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Infectious Diseases

Updated 27 May 2020

Latest on Covid-19 testing in SA: Public sector backlogs more than 6 days – an expert tells us more

According to a report from the National Institute for Communicable Diseases, testing backlogs in the public sector are now more than six days. An expert gives us context into the reasons why.

While coronavirus testing increased week-on-week since early in April, a decrease in testing has been observed in the week ending 17 May, according to a report from the National Institute for Communicable Diseases (NICD).

The week-on-week increase, the NICD said, was on the back of "a larger network of testing laboratories and the implementation of targeted community symptom screening, and referral for testing".

However, according to the NICD, for the week ending 17 May, a decrease in testing volumes has been observed – likely due to a limited number of testing kits, and laboratory testing backlogs. 

In the report, laboratory delays are indicated by an increase in the number of days between the day the test is done and the specimen collected, and the reporting of the result. Currently, the turnaround time for the public sector increased from two days to more than six days (in the weeks leading up to week 20 - the week ending 17 May), while the turnaround in the private sector remained less than two days. 

A reduction in testing volumes was also observed over weekends and public holidays, according to the report from the NICD.

The delay between tests and results was seen in the public sectors of all five provinces where the largest number of tests were done, but a significant delay was reported in Gauteng.

In Gauteng, where it previously took an average of 2.3 days from test to result, it is now more than eight days. 

Test kits not interchangeable

Professor Glenda Davison, head of the biomedical sciences department at the Cape Peninsula University of Technology, told Health24 that test kit availability would definitely be a reason for a decrease in testing.

"I would say the decrease in test kits is one reason for the decrease in testing," she said.

"The test kits are acquired from a number of international companies and are most often imported which could result in delays. The reason being that countries throughout the world are doing these tests and the supply just can’t keep up with the demand."

Another problem, she explained is that laboratories are often locked into using a specific company's test kits as they are specifically designed for the instrument that they have purchased. 

"For example, the National Health laboratory service has a number of GeneXpert machines which should be able to produce test results quickly and within 24 hours. However, these machines can only use test kits/cartridges from the machine manufacturer (Cepheid).

"Cepheid also cannot seem to meet the demand, and although there are a number of other companies (e.g. Roche) who also manufacture test kits, these kits cannot be used on the GeneXpert as they are designed for the machine they are specifically made for.

"In other words, the test kits are not interchangeable."

So why the reliance on kits from international companies?

Professor Davison says although the method to develop our own test kits is available, and we certainly have the capability, this is a long process, and once again they would not be suitable to use on the large commercial automated machines.

"And at this point, we need to be able to process tests on an automated platform".

Understanding how a test is done

Professor Davison tells us that another reason could be in the process of viral RNA extraction.

To understand this, she briefly explains how the test is done.

"The method currently used to diagnose Covid-19 or detect the SARS-CoV-2 virus is a molecular test known as RT-PCR (reverse transcript real-time polymerase chain reaction). Once the nasal or throat swab arrives in the laboratory, the first thing that is required is to extract the viral RNA from the sample.

"This is a long process and is often done manually. It is here that delays often occur as the technologists or laboratory scientist must ensure that the quality and amount of RNA are adequate.

"Ideally, this process should be automated so that the RNA is extracted quickly and the backlog of unprocessed specimens can be cleared. After this has been done, the RNA can be converted to DNA using reverse transcriptase and then using the relevant instrument and test kit, is amplified and detected using PCR."

So, she says a delay could take place at the point where the viral RNA is extracted from the throat or nasal swab, especially if this is a manual method.

Rectifying the situation

With the expectation that things will get worse, before getting better, regarding Covid-19 infections, Professor Davison has expressed concerns about the backlogs.

"This could have huge repercussions. One of the first things I think of is the contact tracing process. If someone is suspected of having Covid-19, one would like to know as soon as possible so that all the contacts can be traced and tested in order to prevent spreading.

"By delaying the tests it makes this process very difficult. It also makes the daily data which is released to the public less accurate and up to date. This makes it difficult to predict how the numbers are going to increase and what action should be taken."

Epidemiologists need up-to-date data to detect hotspots so that they can be contained and controlled. 

Also, worryingly, she tells us that, from a technical point of view, RNA degrades fairly quickly, and so if samples are left too long it could result in a false-negative result. 

"So, it is important that we rectify this situation," she says.

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