Africa’s first COVID-19 wave was atypical. Its second could be, too.

Coronavirus cases are rising again in several African countries and could undo gains made earlier in the pandemic. Experts fear a more devastating second surge could be caused by relaxed restrictions, mounting COVID-19 fatigue, the emergence of a new variant in South Africa, and the upcoming holiday season.

“We are very close to where we were at the peak of the pandemic in July and August,” said John Nkengasong, director of the Africa Centres of Disease Control and Prevention in Addis Ababa, Ethiopia, via a virtual news conference on December 17. “My projection is that, with the holiday season, we will probably exceed that number by January or February."

But Africa’s pandemic response isn’t a continental monolith; rather, more than 50 countries are on separate COVID journeys. National Geographic took a closer look at three of them, in which unexpected outbreaks, death surges fueled by stigma, and puzzlingly places defined by abundant spread but low hospitalization rates have made it difficult to predict the course of the pandemic.

When COVID-19 sprouted in Africa, governments responded swiftly. Most closed their borders, some even before registering a single case. They imposed harsh lockdowns, or at least banned gatherings, and insisted on mask-wearing in public—actions that health experts say helped keep the first wave of the pandemic manageable.

This time around, however, most of the continent is not returning to lockdowns to curb its rising case numbers. And Africa is unlikely to receive a substantial volume of vaccines until the middle of next year, experts say. Adherence to interventions like social distancing and mask-wearing will be vital to preventing rapid spread, Nkengasong said.

Africa’s state of play

Africa’s COVID-19 numbers have remained mercifully low this year. Despite being home to 17 percent of the world’s population, the continent has only reported 3.4 percent of global COVID-19 cases and 3.5 percent of deaths.

The continent’s youth is one obvious reason. Africa’s median age is below 20, half that of the United States, and older adults are more likely to develop severe cases of the disease. Some scientists believe the warmer climate is playing a role, as it allows people to spend more time outside where COVID-19 risk is lower. Other researchers believe exposure to parasitic infections or other widely-circulating coronaviruses—such as those that cause the common cold—could have primed African immune systems to fight COVID-19. But there is little evidence so far to support these theories.

Early in the pandemic, many health experts worried that Africa’s high burden of other diseases and ill-equipped healthcare systems might cancel out the benefits of its youthful population. But those fears didn’t come true. Few African countries have seen their hospitals overwhelmed with severe COVID-19 cases, and the proportion of asymptomatic patients is 80 percent in Africa—higher than elsewhere—says the World Health Organization.

Still, as Nkengasong has repeatedly pointed out in recent weeks, complacency going forward into 2021 could prove deadly. New COVID-19 cases in Africa peaked in July and August at around 18,000 per day before dropping to 7,000 a month later. Since then, they have grown and, in mid-December, are threatening to break records.

South Africa: An unexpected rise

South Africa, one of the continent’s most industrialized countries, had hoped that the combination of summertime and acquired immunity from the first wave would hold the coronavirus at bay over the economically significant Christmas holiday season. In the past month, however, the virus has made an unexpected comeback and is spreading faster than ever.

By the end of August, more than 14,000 South Africans had lost their lives to COVID-19, even though the first wave had peaked a month earlier with fewer active cases than predicted by the country’s most optimistic disease models.

That initial wave abated by September, which was surprising given that the government had begun easing restrictions in May, according to Juliet Pulliam, director of the South African Centre for Epidemiological Modelling and Analysis in Stellenbosch. Pulliam believes the spread was curbed by mask-wearing and handwashing, combined with rapidly rising immunity levels due to fast-spreading infections. This theory was backed by a survey in late July of pregnant mothers and people living with HIV in Cape Town’s poor suburbs, which found that around 40 percent of them had antibodies against the SARS-CoV-2 coronavirus, an indicator of potential immunity.

As spring arrived in the Southern Hemisphere, neither Pulliam nor any of her colleagues on the country’s coronavirus modeling consortium expected a second wave before Christmas—and then a sudden spike in cases arrived in the Eastern Cape province in November. Incidents are rising in December in other coastal cities like Cape Town and Durban, where student end-of-year parties sparked super-spreader events.

“There can no longer be any doubt—the country has entered a second wave of coronavirus infections,” South African president Cyril Ramaphosa announced in a December 14 televised address. Four days later, the county’s scientists identified a new coronavirus variant dubbed 501Y.V2, which they think could transmit more easily between people and could be driving the second wave. While 501Y.V2 shares some mutations with another variant thriving in the United Kingdom, the pair arose separately.

Before the new variant was common knowledge, Pulliam’s best explanation for the resurgence of coronavirus in South Africa was that the country eventually reached a tipping point after the economy reopened akin to other nations in Europe and North America, and people became more relaxed about social distancing and other restrictions. With southern hemisphere summer holidays coming up, there’s a concern that many South Africans who travel to see their families will further speed up the spread, she adds.

The nation’s second wave started in the harbor city of Port Elizabeth, the Eastern Cape’s largest metropolis. By mid-November, infection rates, hospital admissions, and deaths were higher than during the previous peak in July. Several hospitals reported having to turn people away because their wards were full. Many people were likely dying from COVID-19 without a diagnosis: The city recorded 420 more deaths than usual the penultimate week of November—the rest of the province only recorded 250 official COVID-19 fatalities over the same period.

Port Elizabeth’s coronavirus flood spilled into nearby villages and towns as well. In Kenton-on-Sea, a popular beachside tourist town a little over an hour’s drive up the coast, local doctors treated severe COVID-19 patients in their homes because the intensive care beds in Port Elizabeth were full. The community has pulled together to care for the sick, says local physician Eleanor Galpin. She says a retired anesthesiologist helped her with the oxygen setup for very ill patients.

On December 3, Ramaphosa tightened Port Elizabeth’s coronavirus restrictions. To relieve the pressure on hospitals, officials told shops they could only sell alcohol from Monday to Thursday, and nightclubs had to close by 10 pm. A little over a week later, the South African president extended these restrictions nationwide and closed access to many of the country’s beaches—a blow for the seaside communities that depend on December holidaymakers.

Still, the restrictions this time around are a far cry from the harsh lockdown introduced earlier this year, says Tom Moultrie, professor of demography at the University of Cape Town. The government has “shied away” from hard lockdown in the recent surge, he says—something he attributes both to the extensive spread of new cases, as well as the economic consequences of hard lockdowns. The coastal outbreaks, combined with holiday travel, create a “very real” prospect of a nationwide resurgence in early 2021, Moultrie says.

Zambia: Stigma fuels at-home deaths

The first clues arrived in July when autopsies of Zambia’s dead kept testing positive for COVID-19. Though coronavirus takes days to weeks to truly devastate organs, this time window wasn’t large enough, and people were dying before they could even seek care. As a result, the nation’s hospitals weren’t overrun with patients, but their morgues took a toll.

By early September, such “brought in dead” casualties made up almost 75 percent of Zambia’s official pandemic count of 295 individuals. In a paper published in October, biomedical scientist Mischeck Chileshe and his colleagues wrote that Zambians weren’t only reluctant to seek healthcare for COVID-19 but that some were also increasingly embracing a perception that the illness is not real. Chileshe says fear of testing, isolation, and lost income has likely dissuaded many people from looking for medical care. Had they been admitted to a hospital, their outcomes could have been vastly different. “I personally think most of them could have been saved,” he says.

Zambia, a lower-middle-income country with a population of 17 million, has not seen a reemergence in coronavirus since its August peak. As of December 18, its official toll—including those brought in dead—was 18,575 cases and 373 deaths. Yet last month, health minister Chitalu Chilufya warned that Zambians were becoming complacent. He urged them to wear masks in public once more and keep their distance or risk a second wave of COVID-19.

If cases bounce back, Chileshe worries that stigma will once more prevent Zambians from getting tested and treated in time. The hidden toll could be significant in Zambia’s rural areas, where around 40 percent of the population lives, he adds.

People who die in those areas are less likely than town-dwellers to be brought to morgues, a legal requirement in the country, but only urban or peri-urban areas strictly enforce it, he explains. “So in the villages, when somebody dies, they are usually just buried,” he says.

Ghana: Missing the mild cases

In West Africa, Ghana saw an uptick in cases as the country geared up for its December election. Since then, daily incidents have dropped again—but official cases are likely a vast undercount of actual infections, scientists in the country have discovered.

Yaw Bediako is one of the millions of Ghanaians who cast their ballots in the country’s general election on December 7. He says the voting stations had hand-washing stations, and voters adhered to pandemic protocols like social distancing.

“I must admit I was impressed,” says the Accra-based immunologist, who has pivoted from studying malaria to COVID-19 since the start of the 2020. Earlier this year, a different picture greeted Bediako and his colleagues at the West African Center for Cell Biology of Infectious Pathogens (WACCBIP). They set out to test more than 1,300 people for SARS-CoV-2 antibodies in Accra, the country’s capital, from July to September.

“Most people were maskless” in the markets and transport hubs surveyed by the scientists, says Peter Kojo Quashie, the virologist who co-led the study. “If you went out in public wearing a mask, people would look at you funny.”

When COVID-19 arrived in Ghana in March, officials locked down activities for three weeks. As restrictions eased and deaths stayed low, the government became preoccupied with election preparations, possibly to the detriment of Ghana’s testing and tracing efforts, says Quashie. Tidy polling stations were a welcome contrast from the crowded election rallies that many health experts feared would spread the virus. Now, with the election done, there’s hope that the government will once more turn its focus on the novel coronavirus, which Quashie says is much more widespread in the country that its politicians have wanted to admit.

Ghana has documented more than 50,000 infections to date, with cases spiking in July and August. Since the peak, new incidents have, on average, hovered around 100 per day. However, these official numbers are likely a vast undercount. In their study, which has been presented but is yet unpublished, Quashie and Bediako found that one in every five people in their random sample tested positive for SARS-CoV-2 antibodies, indicating that they had likely previously caught the virus.

Even if that infection rate were limited to the capital and its 5 million inhabitants, it would still translate to one million cases—a twenty-fold increase in official countrywide data. Quashie and Bedikao believe such estimates are closer to the truth, and they also think that the drop recorded after the first ‘wave’ might be an artifact of testing efforts that have focused more narrowly on travelers and severe cases in recent months than they did at the start of the outbreak.

However, with only 331 nationwide deaths reported as of December 18 and with hospitals not yet showing significant strain, it’s clear that something unusual is going on in Ghana. “COVID is freely spreading in our community, but it appears that our mortality rates are significantly lower than what we see in a lot of the world,” Bediako says.

Bediako and his colleagues—as well as other scientists around the continent—are puzzled as to why this might be. Bediako’s boss, WACCBIP director Gordon Awandare, says his preferred theory is that people in Ghana could have a higher tolerance to inflammation because they are bombarded with pro-inflammatory infections like malaria.

A few years ago, Awandare was part of a team that showed that Ghanaians who live in areas where there are lots of malaria infections have less intense inflammatory responses to the parasitic disease than those in urban areas where malaria was rarer. Such tolerance could, in theory, help Africans fight COVID-19, as it’s thought to be the body’s overblown inflammatory response that causes severe disease and death, he says. “That’s what may be protecting us.”

Even so, neither Quashie nor Bediako thinks it is time to relax. The epidemic has been managed so far, but it might not remain so, they say, primarily if the virus spreads to remote areas where people have poor access to healthcare.

“Without a vaccine, COVID [will be] in Ghana for quite a while,” says Bediako. “It will not be killing as many people as elsewhere, but people are still dying from it. So we can’t take it lightly.”