Africa’s biggest program to halt the coronavirus is being thwarted by a global shortage of tests and a lack of capacity to process those that have been administered.

South Africa in March unveiled plans to test 30,000 people a day, only weeks after the first infection was diagnosed. Today, with more than 940,000 tests completed and 12 million people screened, its program is by far the most comprehensive on the continent.

But some 80,000 tests haven’t been processed and results can take between five to 14 days, making it impossible to isolate those who are infected and trace their contacts.

Leading epidemiologists are now calling on the government to change its strategy of trying to find infections in communities and instead focus on testing health-care workers and people who’ve been hospitalized. The Western Cape province, which is the worst affected, is already doing that.

The current strategy “would have been the right one if we could have accelerated and expanded the testing,” said Marc Mendelson, head of the division of infectious diseases & HIV medicine at Groote Schuur Hospital in Cape Town. “That just wasn’t possible, we lost that battle.”

Unprocessed Tests

South Africa has more than 50,000 cases and 1,080 deaths. Even though half of those who tested positive have recovered, new cases are rising rapidly, reaching an average of 2,229 a day in the past week.

The National Health Laboratory Service has, in a presentation, detailed challenges ranging from an inadequate supply of tests to its own limitations in processing those that have been carried out. It declined to comment further, as did the Department of Health.

“A major challenge is the speed at which the epidemic is evolving, putting enormous pressure on the response to adapt rapidly, especially in the face of limited information as well as constrained capacity and resources,” said Salim Abdool Karim, the chairman of the Ministerial Advisory Committee on the outbreak, in a May 31 editorial for Johannesburg’s Sunday Times.

South Africa should discard all unprocessed tests that are more than a few days old and immediately focus on testing hospital admissions and health workers, according to Shabir Madhi, professor of vaccinology and director of the MRC Respiratory and Meningeal Pathogens Research Unit at Johannesburg’s University of the Witwatersrand.

The status of those who’ve been hospitalized needs to be known quickly or risks rise that they don’t get the correct treatment and die, he said.

Testing capability with a 24-hour turnaround is about 20,000 tests a day, Madhi said.

“Anything more than that fuels the backlog,” he said. “Using the testing strategy in the community to try to control the rates of spread of the virus is no longer an option for us.”
Pessimistic Scenario

South Africa’s outbreak is expected to peak between late July and early September, with experts predicting last month that deaths could reach between 35,000 to 50,000 this year.

Epidemiologists, including Madhi and Karim, say a stringent five-week lockdown imposed in late March bought the government time to slow down the epidemic and prepare hospitals. Still, there are concerns that the Western Cape will soon run short of intensive care beds. Other parts of the country may follow.

The trajectory of the outbreak “looks very much like the models in the more pessimistic scenario,” said Mendelson. “It’s going to be a huge challenge.”