CAPE TOWN – South Africa was already one of the countries worst hit by the coronavirus, but in the six weeks since a new, more transmissible variant was first publicly announced here, an enormous spike of new cases and deaths has far surpassed previous waves of the pandemic.

The variant is thought to have emerged in South Africa’s Eastern Cape province but has now been found in at least 31 countries, sparking fears its unmitigated spread to new parts of the world could usher in new waves of contagion just as the long slog of global vaccine rollout gets underway.

The variant identified in South Africa is not yet proved to be more lethal than others, including similarly highly transmissible variants recently detected in Britain and Brazil, but mutations that make it around 50 percent easier to catch have allowed it to stage a takeover of what was already out-of-control community transmission in South Africa.

“Of the cases we’ve [DNA-]sequenced in South Africa, more than 90 percent are the new variant,” said Richard Lessells, a lead researcher at the KwaZulu-Natal Research and Innovation Sequencing Platform, or KRISP, which has played a pathbreaking role in identifying coronavirus variants in South Africa and elsewhere. “It’s amazing and terrifying how quickly it came to dominate, and it does feel like we’re in the beginning stages of watching this variant, and the other new ones, become more dominant around the world.”

Its rise has led to dozens of countries imposing bans on travelers who recently have been in South Africa, including the United States.

That move closely followed an announcement by the American vaccine producer Moderna that said the antibodies its vaccine creates were less effective at neutralizing it than previously dominant coronavirus variants. The company said it was developing a new booster shot and testing out a three-shot regimen as ways to boost the vaccine’s efficacy against the variant.


On Thursday, Pfizer and its research partner BioNTech released a yet-to-be-peer-reviewed study showing its vaccine was only slightly less effective against the variant from South Africa, though the findings were limited because it only looked at the vaccine’s effect on two of the 23 total mutations in the variant.

South African studies have also documented dozens of instances of people who contracted earlier strains of the coronavirus being infected with the new variant, suggesting that those who had contracted mild cases or otherwise had low antibody counts might be prone to reinfection.

In South Africa, despite a return to a stricter lockdown and curfew, many hospitals are overwhelmed, especially in Eastern Cape, which has become the epicenter of the new variant’s spread. Harrowing statistics released this week by the South African Medical Research Council show excess mortality numbers shooting nearly straight up in all of the country’s nine provinces.

“Ambulances and family members have said they would drive from hospital to hospital for up to six hours looking for a spot to get some oxygen,” said Imtiaz Sooliman, founder of one of South Africa’s biggest charity organizations, Gift of the Givers, which has been helping distribute oxygen machines. “Doctors will tell you that people died in cars while waiting to be admitted to the casualty ward, or they died in casualty before they could be seen.”

Phumla Mnyanda, who runs a 260-bed hospital in Eastern Cape’s capital, Bhisho, said social media posts had spread misinformation on ways to avoid hospitals where people were dying, keeping an even greater number of people from coming in when they first felt symptoms. But as patients neared death, families would rush them to the hospital only to find that little could be done to save their relatives.

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“They were coming too late and by then their oxygen levels are very low, and you saw it dropping and dropping, and there is nothing we could do,” she said in a telephone interview. “People are so scared because there are so many that have died.”

The SAMRC’s excess mortality figures indicate that more than 110,000 have likely died of covid-19 in South Africa since May, even though the official toll is just above 41,000. More than 30,000 excess deaths have been recorded in January alone.

If most of these excess deaths can be attributed to covid-19, which most South African experts believe they can, then the country’s death toll would be the highest as a proportion of its population in the world.

Debbie Bradshaw, a researcher at SAMRC, said that although South Africa generally had a good reputation of registering most deaths, those that took place outside hospitals often went undiagnosed and thus escaped the official toll.

“We think that most of the confirmed covid deaths are really only being reported from hospitals, whereas there are many who leave hospitals before death or never make it to the hospitals in the first place,” she said.

Despite potentially being the cause of tens of thousands of deaths, the South African variant has been sequenced by researchers fewer than 700 times. The British variant, on the other hand, has been sequenced almost 30,000 times. Nearly 80 percent of the South African variant sequences have been found in South Africa and another 10 percent in Britain.


Twenty-nine other countries make up the remainder, but Lessells at KRISP said it was likely the variant was circulating much more widely, especially in African countries with closer economic ties to South Africa but where sequencing capacity is limited or nonexistent.

South Africa’s land borders have been closed to nonessential travel, but a long list of exceptions means thousands of people still cross them every week. They also remained open through the December holidays, when many migrant workers returned to their home countries on leave.

Some of those neighboring or nearby southern African countries, such as Zimbabwe, Zambia, Mozambique and Malawi, have seen soaring case numbers after months of relative calm.

Lessells said his lab was expecting to release sequences from samples taken from neighboring Mozambique this week.

“We’re engaged in a huge amount of collaborative science with partners around the world trying to understand what caused their rise,” he said.

The consensus, he said, is that it’s no coincidence that new variants emerged in South Africa, Britain and Brazil, which suffered some of the world’s biggest initial waves of the virus. It was likely that in places where the virus was running into large numbers of people who already had antibodies that it mutated to more easily find new hosts.

“Our failures to clamp down on community spread, wherever they may be, will almost certainly lead to even more new variants,” Lessells said.