Lab service vows to reduce testing backlog, currently at over 63,000

South Africa is currently facing a Covid-19 testing backlog of 63,224 samples - a situation caused by suppliers not being able to source the required amount of of testing kits.

This is what the National Health Laboratory Service (NHLS) told parliament's health oversight committee on Wednesday, adding that as of June 8 it had conducted 492,704 kits.

The backlog as of Wednesday stands at 63,244 unprocessed specimens, broken down by province as follows:

• 23,044 in Gauteng;
• 19,431 in the Eastern Cape;
• 17,042 in KwaZulu-Natal; and
• 3,727 in the Western Cape.

Unprocessed specimens are those that are older than three days from the date of registration at the laboratory. A reasonable time to clear a sample through the laboratory, if all reagents (test kits) and resources are available, is 48 to 72 hours, according to a presentation tabled before the committees.

NHLS chief executive officer Kamy Chetty told MPs that the backlog largely impacted tests that had been commissioned as a result of community screening. She said they now prioritised testing according to medical need, high risk individuals, critical frontline workers and essential service personnel.

Chetty said the Western Cape, due to its high numbers of positive cases, has been given priority for testing kits. This has seen its backlog reduced from 15,000 on May 28 to 3,727 on Wednesday.

“We know what happens in the Western Cape now is going to impact other provinces. As a result, we are giving them extra kits in order to reduce backlogs. These are the high-throughput kits. But we are still making sure that we cover other provinces,” said Chetty.

She said the backlog has not impacted on testing for in-patients, who are among the patients prioritised for clinical diagnosis.

“We still have a challenge in the Gauteng province and we are still trying to sort out the backlog. The other priority province is the Eastern Cape, where we brought in a whole lot of new equipment in order to sort the challenges in the province.”

She said they were conducting more than 15,000 tests per day on average and were building up to a capacity of at least 30,000 a day. This would however be dependent on getting more test kits from the suppliers.

While there were local companies manufacturing some of the kits, this was time-consuming and it was therefore easier to seek ready-made kits from international suppliers.

Local small and medium enterprises were getting assistance from the department of science and innovation in this regard, she said.

Chetty explained that the backlog problems started last month when the number of samples the NHLS was getting on a daily basis increased rapidly and the suppliers started to run out of kits.

The NHLS increased the number of tests conducted from 94,203 in April to 232,000 in May. It handled 105,023 tests in the first week of June alone.

Chetty also explained the complex process of testing for Covid-19, which includes RNA extraction and DNA amplification by machines. The extraction and amplification processes were tedious and the machines used were not high-throughput machines. This contributed to the backlog.

She explained that with their separate extraction and polymerase chain reaction (PCR) platforms, the machines can do about 5,000 tests in 24 hours, while their two high-throughput machines can do 15,000 tests during the same period.

“This is where the 36,000 comes from - it's a combination of all those machines. That number represents the capacity that we have - it's the throughput of the machines.”