Last week, Cyril Ramaphosa stood flanked by senior ministers on the tarmac of OR Tambo International Airport, Johannesburg, to welcome the first batch of 1m doses of the Oxford/AstraZeneca Covid vaccine to the country.

“Today marks a major milestone in our fight against the coronavirus pandemic,” South Africa’s president said, effectively firing the starting gun on the immunisation campaign in the continent’s worst-affected nation. “This batch will benefit our healthcare workers who have been at the forefront of keeping us all safe,” Ramaphosa added.

A week later, those plans are in tatters. South Africa has temporarily halted the rollout of the Oxford/AstraZeneca vaccine after a Witwatersrand university study appeared to show that it offered little protection against mild and moderate disease caused by the 501. V2 viral variant first identified in South Africa. The study has yet to be peer reviewed and did not assess severe disease.

That study, first reported in the Financial Times, has left scientists scrambling to figure out its implications for the likely effectiveness of the Oxford/AstraZeneca vaccine, and other jabs, as the virus mutates.

How South Africa, where the 501. V2 strain accounts for at least 80 per cent of new cases, modifies its vaccine strategy in response will be the subject of intense scrutiny.

Line chart showing seven-day rolling average of new cases per 100,000 people in South Africa, Botswana, Namibia and Egypt

“If it is confirmed that the vaccine doesn’t protect against severe disease and death caused by the South African variant, we have a massive problem,” said Peter Piot, director of the London School of Hygiene and Tropical Medicine.

However, Piot stressed that other vaccines, including the Johnson & Johnson jab, showed protection against severe disease and death caused by the 501. V2 variant, meaning that there were still tools to work with.

So far, 45,000 South Africans have officially died of Covid-19 and nearly 1.5m of the 60m population have tested positive for infection. Pretoria’s immediate plan is to switch to the J&J vaccine. J&J has submitted a so-called rolling application to the South African Health Products Regulatory Authority and is expected to submit additional data shortly.

Helen Rees, who chairs the health regulator, told the FT: “There is a consensus among scientists in South Africa, supported by the minister of health, that the rollout of the Oxford/AstraZeneca vaccine should be put on temporary hold, but that the rollout should continue with other vaccines which have demonstrated efficacy against the variant.”

South Africa has also secured 20m doses from BioNTech/Pfizer for delivery in the second quarter, plus 110,000 BioNTech/Pfizer doses through Covax, the vaccine distribution facility, which should start arriving this month. There is no clinical data for BioNTech/Pfizer’s vaccine against the 501. V2 variant but laboratory studies showed a strong antibody response.

Early doses of J&J and BioNTech/Pfizer will go to 1.5m-2m healthcare workers, before the health ministry moves on to its target of immunising 40m people, or two-thirds of the population, by the end of this year in a push for herd immunity. However, even before the Oxford/Astrazeneca setback, several health experts, including Dr Shabir Madhi, leader of the Wits study, had called those plans unrealistic.

After the study was released, Madhi said Pretoria might consider shifting “the focus from the goal of herd immunity against transmission to the protection of all at-risk individuals in the population against severe disease”.

In all, South Africa has ordered 9m doses of the J&J vaccine and is expecting deliveries in time for a mid-February rollout. J&J has also contracted Aspen, a South African pharmaceuticals company, to complete production of up to 300m doses of its vaccine for global delivery, but these are unlikely to start coming off the production line for several months.

J&J said it was “in advanced discussions with the South African government about potential additional collaborations to combat Covid-19 in the country” and that further announcements were expected soon.

Dr John Nkengasong, director of the Africa Centres for Disease Control and Prevention, said Pretoria was right to halt use of the Oxford/AstraZeneca vaccine while it investigated further. “The key word is ‘temporary’,” he said. “They should step back and take a look. It’s not a disaster, it is a cautionary measure.”

But, Nkengasong said the study was of concern not only for South Africa but for the rest of the continent where the Oxford/AstraZeneca vaccine formed what he called “the backbone” of the immunisation strategy. Some 500m doses have been ordered through the African Union and several hundred million doses more through Covax.

The World Health Organization said that it had identified cases of the variant in Botswana, Ghana, Kenya, Comoros and Zambia, as well as in 24 non-African nations. However, many African countries lack the capacity to detect the new strain on a systemic basis, said Nkengasong, adding that the continent needed to dramatically ramp up its genomic testing ability.

Fatima Hassan, founder of South Africa’s Health Justice Initiative, a group campaigning for equitable access to vaccines, said it was urgent for vaccines already demonstrating high efficacy to be tested further in regions where those variants were circulating. “If it does work . . . then those are the vaccines that you have to share with the world and ramp up manufacturing capacity,” she said.

The rapid emergence of variants, said Piot, showed the importance of other measures, including contact tracing, to keep ahead of the pandemic. “Vaccine developers and regulators should as soon as possible start developing effective vaccines against the critical variants,” he said.

Additional reporting by Hannah Kuchler in New York