Government has rolled out an intensified screening and testing campaign in the hope of finding more Covid-19 cases during and after the lockdown period, but the disparity between the country’s testing capacity and the actual number of tests being conducted remains substantial. South Africa probably used less than a third of its Covid-19 testing capacity in the last week.
The extent of Covid-19 testing being conducted in the country will likely be an important factor in the decision over whether or not to extend South Africa’s current lockdown and what measures should follow the lockdown. The World Health Organization advises that when countries weigh up whether or not to lift social distancing restrictions, they should consider whether “health system capacities are in place to detect, test, isolate and treat every case and trace every contact”.
South Africa’s National Health Laboratory Service (NHLS) previously told Spotlight that it is able to do 15 000 tests a day, and plans to increase that to about 36 000 by the end of April. However, statistics released by the National Institute of Communicable Diseases (NICD) indicate that South Africa has been doing only 3 000 to 5 000 tests on most days over the last week.
On Saturday evening Minister of Health Dr Zweli Mkhize said during an online media briefing that just over 7 000 people had been tested over the preceding 24 hours. In the weeks before the lockdown the tests conducted per day mostly varied from 1 500 to 3 000.
According to the figures provided on Saturday evening around 108 000 people have been tested for the Covid-19 virus in South Africa and a total of 123 000 tests have been conducted (the difference reflecting that some people have been tested multiple times – for example to confirm recovery from Covid-19).
Are provinces requesting too few tests?
The NHLS previously explained the gap between their claimed 15 000 daily capacity and the actual number of tests of 3 000 to 5 000 to Spotlight as partly due to the Provincial Departments of Health not requesting more tests and indicated that they would welcome provinces requesting more tests.
Spotlight asked the three hardest hit provinces about this and requested that they share their testing numbers. (Testing refers to taking a sample from the nose or throat and testing it in a laboratory while screening refers to asking people about their symptoms and for example taking their temperature.)
Just over a third of South Africa’s confirmed Covid-19 cases are in Gauteng, with the majority being in Johannesburg.
The Provincial Command Council said on 16 April that during this month the community screening efforts “screened 196 421 people, out of whom 2 591 people were referred for testing and were indeed tested”. This results in a rough estimate of 160 tests per day from community referrals, but the province’s total number of tests being done is unclear.
Spokesperson for the Gauteng Health Department Kwara Kekana said the department is using the resources that they have including mobile units and tents, clinics and hospitals.
DA MPL in the Gauteng Legislature Jack Bloom in a statement said so far “about 30 000 tests in total have been done in Gauteng, with 1 906 tests done on 16 April”. "This needs to be ramped up urgently to at least 5 000 tests a day, and preferably 10 000 tests a day."
The second hardest-hit province, the Western Cape, says it is currently doing about 900 tests a day, increasing from about 350 before community testing and screening was rolled out.
Departmental Spokesperson Mark van der Heever told Spotlight that they have tested approximately 13 752 across all platforms including hospitals and through community testing since the end of January.
Van der Heever said there are “no blockages at moment” in the testing process, given the NHLS’s capacity and rollout of community testing.
In KwaZulu-Natal (KZN), testing was being done at rates of 30 to 100 tests a day before community testing was rolled out on 16 April. This caused a spike to almost 300 tests a day, although spokesperson for the KZN Health Department Ntokoza Maphiza cautioned that it is early in the process.
The province has been screening about 40 000 people a day, exceeding their target of 13 000.
“The way we’ve been doing it, works for us,” Maphiza said. He said that while more testing is possible, they are mindful of not wanting to waste testing resources unnecessarily, but follow protocol by focusing on hotspots and tracing known positive cases.
A slow start?
Prof Shabir Madhi, director of the South African Medical Research Council’s Respiratory and Meningeal Pathogens Research Unit noted the initial delay in testing as one reason for testing numbers not being higher than they are.
Madhi said that while surveillance of the disease started in January, he would have liked to have seen the public and private services scale-up testing much earlier than they did. “Once countries outside of China started showing cases,” he said, “certainly that should have been the warning that we are in for a storm throughout the world and the laboratories should have started doing testing.
This delay in ramped-up testing includes the shift from private and hospital-based tests to include widespread community-based screening and testing. According to Madhi one of the main goals of a lockdown is to do testing while there are movement restrictions.He noted that at the time (start of the lockdown) “the structures weren’t put in place in terms of doing screening at a community level”.
In a series of videos released by the national Department of Health, the chair of the Ministerial Advisory Committee laboratory testing committee, and executive manager of academic affairs at the NHLS, Professor Koleka Mlisana, confirmed that ramping up testing is one of the goals of the lockdown. She said that 80% of testing has previously been through the private sector, but that this will shift drastically given the community health screening.
This shift means decentralisation of testing and an increase in mobile testing unit capacity.
Dr. Glenda Mary Davison, Head of the Biomedical Sciences Department at the Cape Peninsula University of Technology and a laboratory science expert, told Spotlight the main challenges are firstly acquiring test kits and ensuring that as many testing sites are available for tests to be performed.
A related factor is delays within the testing process. According to Madhi the full cycle between someone being tested, that sample going through a laboratory, and the case being counted should take place within a day but currently takes closer to three to five days. “The system is not geared to test rapidly,” he said. This is because of the centralisation and types of testing. This is problematic because it makes contact tracing a lot more difficult and puts those around the positive case, including healthcare workers, at risk for longer.
Chair of the government’s Covid-19 advisory committee, Professor Salim Abdool Karim reminds that there are daily fluctuations in how many tests are processed and it is to be expected because laboratories are “not designed like a car (manufacturing) line where you get standardised throughput”.
The role of testing criteria
Madhi said the second likely explanation for daily testing numbers not being higher, is due to the initial recommendations from the NICD that were very restrictive in terms of who should be tested. Davison agreed that this was a significant contributor to the disparity between NHLS capacity and actual numbers.
According to Madhi the focus on those with a travel history should have been shifted as quickly as possible after the country started seeing community transmissions and that people were being turned away from testing. He said the criteria should have been revised about a week before the lockdown started and that he is not sure why this was only done in the first days of April, although it could have been due to a lower testing capacity at a time.
This theory is widely supported, with the Health Minister Dr Zweli Mkhize calling the previous criteria “reactive and restrictive”. Karim says that the original criteria was “inflexible” and that the authorities were “deliberately trying to hold back” the number of tests at the time, “which is scandalous”.
Closing the gap
It seems plausible that South Africa’s testing rates should keep increasing given the ongoing rollout of community screening and the much wider testing criteria now in use (recent travel to an affected country is for example no longer a key criteria).
Davison said that since it is practically impossible to test everyone, “the more widespread approach of testing all those who have an acute respiratory infection is the best for now”.
“If the plans of the NHLS and the government to set up additional testing sites, roll out the GeneXpert machines, and do community screening are implemented then I would say we are on the right track,” she told Spotlight.
At the media briefing on Saturday evening NHLS CEO Dr Kamy Chetty said that 10 000 GeneXpert Covid-19 tests have already been received and that the tests have already been validated in South Africa. An additional 20 000 tests will be arriving soon. These tests run on GeneXpert machines, of which South Africa already has many distributed across the country since they are also used for tuberculosis testing.
Despite the country’s current capacity not yet being used fully, there is also active work being done towards increasing the capacity of laboratories. In the Western Cape, van der Heever said, they have just brought on additional machines at their Green Point site, which would increase the testing capacity in the province to 2 000 tests a day.
Mlisana said that more capacity is available in general and that the major three private laboratory groups have indicated “they can easily ramp up to 10 000 a day”. This will increase the country’s testing by 30 000 or 40 000 a day.
But is SA scaling up quickly enough?
Madhi argued that the faster rollout of mass testing “has to be done now not in the middle of the crisis”. This, he said is because at the peak of an epidemic the majority of incoming patients will be assumed to be positive and the healthcare system will have to focus on treating as many as possible rather than on testing.
“Testing at scale by the end of May, which I think is what their target is, pretty much becomes a meaningless exercise in terms of what we need to do now,” said Madhi. According to him the focus should be less on bringing down the overall number of positive cases, since this is likely to be the majority of the country eventually, but on reducing the rate of infections and spreading the curve out over time, primarily for the sake of the healthcare system.
Madhi made it clear that despite South Africa’s curve of infection being seemingly different to other countries, we are not special in avoiding the effects of the pandemic. “[What we’ve seen] is more of a uniqueness in terms of our approach, including our lack of testing during a period when we should have been testing. Some of it is due to reducing community transmissions, but the big part of it is the undetection of cases that have been pretty much confined to households that haven’t really had opportunities to access testing.”