CAPE TOWN, South Africa — This city at Africa's southwestern-most tip stands out for a number of reasons — its extreme economic inequality and remarkable scenery among them — but burgeoning hot spots of coronavirus cases have distinguished it anew. The city accounts for 60 percent of cases in South Africa, 15 percent in sub-Saharan Africa and 10 percent in Africa as a whole.

South African epidemiologists are looking to the city — with more than 9,300 cases as of Tuesday — to provide insight into how the virus is spreading on a continent that has largely escaped the waves of death seen in Western Europe and the United States.

The early answer, officials and experts say, is two-pronged. First, the city welcomed more tourists from hard-hit regions of the world than did other places in Africa, meaning the coronavirus was widely seeded here early. Second, major hot spots emerged in two supermarkets and a pharmaceutical factory that supercharged the virus’s spread.

“This is really about a small number of so-called super-spreader events,” said Salim Abdool Karim, an infectious-disease expert and chair of the government’s coronavirus task force. “Too many people were going to the supermarkets, and they didn’t have the right procedures early enough. It just takes one person, and everything in there is contaminated — the baskets, the metal surfaces — just by breathing.”

Karim and others said Cape Town’s hot spots are likely forerunners of what will happen in the rest of the country, and even the continent, in coming weeks as lockdowns and other restrictions are relaxed.

South Africa began targeted testing in Cape Town on April 7, and since then, the number of positives as a proportion of tests has only gone up. While the rest of the country, which is under strict lockdown, is seeing positive rates hover around 2 percent, Cape Town’s rate is regularly above 10 percent and spikes above 15 some days.

The country has more than 16,000 confirmed cases. At first, they seemed to be clustered in Johannesburg and Durban, South Africa’s first- and third-largest ­cities. At that point, cases were growing exponentially, but after a lockdown went into effect on March 27, growth slowed in those cities. Less than a month later, Cape Town had eclipsed them, and it has accounted for most of this month’s positives.

The working-class areas of Tygerberg, which is mostly mixed-race, and Khayelitsha, which has an almost entirely black population, have been the hardest-hit and make up the majority of Cape Town’s cases. Some experts cautioned against jumping to conclusions based on that geography, given that testing is most aggressive in known hot spots, and say there may be areas where cases have been largely asymptomatic.

“The testing centers are very much linked to where the hot spots are,” said Marc Mendelson, who oversees the infectious-
diseases division at the city’s Groote Schuur Hospital. “If you’re screening for symptoms and testing in hot spots, you’re going to pick up more” positive cases.

The high caseload has led some leaders to question the government’s early approach, which allowed tourists from hard-hit countries to enter the city. Flights continued through late March, and testing at the airport was largely limited to temperature checks, which don’t catch asymptomatic travelers.

“We had our temperature tests at the airport, but they weren’t picking up the virus,” said Alan Winde, the leader of Western Cape, the province that includes Cape Town.

Winde is in self-imposed quarantine after coming into contact with a TV cameraman who died last week of covid-19, the disease caused by the coronavirus. On Sunday, Winde met virtually with about 80 epidemiologists, as he does every week, to parse the data. Many in the group caution that beyond the existence of the hot spots, much is still unknown about how and where the virus spreads.

“I get asked every single day, why is this the epicenter?” Winde said. “We don’t have all the answers.”

South Africa began a three-week lockdown on March 27, as the country recorded its first coronavirus-related deaths and the number of known cases rose to 1,000. (Reuters)

South Africa has applied one of the most stringent approaches to containing the virus in Africa with a nationwide lockdown. It sent tens of thousands of health-care workers into communities to screen and test, rather than wait for cases to show up at hospitals. It even banned the sale of alcohol, which sends thousands to emergency wards every month, as a way to keep intensive care beds open. More than 300 people have died of covid-19 in South Africa.

Winde said current projections show as many as 80,000 symptomatic infections in Western Cape by late July.

“It has been building in the last couple of weeks,” Mendelson said. “People say, ‘Are you ready for it?’ The answer is, as best we can, but it is going to get ugly.”

South African President Cyril Ramaphosa announced last week that by the end of May the government will transition its lockdown to a tiered approach, in which areas with hot spots will have more restrictions than those without. The cities of Cape Town, ­Johannesburg, Pretoria, Durban and Port Elizabeth are likely to remain at higher alert levels given current case trends.

A new concern, Winde said, is the growing backlog in testing in both government and private laboratories.

“We have a backlog of about 11,000 and Johannesburg has about 15,000 because all of a sudden our national health laboratories and the private sector are running at maximum,” he said. “If we’re not testing sufficiently and not getting our answers back quickly enough — it’s taking anywhere between six and 10 days to get a result — then that is really useless.”

The lockdown, while credited with slowing the spread of the virus in the rest of the country, may have had the unintended effect of quickening it in Cape Town — evidence of the virus’s unpredictable nature, according to Karim. The hot spots in Tygerberg and Khayelitsha were probably driven by the lockdown’s closure of spaza shops, akin to corner stores, that in turn drove many people to crowded supermarkets.

“That’s how this virus spreads, through hot spots. It’s not like HIV, which goes slowly from person to person. A contaminated environment leads to an outbreak, plain and simple,” Karim said. “It’s a matter of identifying them as rapidly as possible. Sometimes it’s too late — you only see the flames when it’s a full fire.”

Bearak reported from Nairobi.