Testing discrepancies appear to be increasingly common with Omicron and its subvariants, leading many to wonder what to do

In the span of 24 hours this month, I had two positive and two negative rapid antigen tests and a negative PCR test.

After dodging Covid-19 for nearly 2.5 years I knew my time would come. But after all those conflicting test results, I was stumped.

How to explain the wonky results? I asked some doctors, academics and scientists and here’s what they said:

First, testing discrepancies appear to be increasingly common with Omicron and its subvariants, so some common sense comes in handy. If you’re like me and living with people with Covid-19 and feel symptoms develop, you’re likely developing Covid-19. So even if your tests say otherwise, stay home.

For rapid antigen tests, serial testing is the name of the game. Test every day or every other day for up to a week if you can. Once you get a positive you can be confident in it, even if it’s a faint line.

In general, PCR tests are more sensitive than rapid antigen tests and will pick up an infection sooner. But even PCR tests can have false negatives—though the rate is less than 1%—say doctors and scientists.

My negative PCR test appears to fall into that small group. I noticed the testing site I was using wasn’t as thorough. They definitely weren’t counting the 15 seconds per nostril that I did at home and barely pushed the swab up my nose.

They could also have missed a very faint line if they weren’t looking carefully.

“Anything you require humans to do will have some amount of error," says Gigi Gronvall, a senior scholar at the Johns Hopkins Center for Health Security.

But it’s also possible that I experienced rapid viral growth, some doctors and scientists said. So while my morning swab was negative, the virus may have rapidly proliferated in my nose, resulting in my faint positive line eight hours later.

“Viruses grow fast," says Dr. Gronvall. “They make a lot of themselves when they infect cells and blow them up."

The exact timeline on the tests could also have mattered.

I rushed to the closest express PCR site right after I began to feel the first twinges of a scratchy throat. It was negative. Not surprising since the first symptoms in vaccinated people are often your immune system activating. The next morning, I went to my local testing site for a rapid and PCR test. The rapid was negative.

That afternoon, however, the scratchy throat suddenly felt worse. My head started pounding. I took a Flowflex rapid test: There was a faint line. I wanted to confirm it with a second test. I took a BinaxNow test made by Abbott Laboratories: negative.

I went to bed figuring the PCR result the next day would confirm the worst. Only it also came back negative. I was perplexed.

Over the next day, I took more rapid and PCR tests with mixed results. Eventually, my Covid-19 diagnosis was confirmed on a daily basis with multiple brands of rapid antigen tests over the next week.

Mara Aspinall, a professor of biomedical diagnostics at Arizona State University, says another potential explanation of my results was that there wasn’t enough sample in my swab.

“I think people don’t fully recognize that it’s not the mucus you want; it’s the lining of the nose," says Dr. Aspinall, who is on the board of OraSure, a manufacturer of rapid tests. Always blow your nose before a test.

False positive rapid tests are very rare. So you can have confidence in a positive rapid test, no matter how faint the line is, doctors and scientists say. The faint Flowflex test should have been enough confirmation for me.

“If you’re positive on a PCR or an antigen test you are very, very, very likely to be positive for Covid," says Nathaniel Hafer, assistant professor in the program in molecular medicine at the University of Massachusetts Chan Medical School, who is part of a National Institutes of Health project that conducts lab tests of at-home rapid antigen tests.

Dr. Hafer says false negatives are often due to sampling errors.

“There’s a whole lot of things that go from a sample being collected in your nose, transported to the lab, and run by the lab," says Dr. Hafer. “The process is pretty robust but weird things happen sometimes."

So how to explain the two different at-home rapid test results taken minutes apart?

Dr. Hafer says the threshold of virus needed to turn a rapid test positive slightly varies between brands, which could explain why a low amount of virus may result in a faint line in one brand and negative in another.

Blythe Adamson, chief executive and founder of Infectious Economics, a New York City-based public-health consulting firm that conducts infection prevention for private businesses, says “with BA.5 we have noticed more testing discrepancies than with other variants."

Part of the issue is there are more reinfections and some are happening as early as three weeks after an infection, she says.

Wilbur Lam, who is lead investigator of the National Institutes of Health project monitoring rapid tests’ sensitivity to Omicron, says his lab has preliminary data indicating that rapid antigen tests are less sensitive with Omicron compared with other variants. Dr. Lam says with Omicron things can change quickly, resulting in disparate test results.

“Hours do matter," says Dr. Lam. “All of these Omicron subvariants are moving quickly. The windows are suddenly compressed in time."

Another anomaly is happening on the later end of infections, says Dr. Lam. People with negative PCR tests have antigen tests turning positive again.

Rebound infections—where antigen tests go from positive to negative back to positive—appear to be happening even in some people who didn’t take Paxlovid, the antiviral commonly prescribed to people at risk of severe Covid-19, which can result in rebounds.

Dr. Lam said he personally experienced that with a recent infection despite the fact that he didn’t take Paxlovid.

A spokeswoman from Abbott said its assessments, as well as independent researchers’studies, have found that the BinaxNow rapid tests can detect the BA.4 and BA.5 variants with comparable sensitivity as prior variants. Indeed, after my first negative test with Binax it turned up positive in subsequent days.

A representative from ACON Laboratories, the manufacturer of Flowflex, couldn’t be reached for comment.

Dr. Adamson says the Flowflex antigen tests appear to be better at detecting the Omicron variants than other brands of rapid tests, which may explain why I got a faint line so early with that brand. It also may explain why I continued to test positive on Flowflex for well over 10 days.

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