COVID containment
  • South Africa was aiming to immunise 41-million people by the end of the year in order to reach herd immunity, the point at which COVID-19 was no longer spreading.
  • But this level of community protection is hard to achieve when the goal posts keep moving with the emergence of new variants.
  • Instead, South Africa is now rethinking its plan and moving towards a containment strategy to reduce strain on the country’s health system.

Achieving full community protection, or herd immunity, against COVID-19 through vaccinations by 2022 is no longer on the table for South Africa. The country now sets its sights on a less lofty goal called “containment”, which aims to immunise just enough people so that COVID hospital admissions put no more strain on the health system than any other illness would, experts say. 

Health Minister Zweli Mkhize initially aimed to immunise 41-million people by the end of 2021. 

Nearly halfway through 2021, however, South Africa’s vaccination roll-out has immunised only just over a million people with one dose of COVID vaccine. Only about half of them — the 479 768 who received Johnson & Johnson jab via the Sisonke trial; the vaccine consists of one dose only — are fully vaccinated. The other half have received only one jab of Pfizer’s two-dose jab. In other words, only 479 768, which works out to 0.8% of the population, has been fully vaccinated against COVID. 

The immunisation drive has faced various hurdles starting with the February news from a small study that found AstraZeneca’s vaccine is mostly ineffective against the 501Y.V2 variant dominant in South Africa — as a result, the health department sold the AstraZeneca shots. Researchers then rushed to get an implementation study up and running to instead immunise healthcare workers with Johnson & Johnson’s (J&J) jab. But the study lost out on two weeks of its vaccination time, when it was temporarily paused while the country’s medicine regulator, the South African Health Products Regulatory Authority (Sahpra), investigated unusual blood clots linked to the J&J shot. 

The stop-start nature of the roll-out is not the only reason herd immunity is an unrealistic goal for this year — a scarce supply of vaccines and new variants of concern circulating in the country play a role too. 

We explain the maths behind herd immunity and containment with the help of Barry Schoub, chair of South Africa’s Ministerial Advisory Committee on COVID-19 vaccines. 

How is herd immunity calculated?

A community can be protected from an infectious disease such as COVID through herd immunity. This means enough people in the community develop a resistance to the disease which prevents them from falling ill. This resistance means that the spread of the disease is slowed down throughout the community. 

Herd immunity is calculated based on how many people get infected from one person who already has a germ (also known as the reproductive number) — in the case of COVID-19 the germ is the SARS-CoV-2 virus. The goal is to get to a point where each infected person is unlikely to spread the disease to anyone else. This way the virus can be contained and will no longer be spreading within a population.

South Africa had estimated that 67% of people in the country would need to be vaccinated in order to reach this point — but some scientists argued that the figure was actually much higher.

Here’s how Schoub breaks down how to calculate the number of people that need to be vaccinated:

  • The reproductive number in South Africa (factoring in the 501Y.V2 variant) is 1.97
  • The calculation for herd immunity is: 1 – (1/Rt)
  • So for South Africa it looks like this: 1 – (1/1.97) = 1 – 0.51 = 0.49
  • That number needs to be multiplied by 100 to get the percentage: 49%

Now here’s where it gets a bit tricky — because you start making assumptions.

We don’t yet know how many people won’t get re-infected because they have protection (in other words their bodies have produced antibodies that can fight off SARS-CoV-2) from previously being infected.

So based on the assumption that some people will have immunity, you can lower the estimate for how many remaining people need to be vaccinated to 46%.

You work out what 46% of the total population of South Africa is (the population is estimated to be around 59.62-million people) which gives you 27.43-million.

This number then needs to be put into the context of the adult population in South Africa (which is 40.35-million people, according to data provided by Discovery Health) as these are the people who will actually receive the vaccine.

So, if you divide 27.43-million by 40.35-million, we get to the end goal of needing to vaccinate 68% of the adult population in South Africa.

But these calculations are not perfect and the numbers can vary depending on what the epidemic looks like.

“The estimate for herd immunity isn’t based on hard science. It’s based on what we know about other viruses and we’ve just kind of extrapolated it to SARS-CoV-2,” Schoub says. 

How many people you actually need to reach with a vaccine in order to reach herd immunity also depends on the level of protection the jab can provide — and this varies, depending on which jab is being used. You can calculate how much immunity you’ll have by multiplying the vaccine’s efficacy by the amount of people you’ll be vaccinating.

For example, the Johnson & Johnson vaccine has an efficacy of 64% against the 501Y.V2 or Beta variant and we’re planning to vaccinate 67% of the population. Multiplying these two numbers gives you a population immunity level of 43%.

In the case of the Pfizer jab — the other vaccine that South Africa will be using — its efficacy is around 91% against COVID-19 (not caused by the Beta variant), so the level of protection would be 61%. Unlike Johnson & Johnson, Pfizer concluded its clinical trial before the emergence of the variant meaning that there is limited data on the level of protection its jab can provide against this new form of the virus. 

Schoub explains that calculating the herd immunity threshold requires considering a number of factors including how effective a vaccine is, which variants are circulating and how people behave.

Moving towards containment

Within the context of these variables — in calculating a herd immunity threshold and also the barriers standing in the way of achieving it — South Africa has now moved towards a containment strategy.

This means the country is trying to achieve a level of immunisation which will cause the least amount of strain on the country’s healthcare system, Schoub says — in much the same way a winter illness might.

Previously, South Africa tried to use other diseases, such as measles, as a guide for how to respond to COVID.

Schoub explains: “For many of those acute viral infections, we can define herd immunity quite precisely. In the early days, we thought that we could do the same for COVID. But now with all those variables …  it’s become apparent, that it’s going to be impossible to precisely define that figure of herd immunity. So what we are aiming at is containing the virus to a tolerable level, to a level where it doesn’t cause too much hardship.”

Schoub believes South Africa could reach this level of containment by 2022, provided “the vaccine roll-out goes without too many hitches”.

Calculating what the country’s herd immunity threshold should be, is tricky — but achieving herd immunity is even trickier.

Here’s a closer look at some of the hurdles standing in the way.

1. Challenges in South Africa’s roll-out

Schoub says that the supply of vaccines is one of the challenges preventing the country from  achieving herd immunity. 

The country’s staggered roll-out of vaccines has been noted as a point of concern by the South African Medical Association’s chairperson, Angelique Coetzee.

“We really need to be vaccinating about one million people a month, but at the current rate that will not happen,” Coetzee said in a press release issued earlier this year. “We must have a proper vaccination plan in place to meet the demand to ensure we vaccinate as many people as possible in the shortest possible time frames.”

The limited global supply of vaccines means that it’s likely that South Africa will only reach its goal of vaccinating 41-million people by the first quarter of 2022, warns Schoub.

Implementation of the roll-out plan poses a possible challenge too. Early registration for a vaccine on the country’s electronic vaccination data system (EVDS) was interrupted with load shedding, requiring vaccinators to update the system manually. Miscommunication of appointments have also been noted, with people arriving to receive booked vaccinations and being turned away due to glitches in the system.

But despite these early snags, Schoub remains optimistic, pointing to the successes of South Africa’s antiretroviral programme. 

“That’s gone up pretty successfully. I think we’re a world leader,” Schoub argues. “And I think we can reach those goals [with COVID vaccinations] if all the effort is put into it”.  

Vaccine hesitancy could also pose a problem. The National Income Dynamics Study – Coronavirus Rapid Mobile Survey (NIDS-CRAM), is a nationally representative telephonic study of the socio-economic trends of South Africa. The latest wave of the study found that 29% of South African adults were hesitant to get vaccinated. Most hesitant respondents said they were worried about the side-effects of the vaccines (31%), believed the jabs weren’t effective (21%), or didn’t trust vaccines in general (18%).

2. Vaccine nationalism and an uneven supply of vaccines

Wealthy countries hoarding vaccine supplies affect the pace at which we reach herd immunity globally. Half of the world’s vaccine supply is currently held by the wealthiest countries which account for 14% of the population.

Delays in South Africa’s own roll-out are in part due to the fact that wealthier countries secured vaccines from manufacturing companies very early on in their development — mostly prior to results showing if the jabs worked. As a result, less well-off countries, which couldn’t afford to do the same, were placed in a situation where they had to join the back of the queue and wait for more jabs to become available.

This hoarding of vaccines means there will always be regions in the world where the SARS-CoV-2 virus remains circulating, Schoub explains.

This poses its own risk because as long as there are countries that are not able to protect enough of their population and continue to experience new infections, the virus will continue to spread across borders.

Another concern with this uneven distribution of vaccines around the world, is that it could give rise to new variants.

3. The rise of new variants

In the early stages of the pandemic, the coronavirus was thought to be relatively stable. But that changed when new variants — where the virus had mutated and evolved — began emerging in late 2020.

South Africa announced that it had identified a variant — called 501Y.V2, B.1.351 or Beta — in December last year which drove the country’s second wave of infections.

Some of the new variants, such as Beta, are able to spread more easily from person to person and, importantly, can also evade protection provided from previous infection. This means that even people who may have natural immunity to the original form of the virus can still get sick once again.

The rise of new variants poses a problem for reaching herd immunity, as the more infectious the virus becomes, the more people need to be protected in order to stop it from spreading.

Early studies suggested that vaccines could potentially be ineffective at protecting against infection with the Beta variant. 

But new evidence found that most COVID vaccines can provide at least some protection against these variants. For example, South Africa’s roll-out uses both the J&J and Pfizer jabs for which results show that they work against the 501Y.V2 variant.

But Schoub points out that because the Beta variant is one of the more resistant variants, it  means that if you develop immunity against it, the antibodies your body produces could potentially provide protection against other variants too.

4. People may not be protected forever

Calculating herd immunity depends to some extent on the number of people in a population that have natural immunity. But the catch is that we don’t yet know for how long that protection lasts  — and the same is true for people who develop immunity through vaccination.

There is, however, some promising data emerging that shows that protection could potentially last for several years

But for now, we only have evidence that shows that vaccine immunity lasts for six months, epidemiologist Salim Abdool Karim previously told Bhekisisa in April.

Why? Because COVID vaccines haven’t been around for long enough — we’d require a longer period of time to gauge how effective vaccines are in the long run.

“What I think will happen is that we’ll find that the antibody levels will remain high for a substantial period, meaning for a few years — after that we might find the antibodies waning,” Abdool Karim said.

This matters for herd immunity because it affects how often people would need to get vaccinated to remain protected against COVID.

What does this mean for SA?

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