Free rapid COVID-19 test kits sit in a box as they wait to be handed out to residents at Contra Costa County Supervisor John Gioia’s office in El Cerrito, Calif. on Dec. 21, 2021.

The alarming spread of omicron subvariants — particularly BA.5, which has quickly become the dominant coronavirus strain in the U.S. — has again put a spotlight on how well COVID-19 rapid antigen tests work at this stage in the pandemic.

While some early research and anecdotes have suggested that at-home test kits may not be as good at spotting omicron’s sneaky subvariants, Bay Area infectious disease experts say the rapid antigen tests are still an effective way to diagnose infection.

But they add that variants like BA.5 only drive home the importance of using rapid antigen testing as effectively as possible to avoid a false negative result.

Also, experts say it’s still the case that while rapid tests are quicker and easier than PCR tests, they are also less sensitive and therefore more prone to inaccurate results.

That problem has been magnified by this summer’s surge, during which some people with COVID-19 symptoms have reported initially testing negative, said Stanford virologist Robert Siegel.

But the reasons for that may not be limited to BA.5 or omicron subvariants alone, infectious disease experts say.

Rapid antigen tests may generally give a good indication of whether an infected individual is contagious, but as has been the case throughout the pandemic, they are not foolproof.

A recent report combing the results of 155 studies, known as a Cochrane meta-analysis, concluded that antigen tests correctly identified COVID-19 infection in an average 73% of people who were symptomatic and 55% of people who were not.

The study also found that tests were more accurate when used in the first week after symptoms began. As a rule of thumb, rapid antigen tests work best when there is a high “pretest probability” that someone is infected (i.e., that they have symptoms or know they were exposed), when they are done every day, and are from a reliable manufacturer, experts said.

So, how does that change with BA.5? Experts say the answer is complicated.

The subvariant is very new on the pandemic scene, first detected around the beginning of this year. Peer-reviewed and preprint literature on the performance of rapid antigen tests does not yet seem to include anything specifically about BA.5 — though at least one study has shown that a combined nasal/throat swab demonstrated improved sensitivity compared to swabbing the nasal passages alone, said Benjamin Pinsky, director of the Clinical Virology Laboratory at Stanford.

Initial small studies have suggested that in the earliest stage of infection, omicron might be most concentrated in the throat, rather than the nose or nasal pharanyx. However, “I’m not sure (that theory) has panned out with large numbers of individuals,” said UCSF infectious disease expert Peter Chin-Hong.

Although some experts have backed throat-plus-nose swabs for at-home tests, neither the Centers for Disease Control and Prevention nor the Food and Drug Administration has endorsed that approach.

Most infectious disease experts still recommend people follow the CDC’s guidance on proper use of antigen tests, as well as the instructions provided with each test, to ensure their accuracy.

Another factor that could interfere with rapid tests is immunity gained from past infection or vaccination, both of which yield antibodies that could produce an early false negative, Siegel said.

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Experts overall still recommend PCR tests as the “gold standard.” They detect the presence of viral DNA and are not affected by the presence of antibodies — unlike rapid antigen tests, which detect the presence of a viral spike protein and can be greatly affected by timing and human error.

Another possible reason for inaccurate results from rapid antigen tests may relate to the choices people make when they administer it, experts said. Some symptomatic people test too early or too late, or give up after one negative test.

Here are the best ways to use a rapid antigen test if you think you have COVID-19, according to experts:

First, make sure the test you are using is from a reputable manufacturer, and follow all the instructions.

If you feel sick, take an antigen test as soon as possible. If you are symptomatic and test negative, mask up and test again the next day. Don’t assume that one negative rapid test is accurate.

If you are still feeling sick and testing negative, strongly consider a PCR test, which will be the most sensitive. Meanwhile, make sure you are self-isolating, especially from people who may be more vulnerable to COVID-19.

“I think at the end of the day (rapid antigen testing) is a good measure of infectivity,” said Chin-Hong. “The bottom line is for people not to stop at one test, or to think about a PCR if they think they might have COVID-19.”

Annie Vainshtein (she/her) is a San Francisco Chronicle staff writer. Email: avainshtein@sfchronicle.com. Twitter @annievain

Annie is a reporter for The San Francisco Chronicle. She previously was a digital producer for The Chronicle's Datebook section. She graduated from Cal Poly, San Luis Obispo in 2017 with a degree in journalism. During her time there, she spearheaded a culture column, produced radio pieces for NPR-affiliate station KCBX, and was a DJ and writer for KCPR, the campus radio station. Before joining the Chronicle, she was an associate producer at SFGATE and interned at VICE and Flood Magazine. She's particularly interested in communities and scenes that are often misunderstood.