Sudden, unexplained spike in Covid-19 testing numbers as public labs confirm supply shortages

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At the same time, the National Health Laboratory Service (NHLS) confirmed it was experiencing critical shortages of reagents and test kits.

Tests conducted in private laboratories followed a similar trajectory, but not as extreme. 

The sudden spike, just as the media and Health Minister Zweli Mkhize drew attention to the shortage, is unexplained.


It remains unclear whether testing numbers reported on Wednesday account only for tests done on Tuesday, or if the delay is longer than 24 hours.

INFOGRAPHICS | Sharp drop in Covid-19 testing due to kit, reagent shortages

Responding to queries from News24 on Wednesday, the NHLS said it was continuing to experience challenges with the supply of test kits and reagents due to factors “beyond the NHLS’ control”.

“As a result of the global shortage of extraction test kits, the supply of stock is sporadic for some of the key products. The NHLS has placed orders with the suppliers to meet our testing capacity of 36 000 tests per day; however, we are only receiving limited quantities when the suppliers have them available,” the NHLS said.

South Africa manufactures no test kits locally and relies on international companies, such as Roche in Switzerland and Cepheid in the US, for test kits for automated machines manufactured by the same companies, which can conduct tests faster and more efficiently than older equipment.


About testing

PCR testing – polymerase chain reaction – is done by “extracting” the RNA of the SARS-Cov-2 virus, which causes Covid-19, from the swab collected – this requires a small kit containing what is known as reagents.

The NHLS explained the RNA is then reverse transcripted into DNA. This process is called extraction.

The second part of the process is the amplification of the DNA in a PCR machine. Only once amplified, analysis will show whether SARS-Cov-2 is present.

The NHLS uses a range of machines to do this – some fully automated, and some older machines that require separate machines to conduct the extraction process.

Machines such as the Roche Cobas 6800 and 8800 and the Cepheid GeneXperts can conduct the extraction and PCR at the same time but require test kits.

“The NHLS is, on average, conducting 60 000 tests per week with the kits we have available. Kits that are in short supply are extraction kits and kits for the integrated platforms for the Cobas and GeneXpert machines. The NHLS has adequate kits for PCR machines but the limiting factor is the extraction kits,” said the NHLS.

News24 previously reported that the US state department had denied the country was restricting exports of testing kits for the GeneXpert machines, contradicting statements by Mkhize before Parliament.

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