/ 26 March 2020

Test backlog skews SA’s corona stats

Coronavirus Sample Testing At Mgh
Swab duty: Test samples are delivered to a laboratory in Boston. In South Africa, labs are racing to catch up on the large backlog distorting the national Covid-19 picture. (Jessica Rinaldi/Boston Globe via Getty Images)

Since last week Health Minister Zweli Mkhize has been talking about how the country will ramp up testing for Covid-19, yet laboratories have a backlog of more than 5 000 tests.

The impact of this has been confirmed by doctors in the private and public sector, who have told the Mail & Guardian that there is quite a backlog in getting results for Covid-19 tests.

Between February 10 and Tuesday this week, more than 15 000 tests were conducted, with 3% of those tested confirmed as infected with Covid-19.

One of the doctors in the public sector with whom the M&G spoke said the backlogs were due to the sector as a whole being unprepared for the virus.

“Currently we are only confirming cases of those who show symptoms and the rest have to wait. This is the backlog. This is absurd as the virus incubates giving it time to spread. We can’t quarantine people who have not been confirmed yet because the tests are not available and that’s because they are not showing symptoms,” said the doctor.

The department of health’s spokesperson, Popo Maja did not respond to questions about the backlog. In the last few weeks, the department has taken to not answering questions, saying rather that it will address issues in press briefings.

Dr Atiya Mosam, a public health medicine specialist, said that if we are not getting test results on time we won’t know how many people are truly infected. This also means that the numbers given each day are results from days before, and not the number of infected people, or even the number of people who might have tests that will show that they are infected.

Mosam said: “Remember, a few days ago when numbers shot up by more than 100 cases, that was from the backlog and not the tests that had been conducted that day.

“If we are not testing enough, we are not picking up the cases.” This, she said, could mean that the government will end up working with a “skewed picture” of things as it uses the 21-day lockdown to see how Covid-19 has spread. With the disease taking up to two weeks to burn out of people who don’t end up hospitalised, the government would expect the over 700 people who have currently tested positive to either be in hospital or better before the end of the lockdown.

Mosam said this might make it look like numbers “have stabilised — but we will be sitting with a backlog [of tests]”.

The private sector is also battling.

Professor Eftyhia Vardas, a virologist from Lancet Laboratories told the M&G that since March 16 they have received more than 16000 swabs and had tested more than 9000.

This is three times the volumes that other private labs have received or tested, according to Vardas.

The impact of Covid-19 in other countries is also a problem. Testing reagents (the chemicals used to complete the tests) are in short supply everywhere, with countries all trying to get tests. This is being compounded by cancelled international flights. Vardas said that these problems — as well as the number of people asking for tests who did not meet the requirements set by the NICD [National Institute for Communicable Diseases] — “have left us with this problem of low test availability resulting in delayed turnaround times”.

“We regret this deeply and have tried wherever possible to prioritise tests for high-risk individuals, those that are hospitalised, and healthcare workers,” said Vardas.

A private laboratory doctor confirmed this, saying that the backlog was growing. “The backlog is mostly due to people who are panicking and want to be tested for no reason.”

This panic testing will put pressure on an already strained system.

South Africa is not the only country battling with this. Earlier this month, Dr Tedros Adhanom Ghebreyesus, the director-general of the World Health Organisation, said the only way to curb the pandemic was through mass testing. “We have a simple message for all countries: Test, test, test.”

Trying to ramp up that testing has put pressure on rich, poor and middle income countries.

Media in Canada reported on Wednesday that the country was also experiencing backlogs because of a short supply of important testing chemicals. “We all would want more tests,” Canada’s chief public officer, Dr. Theresa Tam, was quoted saying. Nearly 120 000 Canadians have been tested for the novel coronavirus — an average of 10 000 a day.

There are many other countries that are facing this serious hurdle in their bid to flatten the pandemics curve including the United States and Ireland.

In a letter dated March 20, the National Pathology Group — comprising the three biggest private laboratories Lancet, Ampath and Pathcare — told its members that requests for Covid-19 testing were placing extreme pressure on member laboratories’ resources.

“Worldwide demand has created bottlenecks in the supply of N95 and surgical masks, nasopharyngeal swabs, gloves and Covid-19 testing kits. Our laboratories are struggling to meet demand and turnaround times due to the inconsistency in supply of materials required to produce reliable results,” read the letter.

The letter went on to request that laboratories should adhere strictly to the NICD guidelines on making test requests, “testing asymptomatic people is wasting scarce resources” and that there could be a failure to meet turnaround targets to publish test results.

“We are prioritising testing for in-hospital patients, high-risk groups, index cases in community centres such as schools and old-age homes.”

Meanwhile the National Health Laboratory Service (NHLS) said that they will be ramping up testing and that by the end of April, South Africa will be able to process approximately 36 000 tests a day.

The United Kingdom, which has close to 10 000 infected people and seen more than 400 deaths, will be ramping up its testing to about 10 000 people a day, according to their prime minister, Boris Johnson.

More testing has been shown to slow down the infection rate as countries are able to isolate the sick and curb infections. Countries such as Singapore, Australia and South Korea took the decision to test aggressively and widely at an early stage and this has, for now, slowed down their infection rates.

NHLS spokesperson Mzi Gcukumana said that the organisation has adequate testing capacity and equipment to meet the demand. He added that the suppliers have made a commitment that South Africa will be a priority.

The country’s laboratory services have six laboratories performing Covid-19 related tests with 18 state of the art Cobas 6800 and 8800 machines for processing samples and 180 GeneXpert analysers which, Gcukumana said would be available in all provinces for testing by April.

“These are the machines that can process tests in 45 minutes, and the smaller machines can be placed in mobile vehicles, which makes it ideal for community testing,” he said.