How do you know if you have COVID?

How do you know if you have COVID? Through the RAT and PCR tests, how do they work and which one is better?

By Elvina Lau

With the number of confirmed cases increasing dramatically and the regulations on testing severing, it’s no wonder that you may have done the Rapid Antigen Test (RAT) or Polymerase Chain Reaction Test (PCR¹) at least once. Those are the two methods of determining whether you have the coronavirus in your blood.

If you did not know, RAT provides your result within 30 minutes. A single line at C is negative; two lines on C and T is positive². It detects antigens of the 2019-nCoV N protein, which you may find in live cells in your nose or mouth. I.e., the nasopharyngeal³, nasal and oropharyngeal⁴, hence why you or the doctor swabs at your nose or mouth—even spitting, since saliva contains live cells.

Specifically, it utilises the double-antibody sandwich method⁵, quite similar to chromatography. The antigens of the specimens form complexes with corresponding antibodies; they travel along the nitrocellulose membrane to the detection zone on the film (T), and a pink or purple line appears—a positive result.

The PCR test, on the other hand, takes one day at least but is more accurate. Similarly, it requires specimens of your DNA, which one can find in the nasal or mouth. It detects SARS-CoV-2 genetic material, including nucleocapsid⁶, RNA-dependent RNA polymerase⁷ and ORF1 genes. By measuring the cycle threshold of RNA, that is, ‘the number of replication cycles required to produce a fluorescent signal’ (Sethuraman et al., 2020), if it is below 40, deems the person positive for SARS-CoV-2.

And that is how both tests work, RAT using immunochromatography⁵ and PCR diagnosing a sample from swabs. You might wonder which method is better, and essentially both have their strength and limits.

In terms of accuracy, PCR is more sensitive than RAT because it can detect fragments of the virus, including enzymes, when it is still active in the blood, whereas the RAT is more accurate at the start (Cleveland Clinic, 2021).

Regarding the RT-PCR¹, a study found that sensitivity for a specimen from the broncho-alveolar lavage was 93%, 63% and 32% for nasal and mouth swabs, respectively (BMJ, 2020). You may be wondering why the results are low, but note that it has a higher specificity. Note that sensitivity and specificity are different—the former is the ability to identify people with the disease, the latter for those without it. It may also vary depending on where you collect the specimen. So for the outcome to be positive, it has more weight.

For the RAT, the accuracy of the test when you do a nasopharyngeal swab is 98.07%, 97.63% for a nasal swab, and 96.60% for oropharyngeal. That is the colloidal gold method against the PCR comparator method last year. According to a study by Connor et al. (2022), comparing the effectiveness between two RATs and PCR, the RAT is approximately 94% accurate (see figure 1 for sensitivity).

Figure 1

Monthly Trends in Rates With New York City (NYC) Community Infection Rates

Note. From “Comparative Effectiveness of Single vs Repeated Rapid SARS-CoV-2 Antigen Testing Among Asymptomatic Individuals in a Workplace Setting,” by B. Connor, M. Rogova, J. Garcia et al., Jama Network Open, 5(3), p. 2 (https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2790263). CC-BY.

Naturally, these are only a few studies. There are several investigating the likelihood of true and false positives and negatives⁸. Other factors like the time and condition of the test may affect the results, even contamination.

Ultimately, the accuracy and time of the tests give one an advantage over the other. PCR tests would be better for asymptomatic persons too, but since people need to present their results every day to work, only RATs are feasible. And repeated testing would help the reliability of the test.

Footnotes

1. You may see RT-PCR instead, which is a variation of PCR. There is an extra step—reverse transcription—enabling it to be more sensitive.

2. Both C and T have lines; it is a matter of whether it is pink or purple. The C line indicates the validity of the test. If the line at T is colourless, you are not infected, but if it is pink or purple, you have COVID.

3. The nasopharyngeal is the upper part of the throat behind the nose.

4. The oropharyngeal is at the back of your mouth.

5. Link the double-antibody sandwich method to ELISA. Oxford Reference provides the basic principle but search up ‘immunochromatography’ to understand it further.

6. Nucleocapsid, the N protein, binds (surrounds or packages) the RNA or DNA—the virus’ genome and enables replication.

7. RNA-dependent RNA polymerase is an enzyme for the replication of RNA.

8. False positive means the person tested as positive for SARS-CoV-2 when in truth they are not infected. False negative is the opposite.

References

Cleveland Clinic. (2021, August 24). PCR test for COVID-19: What it is, how its done, what the results mean. Retrieved March 21, 2022, from https://my.clevelandclinic.org/health/diagnostics/21462-covid-19-and-pcr-testing

Connor, B. A., Rogova, M., Garcia, J., Patel, D., Couto-Rodriguez, M., Nagy-Szakal, D., & Rendel, M. (2022). Comparative effectiveness of single vs repeated rapid SARS-CoV-2 antigen testing among asymptomatic individuals in a workplace setting. JAMA Network Open, 5(3). https://doi.org/10.1001/jamanetworkopen.2022.3073

Double-antibody method. (n.d.). Oxford Reference. https://www.oxfordreference.com/view/10.1093/oi/authority.20110803095727955

Mayo Clinic. (2022, February 23). COVID-19 diagnostic testing - mayo clinic. Retrieved March 21, 2022, from https://www.mayoclinic.org/tests-procedures/covid-19-diagnostic-test/about/pac-20488900

Sethuraman, N., Jeremiah, S. S., & Ryo, A. (2020). Interpreting diagnostic tests for SARS-CoV-2. JAMA, 323(22), 2249. https://doi.org/10.1001/jama.2020.8259

Surjit, M., & Lal, S. K. (2009). The nucleocapsid protein of the SARS coronavirus: Structure, function and therapeutic potential. Molecular Biology of the SARS-Coronavirus, 129–151. https://doi.org/10.1007/978-3-642-03683-5_9

Watson, J., Whiting, P. F., & Brush, J. E. (2020). Interpreting a covid-19 test result. BMJ, m1808. https://doi.org/10.1136/bmj.m1808

Ye, Q., Lu, S., & Corbett, K. (2021). Structural basis for SARS-CoV-2 nucleocapsid protein recognition by Single-Domain antibodies. Frontiers. https://doi.org/10.3389/fimmu.2021.719037