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Infectious Diseases

Updated 29 May 2020

Scientists warn of false-negative results with Covid-19 virus tests - what are the SA implications?

The RT-PCR test, currently the most commonly used method to test for the Covid-19 virus in South Africa, has a high chance of giving a false negative, according to latest research. What are the implications?

  • Study finds the odds of a false-negative test result is 1 in 5
  • The first four days after infection seem to be the highest risk
  • We spoke to an expert about how this impacts testing backlogs


Health24 recently reported on a general backlog in coronavirus testing in South Africa, and explained how our tests work.

Currently, our laboratories make use of one of the most-used diagnostic tools – the reverse transcriptase-polymerase chain reaction test (RT-PCR). This test makes use of a swab from the nasal passage or throat, where viral particles are then isolated from the sample.

While these tests play a huge role across the globe to help determine the spread of Covid-19, researchers at John Hopkins have found that they might be likely to give a false negative – where a virus cannot be detected through the sputum sample, even when a person is infected.

What are the odds of a false negative?

According to the research that was published in the Annals of Internal Medicine, the odds of a false negative through RT-PCR is one in five, and sometimes, even higher.

In the report on their findings, they found that the probability of a false negative decreases from 100% on day one of being infected to 67% on day four. The false negative rate further decreases to 20% on day eight.

On the day patients actually started to experience symptoms, the average false negative was 38%.

The researchers analysed seven previously published studies on RT-PCR to interpret their current research.

Could this be problematic given SA’s current situation?

As we reported on testing backlogs in several provinces around the country, we asked Professor Glenda Davison, laboratory expert and head of the Biomedical Sciences Department at Cape Peninsula University of Technology, if false negatives could also be experienced in South Africa, and what the implications would be.

She believes that like other countries that currently use the RT-PCR testing methods we are also likely to be experiencing false negatives. But unlike the reasons stated in the research paper, there are other factors that could also cause false negatives:

  • Sampling from the nose and throat may not always be adequate. The reason for this is that individuals may shed the virus in different rates and quantities and that the viral particles in the nose or throat sample are not enough to be detected, which can lead to a false result.
  • The amount and quality of the RNA (viral particles). “It is recommended that once a sample has been taken that it is immediately transported to the laboratory and that if this can’t be done, then it should be stored at 2–8 degrees  for  a maximum of 72 hours or frozen. If a sample is left at room temperature and not processed immediately, the RNA will begin to degrade, again leading to a false negative result as there just isn’t enough to be detected,” Professor Davison explains

She states that this is a difficult situation and that healthcare professionals and community screeners must be made aware of these causes to try and avoid as many of them as possible, avoiding the possibility of a false negative.

Could false negative results increase our Covid-19 spread?

According to Professor Davison, false negative results have all sorts of consequences, not only for those who are sick, but also for the effectiveness of contact tracing and screening.

“In many cases, tests are being performed on people who do not have any symptoms, but who have been in contact with a positive individual. If it is in the early stages (days one to four), or the specimen is not processed properly, they could very well test negative and not go into quarantine. This could, of course, lead to increased spread unless all contacts are made to self-isolate irrespective of a test result,” she told Health24.

But, we shouldn’t only look at testing and false negatives as a reason for increasing rates. “As we go into level three of lockdown and more people are returning to work, taking public transport and shopping, it is inevitable that the infection rate is going to increase,” she adds.

It is, however, important not to become complacent with the current measures and test methods we have in place.

“The fact is no laboratory test is foolproof and all have advantages and disadvantages. I think that when other forms of testing such as rapid antibody and antigen tests are made available, it will offer an alternative way to screen patients and those who have had the infection and recovered.

"However, these tests also have their pitfalls. In the meantime, it is important that we are all aware of the limitations of the RT PCR test and that false negative results are possible,” Professor Davison said.

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

READ | Covid-19: Call to reduce 'unnecessary' screening and testing in SA - and to target areas of concern

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