PORT ELIZABETH, South Africa — At the center of a terrifying coronavirus surge, 242 patients lay in row after row of beds under the soaring metal beams of a decommissioned Volkswagen factory.
Workers at the vast field hospital could provide oxygen and medications, but there were no I.C.U. beds, no ventilators, no working phones and just one physician on duty on a recent Sunday — Dr. Jessica Du Preez, in her second year of independent practice.
In a shed-like refrigerator behind a door marked “BODY HOLD,” carts contained the remains of three patients that morning. A funeral home had already picked up another body.
On rounds, Dr. Du Preez stopped at the bed of a 60-year-old patient, a grandmother and former college counselor. Her oxygen tube had detached while she was lying prone, but the nurses had so many patients they hadn’t noticed. Now, she was gone.
As two porters placed her corpse in a bag, a worker peeked through the door to tell them another patient, a 67-year-old diabetic man, had died.
Meanwhile, the condition of a teacher in her 50s was deteriorating. Dr. Du Preez tried to find I.C.U. space for her elsewhere in the city, to no avail. She called the teacher’s husband, who asked what he could do. “Not much,” the young doctor responded.
“Shame,” she said again and again that day.
For hours, the alarm on the teacher’s bedside monitor bleated. Her oxygen level was dangerously low, her pulse racing and her blood pressure soaring. Still, she remained conscious, saying she could not breathe. That evening, she died alone. A book, “A Heartbeat of Hope: 366 devotions,” lay on her bedside stand alongside a pair of reading glasses.
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, with deaths mounting. 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 Centers 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 World Health Organization, 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 C.D.C., the W.H.O. 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 C.D.C. — is lower than what the United States 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.
“It is possible and very likely that the rate of exposure is much more than what has been reported,” Dr. Nkengasong said in an interview.
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 United States — 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.
“The risk perception has gone from something very scary at the beginning to now something people are not worried about anymore,” said Dr. Chikwe Ihekweazu, director-general of the Nigeria Center for Disease Control.
Some Africans view Covid-19 as an affliction of Westerners and wealthy travelers. In a classroom in a Somali community displaced by drought and war, a fourth grader readily identified the United States as having the most cases. “Donald Trump was Covid-19-positive,” he said.
Sarah Oyangi, 35, an apartment complex manager who lives in what she refers to as a slum in Nairobi, said friends told her they weren’t worried because the virus “is for wazungu and the rich,” using a Swahili word meaning European or white people. “It’s not our disease.”
Dr. Nkengasong said he was very worried about how long it would take to vaccinate enough people on the continent to protect the most vulnerable from unwitting spreaders.
A global effort to help low- and middle-income countries aims for 20 percent coverage at most by the end of 2021, a third of what African leaders say is needed. “The U.S. is not going to target 20 percent of its population. Europe is not going to target 20 percent of its population,” he said. “Why do you think in Africa we should?”
The First Wave
The first case on the continent was detected on Feb. 14 in a foreign traveler from China to Egypt. Two weeks later, Nigeria discovered that a contractor who had flown in from Milan was ill. In South Africa, the earliest cases involved a half-dozen or so people who had gone skiing in Italy. The W.H.O.’s regional director for Africa reported on March 19 that infected travelers from Europe had come into 27 or 28 countries.
Early on in sub-Saharan Africa, only South Africa and Senegal had supplies to perform diagnostic tests, but with aid, every country on the continent was later able to do some testing.
As the virus overwhelmed the West’s advanced health systems, governments across Africa, with some notable exceptions, imposed stringent curfews and lockdowns. Some countries had only a few cases at the time; Zimbabwe declared a national disaster without having announced one.
“They went into shutdown because we were terribly ill prepared,” Dr. Nkengasong said. But that desperate action may have put Africa ahead of the curve in fighting the virus, instead of behind it, as the United States and Europe found themselves.
Dozens of African health ministers agreed on a continental strategy in February, coordinating closely through the Africa C.D.C. West African nations also built on lessons from the Ebola response in 2014 and 2015.
South Africa shut schools, curbed travel from high-risk countries and restricted mass gatherings. “For the first three weeks, our epidemic was growing on track, almost case for case, with the British epidemic,” said Dr. Salim S. Abdool Karim, a top infectious-disease expert. Then “the pandemic just turned,” he added. “It slowed.”
Later, the country prohibited alcohol sales, which led to a drop in car accidents, assaults and shootings, freeing up hospital capacity to treat Covid patients. The police and military enforced the measures, arresting thousands and killing several.
Eventually, the government eased the restrictions, finding the economic cost too steep. Cases soared and hospitals were pummeled. South Africa brought in outside help: 200 physicians from Cuba, medical staff from Doctors Without Borders and scientists from the W.H.O. By late August, the numbers dropped.
Roughly 3,000 miles away, and at the other end of the economic spectrum, Somalia had also imposed a lockdown. The country had a 70 percent poverty rate; the restrictions hit subsistence workers hard and also delayed childhood vaccinations. “African countries have followed the footsteps of all the other countries without understanding if it’s the best thing to do,” said Dr. Mamunur Rahman Malik, the W.H.O. representative in Somalia.
Closed borders and canceled domestic flights impeded the flow of lifesaving equipment and outside experts. Soon, about 150 health facilities in far-flung rural areas ran out of medical supplies, and international agencies had to charter flights to keep them stocked.
The agencies also felt obliged to send ventilators, costing up to $ 25,000 each, to poorly equipped countries. But Somalia, which has one of the lowest ratios of doctors and nurses to population in the world, did not have enough personnel trained to operate them.
That was the case with De Martino, a Covid hospital in Mogadishu, which had no I.C.U. or even basic fever medicine, according to its director, Dr. Abdirizak Yusuf Ahmed. Unable to secure medical oxygen for its patients — a problem throughout Africa — the hospital bought tanks from an industrial supplier, built a Rube Goldberg-like network of pipes to the isolation wards, and assigned technicians to switch out empties around the clock.
the top 50 in Covid deaths
the top 50 in Covid deaths
Somalia exploited one advantage: a system of hundreds of polio workers that extended from the capital to remote rural areas. Employed by the W.H.O., they were redirected to inform people about the pandemic and help identify cases. Community workers have detected about 40 percent of its 4,690 known infections, according to Dr. Malik, the W.H.O. representative.
But about half the country was not reporting any cases at all. Laboratory workers fanned out; in terrain controlled by the Shabab terrorist group, some were driven away. Elsewhere, they found a high number of cases in several districts where the virus had never before been documented.
With widely varying rates of testing and data collection across the continent, public health officials are struggling to assess the pandemic’s reach. In more than a half-dozen countries, antibody tests suggest that the virus has spread far more widely than reported, according to research involving blood donors, pregnant women, H.I.V.-positive people and hospital staff.
Many African countries are planning much broader sampling. But financial and political realities often cause delays. That happened in Hargeisa, Somaliland, when health officials one recent morning debated which districts should bear the cost of notepads, pens, pencils and cellphone airtime.
Participants also objected that some areas were excluded from the survey, which they attributed to planners in Mogadishu, the capital of Somalia, from which Somaliland declared its independence in 1991 after a civil war.
Determining the death toll is especially challenging. Only a third of the nations on the continent record and report annual deaths, according to the U.N. Economic Commission for Africa, many not meeting international standards.
But South Africa offers clues. An estimated 60,000 more people have died there than would normally be expected; fewer than half have been attributed to Covid-19. Disrupted health services may account for some of them, but researchers believe that many fatal Covid cases have gone undetected.
Older adults, people with chronic health conditions and those admitted to public, rather than private, institutions are more likely to die, according to the country’s National Institute for Communicable Diseases. White South Africans have been hospitalized for the coronavirus at higher rates than their share of the population, probably because of their higher average age. But the institute found that when controlling for age, Black, Indian and mixed-race South Africans were more likely than white South Africans to die of the disease in hospitals.
Still, experts generally believe that fatalities on the continent are far lower than in the West, potentially for reasons beyond demographics. For instance, countries that regularly immunize babies with a tuberculosis vaccine also tend to have lower coronavirus mortality, though a causative link has yet to be proved.
To achieve widespread immunity, more targeted vaccines are needed, like those now rolling out in the United States and Europe. Most African countries have not struck direct deals with Western vaccine makers, though some are importing Chinese-made vaccines not yet vetted by stringent regulators. The continent itself has little vaccine-manufacturing capacity. Biovac, a company in Cape Town, was trying to find a partner and would need up to a year to begin filling vials.
But Africans have played an important role in developing coronavirus vaccines. In Durban, Senzo Maloyi, 30, volunteered for a clinical trial of the Johnson & Johnson vaccine, as part of the United States’ Operation Warp Speed. “By us participating, if it does go well, we’ll be helping a lot of people,” he said. There was no guarantee, though, that those who’d be helped would be in South Africa.
A Rattled Health System
Last month, South African officials thought they had a brief opportunity to douse hot spots of infection in the Eastern Cape before they spread across the country.
Crowded post offices, college dormitory parties and migrant farmer encampments were potential sources of outbreaks. So were the traditional three-week initiation retreats where an expected 50,000 18-year-old boys would undergo circumcision in December and January.
The government imposed a nighttime curfew in Port Elizabeth and limited alcohol sales and the size of gatherings. A proposal to screen nearly all adults in the most affected areas, though, was dropped after a pilot project strained labs.
Meanwhile, cases mounted, highlighting the health system’s inequalities. Most South Africans rely on public health services; only 14 percent get medical care from better-endowed private providers. In Port Elizabeth one recent day, 57 of the 59 patients on ventilators were in private hospitals.
Even the private sector was hard-pressed in the outbreak. Dr. Hlanjwa Maepa, the sole pulmonologist at Netcare Greenacres Hospital, spent her day attending to nearly 40 coronavirus patients, inserting breathing tubes and catheters and not stopping once in 12 hours to take off her protective equipment to eat or use the toilet.
The hospital was not proning Covid pneumonia patients — turning them on their bellies — even though evidence shows that it improves oxygen levels and reduces the need for ventilators. “We don’t have enough manpower to do it,” Dr. Maepa said.
The 16-bed I.C.U. was full, and she shifted patients like puzzle pieces to make space for the sickest. A wealthy executive begged her to save him because his affairs were not in order, asking to buy his own ventilator and be treated at home. A middle-aged man sobbed as he visited his dying wife. “There’s a mountain coming, and I may not be able to get over it with her,” Dr. Maepa told him. “But we’re trying either way.”
The scene inside two of the city’s public hospitals was more dire. Dozens of medical workers were out sick, and patients stayed hours, sometimes days, in crowded observation rooms awaiting ward admission. One aging hospital, Dora Nginza, lacked an I.C.U. and was rushing to finish a renovation because it could not properly isolate patients. The physician in charge, Dr. Lokuthula Maphalala, spent her shift pushing stretchers and lifting patients. The other public hospital, Livingstone, had to refuse most patients who needed transfer to the I.C.U. “These cases and faces come back to you,” said its director, Dr. Lizette van der Merwe.
At the nearby field hospital in Port Elizabeth, doctors were forced to ration. Dr. Black, the infectious-disease specialist, saw that an 84-year-old man had been placed on a high-flow oxygen device, a decision he said was “completely against” the protocol tacked to a wall, labeled “Allocation of Scarce Critical Care Resources During the COVID-19 Public Health Emergency.”
“If I need it, I’m going to take it away from him, because he’s not a great candidate,” Dr. Black said.
According to the guidelines, patients more than “mildly frail” at baseline, including those who “often have problems with stairs” and need minimal help with dressing, were to be denied critical care. Other patients were to be divided into low-, medium- and high-priority groups based on pre-existing conditions and degree of illness, with age groups as a tiebreaker.
In practice the procedure was cruder. If you’re 60 with another health condition, “the chance of you getting into an I.C.U. is close to zero,” Dr. Black said. “I have patients dying here in their 30s who couldn’t get into a hospital, and now I.C.U.s are full.”
That night, the nursing staff wound through the wards singing hymns and the Lord’s Prayer. A nurse who sang in her church choir beat an empty water bottle against a cardboard box labeled for compliments and complaints.
‘Killing People Silently’
In Howlwadaag, a rubble-filled settlement in Hargeisa for Somali and Ethiopian refugees displaced by conflict and drought, the risks of transmission were evident. Residents live among prickly cacti, sleeping in crowded corrugated sheet metal shacks and rounded cloth-covered dwellings. Polio outreach workers advised residents to sleep separately if sick and wash their hands often. But community members said they could not afford soap.
A woman complaining of a cough and difficulty breathing rejected the advice of health workers to go to the hospital one day this month. “I’m afraid of people not being able to come see me,” said Khadra Mahdi Abdi, adding that the price of transport was too steep.
In the region, the pandemic often inspires denial. Restaurants are busy, social distancing rare, large family gatherings common. Mask wearing carries a stigma.
“People are watching you and point their fingers at you and say, ‘This is corona man,’” said Hassan Warsame Nor, a senior lecturer at Benadir University, in Mogadishu, who led a Unicef study of attitudes in Somalia’s capital.
And resisting medical treatment is routine.
At Hargeisa’s designated Covid hospital, Daryeel, five patients separated by empty metal frame beds lay beside hissing oxygen tanks, with handwritten medication orders taped to the walls. Nurses swatted away flies that flew in through windows facing a courtyard, where patients were sometimes rolled for a dose of sunshine and bird song. Most had a family member attending them, which the hospital director, Dr. Yusuf M. Ahmed, felt compelled to allow.
He said that about 80 percent of patients scheduled for transfer to Daryeel after testing positive at the main public hospital never showed up. People were dying at home. “The virus is now killing people silently,” said Dr. Hussein Abdillahi Ali, a junior physician there.
Judging by the condolence pages on Facebook, the director said, Covid-19 has come back “with a vengeance.”
At least two of those hospitalized that day later died. “Patients are coming at a late stage,” he said. “It’s much harder than the first round.”
At the Baqiic cemetery on the outskirts of Hargeisa, about 50 men and boys gathered at a grave site this month to bury a family matriarch who had died of unknown causes. Their shovels hit the ground in a frenzy, causing a plume of earth to rise in the air like smoke.
A caretaker at the cemetery’s entrance produced a notebook with handwritten entries for the deceased. Because families often dug graves for their loved ones, he said, he logged only some of the burials and did not share his list with the government.