average daily cases reached a peak of 431 on 25 May, which was much higher than the peaks of the first and second waves in the province. By 6 June they appeared to be starting to decrease.

Daily confirmed Covid-19 cases in Free State. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

The Free State’s third wave also seems to have passed its peak. Average daily cases started to rise in the province in April and reached a peak of 502 on 1 June. This is just 56 cases short of the peak of wave two, 558 cases, on 16 January.

Daily confirmed Covid-19 cases in North West. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

Covid cases are still on the rise in the North West. The 427 average daily cases on 6 June were 56% of the peak of the second wave of 768 cases on 13 January and 73% of the first wave peak of 588 on 13 July 2020. So the third wave has begun.

Daily confirmed Covid-19 cases in Gauteng. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

A third wave has also started in Gauteng. On 6 June the average daily cases of 2,531 were 48% of the peak number of 5,291 cases of wave two on 12 January and 47% of the first wave’s peak of 5,386 cases on 15 July 2020.

Daily confirmed Covid-19 cases in Eastern Cape. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

Average daily cases in the other five provinces are starting to pick up, but they are some way off a third wave. In the Eastern Cape, on 6 June, the average daily cases were 7.5% of the second wave’s peak and 6% of the first wave’s.

Daily confirmed Covid-19 cases in KwaZulu-Natal. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

In KwaZulu-Natal they were 3% of the peak of the second wave and 6% of the first wave.

Daily confirmed Covid-19 cases in Limpopo. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

Limpopo barely had a first wave, but the average daily cases on 6 June were 8% of the peak of the second wave. 

Daily confirmed Covid-19 cases in Mpumalanga. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

In Mpumalanga, the average daily cases on 6 June were 19% of the peak of the province’s second wave, but 32% of the peak of the first wave. So by the first wave’s standards, the province is now in its third wave, but not by the second wave’s.

Daily confirmed Covid-19 cases in Western Cape. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

In the Western Cape, the average daily cases on 6 June were 12% of the peak of the second wave, but 25% of the first wave’s peak.

Up until now, the provinces that have shown sharp increases in their average daily cases have been three (North West, the Northern Cape and Free State) with relatively low populations, so they haven’t had much of an effect on the country’s national numbers. But now that the new confirmed cases in Gauteng, which has the highest population in South Africa, have started to rise, the national curve has begun to rise more steeply. 

KwaZulu-Natal, the second-most populous province, is still reporting relatively low daily case numbers, but if that changes, so will the national picture. And the same will apply if the daily cases in the Western and Eastern Cape, which have the next highest population numbers, start to rise sharply.

How do we know when a wave has ended? 

The MAC has come up with a formula for the end of a Covid wave too. The formula says when the seven-day moving average is 15% or lower than the peak of the previous wave, the wave has ended. 

According to this formula, the third wave hasn’t ended in any province. But in the Northern Cape, it’s slightly more complex than that. 

In that province, the third wave is significantly higher than the previous two waves, so it’s difficult to use the previous wave (wave two) as a measure of whether the current wave is ending. On 6 June the average number of new cases was 30% higher than the number at the peak of the second wave and 44% higher than the peak of the first wave. 

However, the average daily cases on 6 June were 12% lower than they were on 25 May, so there is some good news in that. 

What other ways are there to look at whether a new wave has emerged? 

Abdool Karim says very few countries use formulas such as South Africa’s to determine if a new wave has emerged. Instead, they collectively interpret three measures: the number of new Covid cases, the test positivity rate (the proportion of tests coming out positive) and hospitalisations.

If the new cases, the number of tests (which is an indication that infections are increasing, as more people are coming forward for testing) and positivity rate have all been steadily increasing, there should be reason for concern, particularly when the test positivity rate has exceeded 5%, which the World Health Organisation says is a sign the pandemic is no longer under control.   

South Africa’s seven-day moving average for its test positivity rate was 12.7% on 6 June. 

Abdool Karim says that, based on seroprevalence estimates, only 10% of overall Covid cases are officially reported. “For every case, we know that there are nine other cases which we don’t know about, because they’re asymptomatic and such people are unlikely to have gone for a test, because they probably didn’t even know they had Covid. So that means, as a rough guide, if we have one new Covid case per 10,000 people, the infection rate is one per 1,000 people (in other words, the infection rate is ten times higher than the case rate).”   

Hospitalisations, Abdool Karim says, always lag about two weeks behind new cases, as it takes between 10 and 14 days for an infection to show up on a PCR test and then a few more days before the patient needs to be hospitalised.

How long will our third wave last? 

South Africa’s first wave lasted about three months (from June to early September 2020) and so did the second wave (from mid-November 2020 to mid-February 2021). The gap between the first and second waves was also about three months.

But Abdool Karim says we can’t tell how long the third wave will last by merely looking at the duration of the first and second waves, because we don’t know if the third wave will follow the same trajectory. 

How long the third wave will last, will depend mainly on how long it takes before the Gauteng epidemic spreads to the three other populous provinces and whether a new variant, especially one which can escape past immunity, starts spreading.

Will our third wave be worse than the first and second waves?

This will depend on a number of factors, says Abdool Karim. For one, variants will play a significant role. “If we get a new variant, there are no predictions we can make, because we don’t know how it will behave,” he says. “But if the Beta variant [also known as B.1.351 or 501Y.V2], which is currently our dominant variant, and which was also the dominant variant in the second wave, is the main form of the virus that drives our third wave, then a proportion of people who got infected in the second wave will be protected during the third wave [depending on how long their immunity lasts for].” 

Two other variants, the Alpha variant (also known as B.1.1.7 and first detected in the United Kingdom) and the Delta variant (also known as B.1.617.2 and first detected in India) have also been detected in South Africa. 

“The variant dominating our third wave will be the one which has the most effective combination of mutations to give it the functional advantage of transmitting faster,” explains Abdool Karim. “We know that the Alpha variant transmits faster than the original form of the virus, and this variant has been found in the Northern Cape and Free State, where third waves have reached their peaks. But the Alpha variant doesn’t spread faster than the Beta variant. And the Delta variant we’ve only seen in sporadic cases in South Africa, so we haven’t seen much in terms of local transmission.  

The Alpha and Beta variants will therefore have to “fight it out” to see which one of them can transmit faster and come to dominate our third wave. 

“My guess is that Beta will win because it’s a much more mutated virus and better adapted for survival. In simple terms, the Beta variant is far more scary than the other two variants,” says Abdool Karim. 

How people behave during this wave, so how well they adhere to mask-wearing, hand-washing and social distancing, will also influence how severe our third wave is, because it will impact how fast the SARS-CoV-2 virus, which causes Covid-19, spreads. 

Will we see a fourth wave? 

Abdool Karim says we will almost certainly have a fourth wave and we can likely expect this to happen in December.

“We won’t be able to stop a fourth wave, because you have to have a very high level of vaccination to stop a fourth wave. You’d have to vaccinate 70 to 80% of the population, which we would not likely achieve in time,” he says. “But it will likely be a small, mini fourth wave.”    

He says by the time that South Africa has a fourth wave, the country will have a better idea of whether new variants have emerged and whether the new forms of the virus are able to escape immunity and make vaccines less effective. “Immune escape variants worry me, because they could lead to vaccinated people being at risk again. The fourth wave’s severity is going to depend on a balance between the prospects of a new immune-escape variant versus how fast and how many people we had vaccinated by then.” 

Who should we aim to have vaccinated before the fourth wave? 

Abdool Karim explains: “It’s not necessarily critically important that we get to the government’s goal of vaccinating 40 million people by then, it’s more important that we finish phase two [people of 40 years and older and those living in congregate settings] before December, because the people targeted in phase two are the ones who are going to get sick [research shows older people are more likely to fall severely ill from Covid than younger people]. 

“If you finish phase two, then you’ve more or less done what you needed to, which is to give most people at high risk the individual benefit of not getting severe disease.” 

What’s the reasoning behind the introduction of curfews and reducing the size of gatherings when a new wave is on its way?

When cases are increasing fast, as they are right now, the chances of having a Covid-positive person in a group of people, increases significantly. “The moment you have a positive person in a group, you put the whole group at risk of infection,” says Abdool Karim. 

Here’s why.

Abdool Karim says research shows that about 80% of new SARS-CoV-2 infections occur from only 10 to 20% of infected people. “So it’s a very small group of people doing the transmitting. In a group, particularly in groups that get together indoors, it just takes one or two people to be positive and infect most of the rest of the group.” 

That’s why it’s so important for us to overcome people’s complacency regarding wearing masks, washing hands and practising social distancing. A formal way to deal with that is to increase lockdown levels to control group gatherings, which sends a message that factors driving the spread of the virus have intensified.  

Curfews influence the amount of time that people have to socialise indoors in groups in the evenings in, for instance, restaurants and pubs, which in turn reduces the opportunity for infection. 

Why don’t we implement different lockdown restrictions for different provinces? 

Why would the government not use its risk-adjusted strategy to implement stricter lockdown rules in provinces where infections are spreading the fastest and more relaxed rules in those areas where Covid cases are increasing at a slower rate? 

The short answer: Because it leads to confusion and it’s impractical. 

The longer answer: Abdool Karim says provinces are generally between two weeks and a month ahead or behind each other in terms of infections. Because we don’t have a way to isolate provinces from each other (so that infections don’t spread from one province to another), the infections will inevitably spread from one province to another. “You’ll therefore end up chopping and changing the rules all the time and it all just becomes too complicated. So it makes sense to just have one set of rules for the entire country especially because we don’t have rigid lockdowns anymore, so it doesn’t impact the same way on business.” 

Will we see alcohol sales restrictions during the third wave? 

Banning the sale of alcohol has two main benefits: it decreases indoor social interactions and reduces the number of vehicle accidents and interpersonal violence, which in turn frees up hospital beds for Covid-19 patients. Abdool Karim says because the main advantage of alcohol sales restrictions in a wave is the freeing up of beds, we’re likely to see restrictions on alcohol sales — such as limitations on the hours of sale — when hospital beds are filling up. 

In Gauteng, Free State, Northern Cape and North West, hospital admissions have been rising for the past few weeks, according to the National Institute for Communicable Diseases’ daily hospital surveillance report. Admissions in the Western Cape are also starting to rise. DM/MC

Hospitalisations from 10 April 2021 to 29 May 2021. (Graphic: Supplied by Bhekisisa Centre for Health Journalism)

This story was produced by the Bhekisisa Centre for Health Journalism. Sign up for the newsletter.