How Omicron Affects Testing for the Coronavirus

(Bloomberg) -- The rise of the omicron variant of the coronavirus has refocused attention on the importance of testing as a tool for bringing the pandemic under control -- and keeping it that way. At the same time, some tests used to identify infections may be less accurate detecting omicron cases.

1. How has omicron affected test performance?

The U.S. Food and Drug Administration has notified health care professionals of a handful of tests that, in the absence of modifications, are expected to fail to detect the variant or that were modified in order to pick it up. These are all so-called molecular tests, the gold-standard for diagnosing a coronavirus infection. The FDA said Dec. 28 that early data suggest that antigen tests -- which are faster, cheaper and more accessible -- detect omicron but possibly with reduced accuracy. A study posted Dec. 24 suggested that saliva samples may be better for diagnosing omicron than nasal specimens, whereas the opposite was true for delta, the variant that became the dominant strain worldwide in mid-2021.

2. What if I get a negative result with an antigen test? 

If you’re experiencing symptoms of Covid or have a high likelihood of infection due to exposure to the coronavirus, the FDA recommends following up with a molecular test. Even before omicron emerged, it was clear that antigen tests are generally less likely to pick up early infections than molecular tests. In a small study posted Jan. 5, among 30 people who became infected during omicron waves in the U.S. and received both types of tests, the median time was three days from a first positive on a molecular test to a positive on an antigen test. In four cases, individuals were confirmed to have spread the virus to someone else after receiving false negatives on antigen tests. 

3. How do the tests differ? 

Both look for the presence of the coronavirus in your nose, throat or mouth, but they do so in different ways. Molecular tests seek bits of the virus’s nucleic acids, or its genetic material, in a sample of secretions. Antigen tests search out proteins on the surface of the virus.

4. Why not just rely on molecular tests?

Molecular tests typically require several components, including chemical reagents, small plastic containers and swabs. One widely used type relies on trained lab technicians to perform a complicated process called reverse transcription polymerase chain reaction (RT-PCR), which amplifies the virus’s genetic material so that it can be studied in detail. A lack of components, machinery or technicians can limit the availability of these tests. While some molecular tests can churn out results in 30 minutes or less, they don’t scale very well. Thus, countries have increasingly embraced antigen tests, some of which people can perform at home. One version of an antigen test is called a lateral flow test. Similar to a home pregnancy test, it runs a liquid sample over a reactive surface. 

5. What are the benefits of antigen tests? 

Advocates of antigen tests argue that, while they’ll probably never be as sensitive as molecular tests, they compensate for that with their speed and accessibility. In a pilot study in Liverpool, England, in late 2020, rapid antigen tests identified nearly 900 people who didn’t realize they had a coronavirus infection -- and presumably wouldn’t have otherwise gotten tested. For these tests to function best, people may need to perform them regularly.

6. How do we keep track of variants?

The best way to identify new variants of concern and monitor their spread is to take samples from infected people and sequence the genome of the entire virus or at least the spike protein that gives it its crown-like appearance. That, however, can be expensive and time-consuming. As a shortcut, researchers use other techniques, such as subjecting samples to molecular tests that have been slightly tweaked to identify specific mutations. That helps get a faster and fuller picture of what virus strains are fueling a region’s outbreak, though it’s important for researchers to confirm some of those results with genetic sequencing. 

7. What other type of coronavirus tests exist? 

Another type, generally a blood test, measures how much -- if any -- immunity a person has against the virus, either from a previous infection or from a vaccination. A person infected by a virus or vaccinated against it summons, among other tools of the immune system, antibodies designed specifically, like keys for a particular door, to latch onto and neutralize the proteins that form the bulk of that particular virus. These antibodies can linger for months -- or even years in some cases -- though their levels tend to fall over time, a key factor behind vaccine booster campaigns. If a person has already fought off the virus or been inoculated against it, their blood should contain antibodies that will latch onto proteins that appear naturally on a particular virus and exist in these antibody tests. While there are also tests for detecting other parts of the immune system, such as T cells, they’re more expensive and are used less often.

The Reference Shelf

• Related QuickTakes on the omicron variant, Covid treatments and vaccine mandates.
• The FDA’s statement about the effect of omicron on tests.
• Guidance on testing from the U.S. CDC and the FDA.
• The OECD’s guidance on how to best use coronavirus tests.
• Bloomberg’s Virus Tracker monitors the state of the pandemic.

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