The vaccine doesn’t seem to offer protection against the variant.

This month, South Africa received over a million doses of the AstraZeneca COVID-19 vaccine. This much-anticipated shipment was supposed to boost the country’s vaccination program, which is lagging far behind that of other countries. But in a surprising turn of events, the country’s minister of health announced on Sunday that it would halt mass vaccination using AstraZeneca’s product citing insufficient protection against mild disease caused by the new coronavirus variant circulating in South Africa.

Disappointing results and an unwelcome confirmation of our wildest fears

The vaccine produced by Anglo-Swedish pharmaceutical giant AstraZeneca in conjunction with the University of Oxford, known as ChAdOx1 nCoV-19, is one of the cheapest, easiest to distribute, and widely available COVID-19 vaccines. Over three billion doses are supposed to be manufactured this year, so this is deeply worrisome news. But there seems to be a problem.

Concerns about vaccine effectiveness in the face of the new South African coronavirus variant, known as B.1.351, have been voiced ever since the mutations had been identified at the beginning of the year.

Now, a new analysis performed by the Wits Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, which runs the Oxford Covid-19 vaccine trial in South Africa, seems to confirm some of our most negative scenarios.

According to the non-peer-reviewed study, which involved 2,000 volunteers with a median age of 31, the number of mid cases of disease were reduced by only 22% based on 42 cases of symptomatic COVID-19. Previously, before the B.1.351 become widespread in South Africa, the AstraZeneca vaccine was 75% effective.

In this context, mild disease was defined as having at least one symptom of COVID-19. Protection against moderate to severe disease, which involves hospitalization or death, was not assessed at all because the cohort was comprised of young individuals who are at very low risk.

“The AstraZeneca vaccine rollout needs to be put on a temporary halt while we get the clinical efficacy information in,” said Salim Abdool Karim, an epidemiologist at Columbia University and part of a commission advising the South African government. “And the way that we can do that is with the new approach to rollout.”

Sounds like bad news, but protection against severe disease may still be enough to save the most vulnerable

First of all, it should be said that this study assessesed vaccine efficacy, not safety. The AstraZeneca vaccine is just as safe as when it was approved by regulatory bodies — nothing’s changed there.

Secondly, the study was small and has yet to be submitted for scientific peer-review. The rather small number of recorded cases led to a broad confidence interval ranging from -50% to +60%, meaning the 22% recorded efficacy against the South African variant could vary wildly in reality, up or down.

Although protection against mild disease seems sub-optimal, to put it lightly, the efficacy in reducing the number of cases of moderate to severe disease may still be significant.

Recent data from a study sponsored by Janssen, which assessed protection against moderate to severe disease using a similar vector like AstraZeneca, found that “protection against these important disease endpoints was preserved.”

“This study confirms that the pandemic coronavirus will find ways to continue to spread in vaccinated populations, as expected, but, taken with the promising results from other studies in South Africa, such as those using a similar viral vector, vaccines may continue to ease the toll on health care systems by preventing severe disease,” said Andrew Pollard, Professor of Paediatric Infection and Immunity, and Chief Investigator on the Oxford vaccine trial.

However, this isn’t the first assessment that concludes the new South African variant is putting a dent in vaccine efficacy. The Novavax vaccine was found to have an efficacy rate of under 50% for the South African variant in a study involving 4,400 participants, compared to 86% against the British variant and 95.5% against the original coronavirus strain for mild-moderate disease. Johnson&Johnson reported a 57% efficacy against moderate-to-severe disease due to the new variant, compared to 66% for overall protection against other strains. Even the mRNA vaccines, which are the most advanced and effective against COVID-19, have run into trouble.

AstraZeneca and Oxford University are taking this threat seriously, even though their product might still offer ample protection against moderate-severe disease. Researchers have started to adapt their vaccine to B.1.351, and propose a ‘booster’ vaccine if subsequent, more robust trials determine dangerously low efficacy that may impede herd immunity.

For now, what’s clear is that the South African government is very disappointed with the results, which is why they’ve halted their vaccination program with AstraZeneca until they have better data that says otherwise. However, they ought to make a decision soon.

According to Maverick Citizen, the batch of one million doses that arrived on 1 February has an expiration date in April. The vaccine requires two shots spaced several weeks apart, which means they should be used in early March at the latest. Perhaps the vaccine doesn’t work ‘as advertised’, but can the government afford to throw them away? These will be some stressful weeks in the ministry of health cabinets in South Africa, that’s for sure.