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COVID-19 PCR testing – what is it, what are false positives and false negatives, and why do they matter?

SARS-CoV-2 is the virus that causes the disease COVID-19 (see my previous blog post for how we know this). Each particle of the virus is essentially a ball-shaped shell containing a bit of material called RNA (similar to DNA). Imagine the virus as being one of those chocolate eggs that kids break open to retrieve a plastic toy; the toy is RNA. When the virus attaches to a cell, the shell breaks open and the RNA is delivered into the cell. The RNA is then seized upon as a new toy, with disastrous consequences for the cell.

RNA contains instructions telling a cell what substances to make and how to make them. All the cells in our bodies use RNA in this way. The SARS-CoV-2 RNA contains the instructions for making new virus particles, and when it gets into a cell the cell unwittingly uses those instructions to make new virus particles - hundreds of them. Eventually, so many new virus particles are made that the cell explodes and releases all the new virus particles. They can then get into other cells, and the process repeats itself. In this way, one virus particle can make millions.

PCR is a test used to find out if someone has the virus. It does this by detecting the virus RNA (and only the virus RNA). However, for the test to work, there need to be a lot of virus particles in a sample – it needs lots of RNA.

The test itself works extremely well. If you add virus RNA to a PCR test, it will show a positive result 100% of the time.

Unfortunately, in the real world things are not so simple.

False Positives

These occur when the PCR test ‘detects’ the virus in a sample taken from someone but the virus is not actually in the person. This can be caused by contamination (e.g. virus RNA in a lab that is doing the tests getting into samples by mistake, or material from one sample being mixed with another). A recent study estimates that the number of false positives in UK testing is between 0.8% and 4%. That means that up to 4% of people who have had a PCR test are self-isolating but do not need to.

Too many people isolating does not pose any danger to public health. False negatives are more of a problem, and are much more common.

False Negatives

False negatives are caused by a lack of virus particles in a sample taken from someone an infected person. This can be because the body has not made enough virus particles or that the swab was taken from the wrong place.

When one virus particle infects a person, it takes time for that one particle to cause the production of millions of virus particles. Symptoms only start to appear when there are millions of the particles (and millions of dead human cells). The PCR test only works when there are millions of the particles. Below this level, there is not enough RNA for the test to work.

You can see from the graph that it takes about five days for symptoms to appear after someone is infected. And it takes about four days for there to be enough virus RNA for the PCR test to work. So, if you take a test in those first four or five days, you may get a false negative – you have the virus but the test cannot detect it and says that you are negative.

Studies suggest that the 8th day after infection is the day that produces the least false negatives. But even on that day, there is a chance of a false negative and that is caused by the way the virus moves through body’s breathing system.

The virus initially infects the nose. As it progresses it moves further down the body, into the windpipe and then to the lungs. It does this at different speeds in different people (something that scientists think is caused by the genetic differences between people). So, if you have the virus and you have a test on the 8th day after infection, it is possible that the virus has cleared from your nose and throat (from where swabs are taken) and is now lower down in your breathing system. It is therefore not detected.

So what?

The obvious conclusions from all this are that PCR tests may need to be repeated to check results and this is what is done in hospitals. It also means that if you are told that you have been exposed to someone with COVID-19 but your PCR test comes back negative, you should continue to exercise caution in terms of who you come into contact with.

Text: Mark Levesley   @marklevesley

Photo:  Infektionsschutzzentrum im Rautenstrauch-Joest-Museum, Köln-6313 (cropped).jpg by Raimond Spekking under CC BY-SA 4.0