Rapid at-home Covid-19 test kits are distributed by the GreenRoots environmental protection organization and Chelsea Community Connections in Chelsea, Massachusetts, on December 17, 2021.
CNN  — 

With Covid-19 cases up across the country, many people are once again relying on home tests to guide decisions about going to work and sending their kids to school and other activities.

A lot of those tests will come back negative, even when a person is 100% sure they have Covid-19. They have had a known exposure, for example, or telltale symptoms they recognize from a previous bout.

That has led to speculation on social media that perhaps rapid tests have lost their ability to detect some of the newer coronavirus variants.

“Each time a new variant comes around, I see this exact same conversation spark up on Twitter,” said Dr. Michael Mina, an immunologist and epidemiologist who is the chief science officer at the telehealth company eMed. Mina was an early proponent of selling rapid lateral flow tests to the public as a way to help people understand when they were contagious.

Mina says people who notice this aren’t crazy. There are reasons why your test might say you’re negative why you actually have Covid.

For one thing, people are using rapid tests differently than they used to. Our immunity factors, in, too. Nearly all of us have some kind of underlying immunity to the coronavirus now, and that affects the performance of the test, too.

But ultimately, the tests are still capable of picking up infections, said Todd Merchak, who co-leads the RADx program at the National Institutes of Health. The program, whose name is short for “rapid acceleration of diagnostics,” was created during the pandemic to quickly develop tests for the coronavirus.

“To date, the performance of currently marketed COVID-19 tests has not been adversely impacted by any new variants,” Merchak said in a statement.

RADx works with the US Food and Drug Administration to monitor new variants and continually assesses the performance of the Covid-19 tests sold in stores.

Tests are less vulnerable to variants

The reason Covid-19 tests continue to work when other tools don’t, such as the vaccines and monoclonal antibodies that have become ineffective over time, is that the vaccines and antibodies target the spike proteins that stick up from the round envelope of the virus. These spikes are under constant pressure from the environment to change, and they do.

Most rapid tests, on the other hand, target the nucleocapsid proteins, or N-protein, of the coronavirus. N-proteins don’t change as much as spike proteins do.

If the N-proteins do change, researchers are prepared.

In a large study published in September 2022 in the journal Cell and funded by RADx, researchers developed a tool that’s essentially a library of every conceivable change to the N-protein over time. They used deep mutational scanning to predict how each of those changes would affect the ability of 17 antibodies used in 11 commercially available rapid tests to latch onto the virus. Now, scientists can cross-reference changes in each new variant of the virus to quickly assess whether a given test will still work.

If the FDA suspects that a test has stopped working to detect a common variant, it conducts further analysis and may revoke authorization for the test.

When you test matters

The CDC recommends that people take a rapid test five days after a known virus exposure.

“If you look at viral kinetics … on average, it usually takes three, four or five days for the virus to go from being very low levels to getting high enough for any test to pick up,” Mina said.

That hasn’t changed, even with new variants, he said.

The new variants may copy themselves a little faster in the body, but it’s a difference of hours, rather than days with the original virus, he said.

Now that our immune systems recognize the virus, Mina thinks they begin to respond faster, and thus people get symptoms sooner than they used to.

That may be leading them to test earlier in their infections, before the virus has a chance to build up enough copies that a test would catch it.

“So people are now starting to test really fast, like day one, day two post-exposure, when we know that the average person won’t get a viral load that’s high enough to be detectable on PCR or antigen tests until day 3, 4, 5 or 6,” Mina said.

“It’s a bias that’s happening as a result of easy access to testing at home,” he said.

Repeat testing improves accuracy

That’s why, late last year, the FDA issued a safety communication to the public, advising anyone who uses a home test and gets a negative result to repeat it within 48 hours. In November, it added the same direction to the emergency use authorizations for all Covid-19 home tests.

The advice to repeat test came from another government-funded study. Researchers at the University of Massachusetts studied more than 5,000 people who had been recruited to find out how well home tests for Covid-19 work in the real world. The study was conducted during the winter of 2021 and into 2022.

People in the study tested themselves with rapid home tests every 48 hours for 15 days. They also submitted samples for PCR testing, which is a more sensitive way to detect infections.

“They can detect sort of vanishingly small amounts of a virus, and so they tend to perform better in the early stages of an infection,” said study author Dr. Nathaniel Hafer, an assistant professor of molecular medicine at UMass Chan Medical School.

During the study, 154 people tested positive on PCR tests; 57 had symptoms, but 97 did not.

Rapid home tests were more accurate in people who had symptoms. They caught the infection about 60% of the time when a single test was taken on the first day of infection when a person had symptoms. When the rapid test was repeated two days later, the tests caught an infection with symptoms around 90% of the time.

Rapid tests were less helpful in people who didn’t have symptoms. A single test caught positive but asymptomatic cases only about 9% of the time. A second test two days later caught people who were positive but didn’t have symptoms about 62% of the time. A third test another two days later caught more than 75% of positive cases without have symptoms.

“Early in an infection, the amount of virus can still be pretty low. And PCR tests could detect that the presence of the virus, but the rapid test is not quite sensitive enough,” Hafer said. “That’s why the repeat testing 48 hours is so important.”

Why rapid tests are often negative in kids

Another real-world study of rapid tests identified another reason the tests sometimes don’t work well: operator error.

The study followed more than 200 parents and 426 children treated at a family clinic in Taiwan as Covid-19 spread through their households. The families were given rapid home tests and instructions on how to use them. The average age of children in the study was 5, parents were around 40. More than 98% of the adults were vaccinated, but most of the children were not because Taiwan hadn’t recommended vaccination of children under 5 at the time.

Covid-19 cases were confirmed by PCR tests, which were helpful in determining a person’s viral load.

Then, investigators looked to see how well the rapid tests performed in detecting those cases. Despite having more infections and more symptoms than their vaccinated parents, kids’ rapid tests often read as negative. In this study, negative rapid tests correctly meant that a child was healthy only 38% of the time.

Researchers were puzzled by this result. PCR tests showed that the infected kids had viral loads that should have been high enough to turn positive on rapid tests. What’s more, kids who tested negative often had the same high viral loads as children who tested positive, giving researchers a clue about the problem: As many parents can attest, sometimes the kids weren’t exactly cooperative when it came to getting a good sample.

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“This finding indicates that it is difficult for some parents to obtain a good nasopharyngeal swab sample from children, resulting in false-negative test results,” the study authors wrote.

Squirmy toddlers aside, Mina says he’s looking forward to the day when it’s common for rapid home tests not to show a positive result, even with repeat testing.

“We could actually call that a victory of our immune system, because it means that our immune system actually kept the virus at bay enough that it never grew up to a high level” to turn the test positive, he said. “I think for a lot of people, that’s actually happening.”