By Zaurez Khan M.D.
Confused about testing ? When to get tested? What kind of test? Rapid test?
PCR test? Which one is more accurate? Saliva or nasal swab? When to get retested?
First off, what's the difference between an antigen test and PCR test?
In PCR (polymerase chain reaction) test,
we amplify the genetic material so that even a small amount of virus can be detected. The sample ( nasopharyngeal or saliva) taken from patient is treated with an enzyme called reverse transcriptase to make the RNA into DNA. The DNA is then mixed with polymerase and heated , it separates into two strands. Then it is cooled and the primer copies it so we get a double from each strand. Now keep repeating the process. It goes through many such cycles and we get billions of copies in about an hour. Fluorescein dye enables the copies to generate fluorescence which is measured by a machine.
Antigen tests are much faster (15-20 minutes), easy to perform and can be done at home but have some drawbacks. First, you mix the sample with a solution and then apply that to the test strip which has antibodies. If there are Coronavirus antigens in the sample, they will bind to the antibodies and change color on the strip. They don't amplify so that means there needs to be enough amount of virus to make the test positive. That makes them less sensitive.
What do antigen tests detect?
If you are thinking it is testing the famous spike protein…then you guessed it wrong. Antigen tests detect the N or nucleocapsid protein of coronavirus.
Where omicron has 32 mutations of spike protein, there are only 4 mutations on the N protein. So that answers your next question.
Can antigen tests detect Omicron?
Yes, but how sensitive are they? I’ve discussed that later.
What are some antigen tests available?
You can find all the FDA approved antigen kits using this link:
Throat or nasal swab?
A preprint study from South Africa showed saliva swabs are more sensitive than nasal swabs and should be preferred for omicron detection.
Throat swab at home ?
Some experts recommend swabbing the throat and then the nose.
It is a bit difficult to do on your own and then there is risk of using the wrong technique. Best if a professional does it or someone else.
To avoid a false positive test, it is recommended that there is no food/ drink/ gum/ tobacco use 30 minutes prior to throat swab.
The FDA and CDC have warned against doing throat swabs at home by yourself. Some factors here – because they didn’t approve it that way. They can give a green light only after they have tested something…since they approved nasal swabs initially and didn't test otherwise, plus there are safety concerns.
You can get false negatives with antigen tests.
Here's why: Firstly, antigen tests lag behind PCR tests.
Secondly, they are likely not as sensitive as depicted by manufacturing companies. Now, is that due to the assay quality or because we are not testing saliva?? We don't have published data yet.
If you are thinking about screening for students or workplace, antigen testing is not the right option because you will likely miss the asymptomatic phase and first 2-3 days of symptomatic phase.
Test timing
Below is a pre-omicron era graph from a Lancet study. Omicron has a shorter incubation period. This needs to be adjusted for omicron as the antigen test has a lag of ~3 days after a positive PCR test according to a study later mentioned. But it gives you an idea of the infective period and when to expect a positive test.
High risk individuals need to test early!
The first few days are important for the antivirals to be effective. You may still be in the monoclonal window but you may miss the antiviral window.
Read my previous post on antivirals:
Individuals who are immunocompromised need to get tested early so they can benefit from the treatment options we have.
According to a preprint study (small population) posted Jan 5, 2022, the antigen test lags behind the PCR by 3 days for omicron. See the graph below.
What's the use of antigen tests?
They are useful when done correctly and if the test is positive especially when symptomatic and the fact that wait times are longer for PCR tests.
Some may say that if an antigen test is negative it means you are not infectious because you did not have enough viral load to spread. But was the timing right ? ...and did you use the right technique to swab? We don’t have published data on current antigen tests and omicron sensitivity except for the preprint study I shared with you.
To me a negative PCR test is more reassuring.
Ummm... you still have to wear a mask!
Can PCR test be done at home?
There are FDA approved molecular self test kits available like Lucira and Cue Health. They are more costly compared to antigen tests but more sensitive and accurate.
You don't have access to PCR testing?
Use serial antigen testing and discuss with your physician about the best way to proceed.
Exposed to Covid? What to do next ? Watch this video
In this video, I have shared latest CDC guidelines and my personal algorithm for January 2022 Covid Wave. Keep in mind this can be tweaked around depending on the severity of symptoms.
Article by,
Dr.Zaurez Khan
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