When the pandemic began, global public health officials raised grave concerns about the vulnerabilities of Africa. But its countries overall appeared to fare far better than those in Europe or the Americas, upending scientists’ expectations.

Now, the coronavirus is on the rise again in swaths of the continent, posing a new, possibly deadlier threat.
In South Africa, a crush of new cases that spread from Port Elizabeth is growing exponentially across the nation. Eight countries, including Nigeria, Uganda and Mali, recently recorded their highest daily case counts all year.

“The second wave is here,” John N. Nkengasong, the head of the Africa Centres for Disease Control and Prevention, has declared.

When the virus was first detected, many African countries were considered particularly at risk because they had weak medical, laboratory and disease-surveillance systems and were already battling other contagions. Some were riven by armed conflict, limiting health workers’ access. In March, Tedros Adhanom Ghebreyesus, the first African director-general of the WHO, cautioned, “We have to prepare for the worst.”

But many African governments pursued swift, severe lockdowns that — while financially ruinous, especially for their poorest citizens — slowed the rate of infection. Some deployed networks of community health workers. The Africa CDC, the WHO and other agencies helped expand testing and moved in protective gear, medical equipment and pharmaceuticals.

The reported toll of the pandemic on the continent — 2.6 million cases and 61,000 deaths, according to the Africa CDC — is lower than what the US alone currently experiences in three weeks.

But that accounting is almost certainly incomplete. Evidence is growing that many cases were missed, according to an analysis of new studies, visits to nearly a dozen medical institutions and interviews with more than 100 public health officials, scientists, government leaders and medical providers on the continent.

Now, as they battle new outbreaks, doctors are convinced that deaths have also gone uncounted. Dr John Black, the only infectious-disease specialist for adults in Port Elizabeth, said he and other physicians feared that many people were dying at home. Indeed, a government analysis showed that there had been more than twice as many excess deaths as could be explained by confirmed cases in South Africa. “We don’t know what the real number is,” he said.

Scientists are also considering other explanations for the continent’s outcome. These range from the asymptomatic or mild infections more common in youth — the median age in Africa is just 19.7, about half that of the US — to unproven factors, including pre-existing immunity, patterns of mobility and climate. If those conditions helped protect against the virus earlier, officials ask, will they do so now?

In South Africa, the continent’s leader by far in coronavirus cases and deaths, the growing devastation in its medical system has led to the rationing of care for older adults. Last week, officials announced that a new variant of the virus that may be associated with faster transmission has become dominant.

With stricter control measures lifted and many people no longer seeing the virus as a threat, public health officials fear that Africa’s second wave could be far worse than its first.

New York Times News Service