Will a PCR test pick up if I have the Omicron variant?

As scientists and health experts continue to study the Omicron Covid-19 variant to understand its severity and how contagious it can be, preliminary data suggests rapid antigen tests should pick up the new variant.

According to the National Institute of Communicable Diseases (NICD), indications are the variant can be detected by polymerase chain reaction (PCR) tests.

The tests are used to determine if there is specific genetic material from the coronavirus present.

“A PCR test is a nucleic acid-based test, RNA in the case of Covid-19. The test uses a set of enzymes technologies to accurately detect Covid-19 specific genetic markers,” the Council for Scientific and Industrial Research (CSIR) told TimesLIVE.

The government requires a PCR test to be taken by those travelling into SA.

The NICD said the tests check for multiple targets in case there is a variant present.

“These PCR tests typically detect at least two different SARS-CoV-2 targets, which serve as a backup in the case of a mutation arising in one.

“Analysis of the mutations in the nucleocapsid (N gene) of B.1.1.529 viruses suggests rapid antigen tests should be unaffected. However, verification of this is under way,” it said.

The World Health Organisation (WHO) said the PCR tests can detect Omicron while studies into the variant’s affect on rapid antigen testing are ongoing.

“The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any affect on other types of tests, including rapid antigen detection tests.”

Speaking to experts, Time Magazine explained how a PCR test can detect the variant.

It said a commercial test from Thermo Fisher Scientific, which is used in SA and was reportedly instrumental in early detection of Omicron in the country, looks for three different parts of the virus: two relatively stable areas, and a more variable spike protein.

“It turns out Omicron will show positive matches on the two more stable regions, a pattern similar to the one from the Alpha variant, but will show a mismatch on the spike protein portion,” it said.

The Delta variant will show a match on all three areas. If a patient got three matches out of three they would likely have the Delta variant, but if they had two matches they would likely have the Omicron variant.

“This happens to be good fortune that this pattern can flag the presence of Omicron. It’s a good early warning system,” Mark Stevenson, executive vice-president and chief operating officer at Thermo Fisher, told the publication.