In Eastern Cape, more than 20,000 still await their Covid-19 results

Testing for coronavirus infections has slowed down at an alarming pace in the Eastern Cape after no extraction and test kits could be delivered to the province’s laboratories due to “logistical challenges”, according to the National Health Laboratory Services (NHLS).

The area manager for the NHLS in the province, Tabita Makula, stated in a letter addressed to the Eastern Cape Legislature’s Health Portfolio Committee that the province’s testing strategy will have to change.

In an article published in Daily Maverick on 1 June, several experts in infectious disease also called for a change in testing strategy.

Health Minister Dr Zweli Mkhize said on Monday that the province now had 4,111 patients who had tested positive for the coronavirus.

According to the Department of Health, more than 21,000 test results are outstanding. Data from the province’s two metros, Nelson Mandela Bay and Buffalo City, shows that between 3% and 5% of tested cases have a positive result.

The current waiting period for non-prioritised samples in the province is more than two weeks. This has led to the prolonged closure of clinics as nurses refuse to return to work until they have received their results.

“The testing strategy or priorities for Covid-19 testing in the province needs to change. This will reduce the number of samples received and improve turnaround time for results,” Makula wrote.

According to the National Department of Health, on 14 May laboratories in the province registered 7,000 unprocessed tests. This increased to 21,904 on May 21 and to 22,802 on May 25.

A spokesperson for the National Health Laboratory Services, Mzimasi Gcukumana, said extraction and test kits could not be delivered “due to logistical challenges that were outside of the NHLS’s control.”

He said they had ordered enough test kits for 36,000 tests per day but were only receiving limited quantities.

“We continue to engage with international suppliers to expedite the delivery of the test kits.””

He said the kits that were in short supply were extraction kits and kits for integrated platforms for Roche Cobas and GeneXpert. These are the machines that perform rapid testing.

“The NHLS has adequate kits for PCR machines but the limiting factor is the extraction kits. The testing process requires two steps: Firstly, the RNA of the virus is extracted from the swab, and the RNA is reverse transcripted into DNA – this is called extraction. The second part of the process is the amplification of the DNA in a PCR machine. Once amplified, the DNA can be analysed to determine the presence of the virus,” he said.

He said machines like the Cepheid GeneXpert and the Roche Cobas 6800/8800 are integrated machines and able to do both the extraction and PCR process in one automated test.

“The PCR machines that do not have their own extractor are Abbott M2000, BioRad CFX, QuantStudio and Roche LightCycler. Separate extractors (Nimbus and EasyMag) have been procured to extract the RNA from the virus before it can be put into the PCR machines for amplification.”

This test takes longer than those done on the GeneXpert and Roche machines.

It is understood that due to the lack of test kits, the PCR machines with separate extractors must now be used, which slows down the production of test results.

In a letter written to the Eastern Cape Legislature’s Health Portfolio Committee, area manager Tabita Makula stated that Health Minister Mkhize had contacted the US ambassador to assist and had chartered planes to fetch test kits.

“The testing strategy for the province has changed from the initial guidelines [set by the National Institute for Communicable Diseases] to include testing of asymptomatic patients. This has resulted in delays and laboratories incurring backlogs. Test kits that could have been utilised for priority samples, eg, hospitalised patients or primary contacts, were used for testing asymptomatic patients.

“The current system of prioritising urgent specimens should alleviate this problem when fully implemented.

“In addition, private organisations such as Volkswagen South Africa are in the process of assisting us with getting high throughput equipment from other countries to expedite the testing,” she stated in her letter.

“The laboratories are receiving samples on a daily basis and there is no time to catch up and clear the backlog,” Makula said in her letter.

She added that laboratories were running out of storing space.

A spokesperson for the Democratic Nurses Union of South Africa, Khaya Sodidi, said many nurses are stuck at home for more than two weeks awaiting results.

“It is not that they don’t want to work. The department is trying to force them to come back before they have received their results, but this would be irresponsible,” he said.

“The lack of leadership in the health department is becoming more glaring every day. Lack of coordination and the distinct lack of a targeted and consistent approach to screening, testing, tracking and tracing has left healthcare workers confused and angry, particularly as they have been put at risk by these failures.