And another thing…on false positives

Sometimes the full story can’t fit into a media article. A lot of words can be said during an interview with a journalist but sometimes it’s just really hard to convey the full story. So here, I add some of the missing content to a recent piece I was quoted in about false positive test results.

Testing for current, active, right now, SARS-CoV-2 infection relies on detection other viruses genetic material. This doesn’t have to be present in an intact virus, because the test can detect virus even if its is not longer able to replicate or when there’s likely to be too little to infect someone else.

The article entitled “Coronavirus false-positive test results rare, experts say — so how do they get COVID-19 wrong?” sought to explain where a false-positive laboratory test result comes from. The ABC has been providing extraordinarily comprehensive coverage of every aspect of the COVID-19 pandemic. This was a good question to ask since media worldwide have been talking about false positives and false negatives throughout, but often without much detail to help out the public. I was happy to chew the ear of an expert journalist.

We don’t throttle our PCRs

First off, this comment was a bit wrong so let’s delve more deeply.

“Scientists could adjust the test to find smaller amounts of the virus RNA but that would increase the chance of a positive result where the virus wasn’t actually present.”

Scientists and companies create and optimize these sorts of virus detection tests – called PCRs (lots to read about these here, here, and here) to be as sensitive as possible, right out of the gate.

There is no adjustment.

And with these tests – which don’t guarantee detection of infectious virus, just bits of their genetic material – that high level of sensitivity has been a problem sometimes. Finding traces of the virus in people who are well can really confuse matters.

How can a false positive occur?

The most common way they happen is usually as per this quote…

University of Queensland virologist Ian Mackay said false positives were rare and usually only caused by contamination of the test once it was back in the lab.

There was another part to this which didn’t make the final cut. That’s around the nature of the test. Sometimes, a test might cross-react with other, related viruses. This can be both a design issue or a lack of pre-release testing.

Sometimes one “test” is actually a combination of multiple tests. These are called multiplexed tests and they aim to detect two or more different parts of the virus genome, sometimes with other targets included ensuring the test is working. A multiplex test can behave a bit differently sometimes.

All of these “sometimes'” can be mitigated, overcome – or at least predetermined – by doing lots of pre-release testing of:

  • different sample types (throat swabs, nose swabs, saliva, sputum, blood, urine – you name it. Put that test through the hoops!),
  • different viruses (rhinoviruses, other coronaviruses, or other things you might find at the sampling sites)

…and looking for unexpected results.

This is the process of validating the test. Validation is a kind of pressure testing and it’s essential.

In Australia, validation required of tests for human use (see here and here for example). Australian labs are well aware of all this and constantly work hard to address all those needs to deliver the best results for the community (of which they are also a part!).

It’s not possible to “fix” a commercial assay if problems are found during its evaluation – kits are sold “as is” and are more of a closed box. One hopes they have been thoroughly validated. Sometimes they might not have.

Tests made by labs (“in-house tests”) can be fixed – or thrown out and redeisgned – if problems are seen during their development.

But it’s important to note that whether commercial or in-house or well-validated or not – sometimes a test may just throw up extremely rare problems not seen until used on thousands of tests.

It might be the sample not the test

Another cause – mentioned in the article – is the contamination of the sample at the point of collection. This scenario could happen if another infectious person’s sample got into a negative person’s sample tube in some way. Both samples could test positive by RT-PCR.

False negatives

This bit was confusing.

If a sample was taken too soon after someone was exposed to COVID-19, there may not be enough of the virus in the nose or throat to be detected.

This is actually about how a false negative result might arise. Not a false positive.

The same thing can happen at the other end of illness; a person is well and has so little virus left from their resolving illness, that it’s right at the limit of the test’s capability to detect.

Sick weeks ago, healthy now, still testing positive

Here we may see one sample positive, the next negative and so on in a random-looking pattern. We’ve all read a lot of these examples. They are happening in this pandemic because so many labs all over the world are concurrently hunting the same viral beast using RT-PCR – the scrutiny on results is more intense and rapidly communicated than ever before. We’re also testing samples from people who are basically well (looking to satisfy discharge criteria), and whom we wouldn’t normally test.

We’re asking and expecting an awful lot even from RT-PCR, the most sensitive virus test we’ve ever known.

A well contact example

As part of screening contacts, for example, a person may test positive even when they are currently well. From a medical point of view, this could look like a false positive. But it may be that after delving into this person’s story, they were sick, but weeks ago. We know from lots of experience now that some people shed viral genetic material weeks even when an infectious virus cannot be found using methods to try and amplify or “grow” it and the patient looks, and perhaps feels, clinically well.

As Prof Bill Rawlinson noted in the piece..

Our lab and other labs are doing thousands and thousands of tests every day and we are only seeing a couple of false positives.

It’s really a rare event

The main point

Can we rely on our lab results? Absolutely. Australian labs are every bit as good – and often better than labs the world over.

This is the point I really wanted to stress in this interview…

Our labs are good, and have good processes, so you won’t see many false positives.

…and we don’t.

The fact that we know this should tell you something about how expert the labs in Australia are and how well they work with doctors and public health authorities to each check other and resolve in “funny” results through communication.

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