Lateral flow vs PCR: how do they work?

Lateral Flow Test

There has been some controversy in England this week surrounding the mass testing of pupils for COVID-19 as they return to school. The problem is that the government seems to be contradicting itself regarding the relative reliabilities of the lateral flow test (LFT) and the polymerase chain reaction test (PCR). If a student has a positive LFT from a test done at home, and they subsequently have a negative PCR test, they can return to school. If a student has a positive LFT from a test done at school, then they must self-isolate for ten days even if a subsequent PCR is negative. In this post I am going to explain how the two tests work, and why a positive LFT is always followed up by PCR.

When a new LFT for detecting small amounts of EPO was developed, Lance Armstrong decided to confess.

LFT or, to give it its full title, lateral flow immunoassay, is not new; in fact, it’s been around for years. LFT is a quick, cheap and simple method used to detect specific analytes or biomarkers. Prior to COVID, the most common use of LFT was in pregnancy testing. Lateral flow testing is also used in drug testing, for example in testing athletes for performance enhancing drugs such as EPO. In fact, it was the development of LFTs that could test for EPO that led Lance Armstrong to confess to having used it in his 7 Tour de France wins; he knew that when stored urine samples were tested using the new method, the game would be up.

LFTs are used to check for substances or biomarkers in bodily fluids or swabs. Urine is commonly used in drug testing, while swabs are used to test for pathogens. LFTs use two lines: one is a control line, which confirms that the test is working; the other is the test line. The lines are made up of labels; these are nanoparticles of substances which will bind to the substance being detected and cause a visible line to appear. Labels include nano-beads of coloured polystyrene or latex (a nano-bead is a bead that is around one millionth of a millimetre in diameter!).

This LFT is positive for COVID. You can clearly see the control and test lines.

So, how does it work for COVID? When you have done your throat and nasal swab, you or whoever is carrying out the test will swirl the swab tip in a small amount of extraction buffer. This is a solution which will break down any virus particles, releasing their RNA; it also maintains the pH (acidity) at a constant level, because changes would affect the result. When you do your test, the control line will appear within a couple of minutes to show that the test is working. If the test is positive, the test line will appear within about 30 minutes.

Polymerase Chain Reaction

The enzyme used in PCR was isolated from bacteria that live around underwater thermal vents. This means that it can withstand the high temperatures used in PCR.

PCR is basically a process which uses an enzyme called polymerase to make multiple copies of DNA or RNA; this is called amplification. This means that PCR can detect extremely small amounts of either substance. One of the most widespread uses of PCR is in forensic science where it is used to amplify minute amounts of DNA to a level where it can be analysed.

In forensics, PCR is particularly useful in solving cold cases. Famously, PCR was used to identify the remains of Tsar Nicholas II and his family from very small samples of mitochondrial DNA.

PCR was used to identify the remains of the Romanovs.

The major advantage of PCR in testing for COVID is that it can detect the virus at much lower levels than LFT. This means that it is particularly useful in testing close contacts, who may have the virus but whose viral load is too small to cause symptoms or a positive LFT. Analysis of the swab is also carried out entirely by professionals working in sterile laboratories, so the potential for human error or contamination is very low.

A PCR machine

PCR has several disadvantages. It requires specialist equipment so must be done in a lab, making it more expensive. It also takes much longer. Amplification of the virus’ RNA using PCR requires multiple cycles of heating and cooling, taking several hours. Some people argue that because PCR is a multi-stage process, there is actually more potential for human error than with LFT; personally, I do not agree with this. PCR has been used for many years in forensic and diagnostic applications, and has consistently been found to be reliable.

So, should students who have had a positive LFT in school but a subsequent negative PCR be allowed back to school? Having considered all the scientific evidence, my opinion both as a scientist and as a teacher is yes they should. The argument is that LFTs in school are administered by staff, so they are more reliable than those done at home. That may be the case, but it certainly does not mean that they are more reliable than PCR, which is widely regarded as the ‘gold standard’ within the scientific and medical communities. To me, this is yet another example of the lack of medical and scientific understanding at the highest levels of government, but don’t get me started on that one!

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