What is PCR?

Polymerase Chain Reactions (PCRs) are often used in research to amplify genetic material, and, as a scientist, you probably don’t give the process a second thought. However, the term PCR has now left the laboratory and worked its way into every household due to its use in the COVID-19 test.

So now perhaps we should give a thought to exactly how the PCR process works and how you could explain it to someone who doesn’t use it on a daily basis.

If we return to the book example from ‘Under the Microscope: What is DNA, RNA, and Proteins’, we can refer to PCR as a photocopier, which can copy pages from this book. But it’s not simply a photocopier.

To expand upon this point, let’s assume that it takes one second to make a photocopy. One billion copies would then take one billion seconds, which is a couple of days shy of 32 years!

However, in a PCR reaction, once the photocopier has made a photocopy, those photocopies can be used to make more photocopies. Therefore, after the first second you will have two copies of the page, after two seconds you will have four copies, and after ten seconds you’ll have 1,024 copies.

Diagram of exponential growth using photocopiers

Therefore, at one second per cycle, it would take approximately 30 seconds to make one billion copies! This means that it’s about 33 million times faster than making single copies for 32 years.

That’s the power of exponential growth.

And the power of PCR.

Fun Fact: Kary Mullis won the Nobel prize for PCR in 1993.

PCR and COVID-19

When you run a PCR in the lab, you specify the genetic material you want to copy. Using our book example, this is equivalent to telling the photocopier to only copy a billion copies of page 32 from a specific book. If the book isn’t in the room, or page 32 is missing from the book, then do nothing.

In the COVID-19 PCR test, the photocopier is told to copy a small piece of the virus that is unique to COVID-19. If that page in that book is there, then at the end of 2 hours we’ll have a billion copies of that small fragment. If it wasn’t there, we’ll have nothing.

To make sure the test is accurate, the COVID-19 PCR test often involves three different fragments (ie three different pages) that are unique to COVID-19 and only call it a ‘positive’ result when all three fragments are amplified.

Once the PCR has finished running, an assay is used to see if a billion copies have been made. If it is positive, and you didn’t contaminate the tube, then COVID-19 must have been in the sample.

SARS-CoV-2: the ‘RNA virus’

SARS-CoV-2 is not encoded by DNA, like a lot of viruses. It consists of RNA. That’s why it’s called an ‘RNA Virus’. RNA viruses aren’t rare, in fact a lot of plant viruses are RNA.

Fun Fact: There are interesting differences between why some viruses are RNA and some are DNA. For example, RNA viruses mutate much faster than DNA viruses. Although, before you tell this fact to your relatives, make sure to emphasize that, like in humans, most mutations are defects that are bad for the virus.

As PCR can only be used for DNA, there’s an extra step in the PCR test for COVID-19 to convert it from RNA into DNA. Not too hard, just kind of a pain because RNA is harder to work with. The RNA in the SARS-CoV-2 virus is surrounded by a protective membrane shell, but the RNA itself is easily destroyed by proteins on your hands.

Detecting SARS-CoV-2: the PCR and Antibody Tests

PCR test

Up to this point in the article, we have focused on the PCR test. However, your friends and relatives may ask you what the difference is between the PCR test and the antibody test for COVID-19.

The PCR test is to see if you have an active, on-going COVID-19 infection. However, if you are in the early stages of infection (ie the first day or two), you may have the disease and still test negative for the PCR test, but this situation is rare.

The virus seems to replicate really well in nasal tissues, which is why the preferred method for PCR testing is to use a long cotton swab as far back into your nose as is possible. The swab is then put into a tube that contains a solution that destroys the membrane shell, preserving the RNA until it can be converted into DNA for the PCR reaction.

If you have COVID-19, the PCR test will show a positive result once the virus has built up a presence in your system, for the couple of days that you are actually sick, and possibly for two or more weeks after you’ve recovered. After probably a month, the virus will have cleared your system and you will likely be back to being negative on the PCR test.

An advantage of the PCR test is that it is not expensive to perform, with the tube of materials to do the test costing around $0.19. And most of that cost is the tube. However, the PCR machines required for the test can cost anywhere from $5,000 to $50,000, but these are standard pieces of equipment in most labs.

Antibody test

The antibody test is to see if you have had COVID-19. It does this by measuring to see if your body has a history of fending off an active infection. This is called a surrogate assay: it’s not measuring the actual virus but instead measuring whether you fought the virus. Since some people are asymptomatic it is possible that you may have had COVID-19 and didn’t even know it.

The antibody test is looking for factors (antibodies) in your blood that recognize the virus. This is in contrast to the PCR test, which recognizes the virus itself. You probably become positive for the antibodies that recognise SARS-CoV-2 a few days into the illness and will remain positive for quite some time.

The cost for the antibody test is similar to the cost for a pregnancy test or some drug tests. It uses a lancet to initiate the collection of the blood sample. No machine is required. However, testing accuracy is currently not 100%, dependant on who has made the test and their quality control. It differs, of course, from test-to-test, but the errors on the antibody test are mostly false negative; you had COVID-19 and the test didn’t pick it up.

So that’s how the PCR and antibody tests for COVID-19 work in a nutshell. Of course, although we are trying to make these posts as accurate as possible at the time of writing, COVID-19 is a rapidly evolving field of study. So please don’t treat these posts as medical advice or use them as a basis for making a medical, or even political, decisions.

That’s all for now but keep an eye out for the next Under the Microscope post!

About Dr Michael Weiner

Dr Michael Weiner is Abcam’s Vice President of Molecular Sciences. Throughout his career he has founded more than four biotech companies, including Affomix, GnuBio, and AxioMx.

Throughout his career, Dr Weiner has developed several tools widely used in molecular biology. These include the first commercial Next Generation DNA sequencing instrument, a bead-based genotyping method, and improved methods for the production of monoclonal antibodies.

Beyond his career as a scientist, Dr Weiner is a dedicated mentor to multiple bioscience professionals. He is also an inventive artist!