Joe Phaahla | Covid-19: This agile, mutating virus is outsmarting the world’s best scientists

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Scientists work in a lab testing COVID-19 samples.
Scientists work in a lab testing COVID-19 samples.
Brendan McDermid/Reuters

The unparalleled speed at which vaccines have been manufactured, tested and distributed to combat an ever-changing virus presents unprecedented challenges to all of us, writes Deputy Minister of Health Dr Joe Phaahla.


Vaccines are most effective against static targets and SARS-CoV-2 is anything but stationary. The massive scale of human infection has provided Covid-19 with bountiful opportunities to generate variants. This agile, mutating virus is outrunning and outsmarting the world’s best scientists.

The Department of Health’s decision to modify its rollout of the AstraZeneca Covid-19 vaccine, after research suggested it offers diminished protection against the 501Y.V2 variant prevalent in South Africa, is disappointing. But it should not be surprising given how quickly this virus transforms.

A no-win situation

AstraZeneca’s vaccine research began at the end of the South Africa’s first wave of infections last year and continued through to the second wave which occurred at the end of 2020. We now know that the second wave was largely fuelled by the 501Y.V2 variant which first emerged in the Eastern Cape and then spread rapidly throughout the country. It was only in the latter part of 2020 and early January 2021 when researchers began to focus on the effect of vaccines against the 501Y.V2 variant.

The results of their studies only became available on Friday, 5 February, and were publicly and transparently released two days later at a media briefing hosted by Minister of Health, Dr Zweli Mkhize.

It was through this research, which the government has directly invested in, that it was established that the AstraZeneca vaccine was largely ineffective on the 501Y.V2 variant. By this time, a million doses of the vaccine – designed to fight the original virus and developed before the new variant was discovered - had already been delivered to South Africa.

READ | Explainer: Covid-19: Did the 501yY.V2 variant come from SA? We ask the experts

As the rollout of vaccines began worldwide in 2021, government found itself in a no-win situation.

In early January, we were chastised for failing to enter into bilateral agreements with pharmaceutical companies to secure vaccines, even though nobody knew with any degree of certainty if they would be effective against the new strain.

We had no idea at that time whether or not vaccine evasion was a feature of the 501Y.V2 variant. That data was still coming. The only information we could access was from day-to-day trials. This made it impossible to anticipate anything since tests were being conducted on the go while the virus was mutating.

If we waited and the results then showed that the vaccine was effective against the new variant, we would have missed an opportunity to procure a possible antidote. Understandably, South Africans would have been outraged. 

The decision to purchase the AstraZeneca vaccine was based on data that showed 76% efficacy after just one dose. For us, it was a low-risk, short-term, relatively small investment that we had to make to secure the safety of our healthcare workers and frontline defenders. At the time when the decision was made, it was the right thing to do.

Timing and expiry dates

Suggestions that government has been sold expired vaccines are absurd.

If the vaccines were appropriate for South Africa’s Covid-19 context and we had proceeded with the AstraZeneca vaccine rollout as planned, the Department of Health would have safely jabbed a million doses into frontline healthcare workers long before 30 April, when the vaccine expires.

The April expiry date was also not discovered by accident. Through the implementation of quality assurance and control protocols, government was well aware of when the stock expired. That the shipment expires in April isn’t alarming. Its drastically-reduced efficacy of 22% against the 501Y.V2 variant is the concern.

What now?

Right now, the immediate priority is to reduce the risk of severe disease, and help ease the burden on our healthcare systems. We will continue with Phase 1 of the vaccination programme as planned, using the Johnson & Johnson and Pfizer vaccines instead of AstraZeneca. These vaccines have been proven effective against the 501Y.V2 variant and the necessary approval processes for use in South Africa are already underway.

In partnership with the Medical Research Council and the National Department of Health, the vaccination rollout will begin in the form of an implementation study at vaccination sites across the country. This study will provide valuable information about breakthrough infections - should they occur - amongst vaccinated health workers.

READ | SA's first Johnson & Johnson jabs could arrive next week. Here's what our rollout plan looks like

Such a nimble virus demands a range of responses, so we are also engaging Sinopharm, Moderna and the manufacturers of the Sputnik V candidate. There are vaccines coming out all the time, and this is an iterative process. We always knew that first-generation vaccines would be far from perfect. Scientists have warned all along that this is a long game with gradual gains. All of us must, therefore, manage our expectations.

What about AstraZeneca?

So, are we burning the AstraZeneca vaccine?

Depending on the advice we receive from the experts, the vaccine will either be exchanged before the expiry date, or sold to countries where the 501Y.V2 variant is not present. At a recent World Health Organisation (WHO) press conference that discussed South African’s findings about AstraZeneca’s efficacy against the 501Y.V2 variant, scientists and public health experts emphasised that the vaccine still has an important role to play. The storage and cost of AstraZeneca makes it particularly suitable for developing countries, which have been pushed to the back of the procurement queue after developed countries stockpiled billions of vaccine doses.

READ | Covid-19: Astrazeneca vaccine provides minimal protection against 501Y.V2 variant - new study

With so much research focused on the development of vaccines to beat this pandemic, there is huge reason for optimism. But vaccines are just one of a range of responses we will need to get the pandemic under control.

Right now, we all need to perfect non-pharmaceutical interventions: maintaining social distancing; wearing masks; keeping to out our social bubbles; and hand-washing.

There are no quick-fixes or magic bullets in the fight against Covid-19. This is a long battle.

- Dr Joe Phaahla is the Deputy Minister of Health.


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