Antigen Versus PCR for SARS-CoV-2: Introduction, Principle, Differences, and Keynotes

Introduction of Antigen Versus PCR for SARS-CoV-2

Antigen and PCR tests in COVID-19 patients are the most common assays applicable for laboratory diagnosis of COVID-19 caused by a virus, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2). The antigen is a foreign substance that induces an immune response. The nucleocapsid (N) is the most common antigen for the SRAS-CoV-2 antigen test and is also called antigen-detecting rapid diagnostic tests (Ag-RDTs). These Ag-RDTs work in the principle of immunochromatographic (lateral flow) assay. Ag-RDTs for COVID-19 will most often be positive when viral loads are highest and patients are most infectious – typically 1−3 days prior to the onset of symptoms and during the first 5−7 days after the onset of symptoms – and will become negative as the patient clears the infection and recovers. The nasopharyngeal swab is used as a specimen.

PCR stands for a polymerase chain reaction and PCR assay applies to detect genetic material from a specific organism but here for a virus, SARS-Cov-2. The test detects the presence of genes of a virus if you have been infected at the time of the test. This PCR is also applicable to detect fragments of the virus even after you have no longer been infected. Test specimens are nasopharyngeal swabs,  oropharyngeal swabs, bronchoalveolar lavage (BAL), sputum, etc.

Principle

Antigen test works on the principle of immunochromatography while polymerase chain reaction (PCR) itself is a technique in which three common steps are denaturation (template into single strands), annealing ( primers to each original strand for new strand synthesis), and extension (new DNA strands from the primers).

Differences-Antigen Versus PCR for SARS-CoV-2

The differences between antigen tests and PCR are as follows-

S. No	Antigen Test	PCR
1	Immunochromatographic test	Molecular Test
2	It is a rapid diagnostics test (RDT).	PCR stands for a polymerase chain reaction and it is a technique.
3	It detects antigen/s.	It detects gene/s.
4	It is less sensitive.	Highly sensitive
5	Rapid assay	Time taken
6	Reports in minutes ( average 3o minutes)	Reports in hours (4 hours)
7	Presumptive test	Confirmatory tests
8	It can be assayed in an ordinary setup.	It needs a high level of setup.
9	No need for highly qualified laboratory personnel.	There is a need for highly qualified laboratory personnel.
10	One staff can perform the test.	Numerous laboratory personnel is required.
11	Relatively inexpensive	Expensive
12	Less accurate	It is a highly accurate test with accuracy that approaches 100% and this is the reason, it is the gold standard for diagnosing SARS–CoV–2.
13	It is a qualitative test.	It is both a qualitative and semi-quantitative assay and thus positive report is mentioned with ct (cyclic threshold) values.
14	can miss early cases of COVID-19 ( low viral load)	Rarely occur so ( can detect even low viral load)
15.	It can detect a viral load of a ct value less than 30.	It can detect a viral load of ct value up to 40.

Keynotes on Antigen and PCR for SARS-CoV-2

Antigen Test

• Antigen test occurs as positive typically 1−3 days prior to the onset of symptoms and during the first 5−7 days after the onset of symptoms thus it is known as an early marker of lab diagnosis.
• It is a marker of active infection.
• It is applicable at the point of care i.e. outside clinical laboratories.
• Easy to perform
• Quick results (within 30 minutes) enabling rapid implementation of infection control measures, including contact tracing
• Less expensive than nucleic acid amplification testing (NAAT), e.g., RT-PCR assays

PCR Test

1. PCR test detects active as well as inactive SARS-CoV-2 infection and therefore there is the significance of cycle threshold (Ct) values.
2. Ct < 25 indicates high viral load, Ct 25-30 medium viral load, and Ct > 30 low viral load.
3. This test is highly sensitive and specific.
4. It is also a gold standard test for diagnosing COVID-19.

Further Readings

1. WHO-2019-nCoV-Antigen_Detection-2020.1-eng.pdf
2. https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays
3. https://covidreference.com/diagnosis
4. https://www.umassmed.edu/news/news-archives/2021/11/whats-the-difference-between-a-pcr-and-antigen-covid-19-test/
5. https://academic.oup.com/femspd/article/79/1/ftaa069/6123719
6. https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-020-01810-8
7. https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05419-3
8. https://my.clevelandclinic.org/health/diagnostics/21462-covid-19-and-pcr-testing
9. https://apps.who.int/iris/handle/10665/337948
10. https://jcm.asm.org/content/58/11/e01695-20
11. https://universe84a.com/antigen-antibody-pcr-tests-covid-19/
12. https://link.springer.com/article/10.1007/s00540-020-02875-8