COVID-19 testing in clinical settings:

When to use PCR versus rapid antigen testing

Polymerase chain reaction (PCR) tests and rapid antigen tests are both useful tools for detecting SARS-CoV-2 infections. It is worth knowing the differences in their abilities, as well as the best circumstances in which to use them.

PCR tests use nasal or throat swabs to detect viral genetic material (specifically RNA from SARS-CoV-2), and are done in laboratories. They usually take between 24 and 48 hours. Rapid antigen tests are much quicker, usually taking only between 15 and 30 minutes to complete, and can therefore quickly determine if you have COVID-19. They can be done at home or done by a medical professional (such as in a clinical setting). Rapid antigen tests use nasal swabs to detect a protein found in SARS-CoV-2.

The differences in how PCR tests and rapid antigen tests work mean they are best used in different circumstances. PCR tests are highly sensitive (detecting a small amount of what is being tested for, nucleic acids) and highly specific (only detecting what it sets out to detect). Because of this, PCR tests are reliable in detecting a SARS-CoV-2 infection whether or not symptoms are present. They can be used when you suspect you may have COVID-19, or after close contact with someone who has COVID-19. If a PCR test is done after close contact, it should be done 3-5 days after the last time you were in contact with that person, as the virus may not have replicated enough within your body to be detectable before then.

An important caveat to PCR tests is that they are less reliable when testing after a recent SARS-CoV-2 infection. PCR tests can show as positive up to 90 days after an infection, even after someone has fully cleared the infection. This is because small amounts of genetic material (in this case, viral RNA) can remain in a person’s body after an infection, and even though they are not from a live, replicating virus, the PCR test will still be able to detect it. The sensitivity of a PCR test here can end up being a slight drawback. Rapid antigen tests do not face this issue, meaning they can be used during this period more reliably than PCR tests can.

In a perfect world, a viral plaque assay would be performed, where cells grown in culture would be inoculated with a patient sample to determine if intact and replicating virus is present. Unfortunately, this is not a feasible method outside of research scenarios - the time to conduct this can take days (in order to allow the potential virus in a sample to replicate), and can be very cost prohibitive as well. As such, clinicians must rely on a balance of PCR and antigen testing when most appropriate.