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Jan. 17, 2022, 11:12 a.m. EST

COVID-19 vs. the flu. If you test negative on an antigen test, don’t assume it’s a common cold or influenza. Here’s why

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By Quentin Fottrell

You have a blistering headache. Your body aches. You’ve developed a cough. You’re sneezing. But you test negative on an antigen test. Do you have COVID-19, the disease caused by the virus SARS-CoV-2? Or the flu?

It’s a stressful dilemma and an increasingly common question. Flu season is upon us. Omicron is upon us. If you have a COVID-19 vaccine, your immune system will kick in faster to fight the virus. That’s when you start feeling sick.

You isolate for at least 5 full days — day zero being the first day of symptoms — because that’s the responsible thing to do. Yet you still have your sense of taste and smell, but you know that doesn’t mean you don’t have COVID-19.

A COVID-19 vaccine and booster shot help reduce the risk of severe symptoms, and hospitalization, studies suggest. If this is what omicron feels like with a vaccine, you may be thanking your lucky stars that you got your shots.

As the omicron variant sweeps across the world, and flu season takes hold, how can you tell the difference between COVID-19 and the flu? The truth is unless you finally get a positive COVID-19 antigen test, it’s almost impossible to tell.

COVID-19 and flu symptoms are practically the same

Here’s why it’s tough: Both COVID-19 and flu may result in fever, coughing, shortness of breath/difficulty breathing, fatigue, sore throat, runny or stuffy nose, body aches, headache, vomiting, diarrhea, change in or loss of taste or smell.

The CDC says a loss or change in taste or smell is more common in COVID-19, but it’s not a precondition for having omicron, the highly transmittable variant that’s blazing a trail across schools, workplaces and family gatherings.

One sign you could have COVID-19 rather than the flu: A persistent dry cough, and shortness of breath or difficulty breathing are two symptoms that could point to COVID-19, especially if you were exposed to someone who tested positive.

It’s a Catch 22. The flu and COVID-19 have near identical symptoms. Despite all the guidelines helping people to distinguish between the two, a positive rapid antigen test is still the only surefire way of knowing which illness you have.

But here’s the rub: Tests are not one and done. If you have COVID-19 and have symptoms, you may still test negative on antigen tests for days. What’s more, your immune system, helped by a vaccine, may actually defeat the virus.

Repeatedly testing negative with COVID-19 or flu symptoms

Therein lies the silver lining to feeling ill. Early in the pandemic, our immune systems fought the coronavirus and we felt ill. Without any preexisting immunity we likely had a large amount of virus in our systems by the time we felt rotten.

Vaccines were a game changer. Michael Mina, an epidemiologist, says feeling sick can be a good thing. Vaccines help our immune system to more quickly recognize and fight the virus, and that makes us feel sick — not necessarily the virus load.

Mina said you can be symptomatic and pre-infectious, infectious, post-infectious or never infectious. “Symptoms don’t = contagious virus,” he wrote on Twitter. “This is literally a reflection of the fact that vaccines are doing their job!”

That’s why we feel horrible even when we’re negative. “We recognize the virus quickly after it lands in us, we develop symptoms, we kind of fight it off, then it often eventually wins, and grows fast AFTER immunity/symptoms started,” he added.

“Thus, if you are symptomatic and negative — although it means you’re probably not contagious at that moment, be very very cautious,” Mina adds. “Quarantine even if possible and test the next morning or that night. (Sometimes even longer.)”

Emily Landon, executive medical director for infection prevention and control at University of Chicago Medicine, told UChicago News in a Q&A that antigen tests detect COVID-19 when people have a higher amount of virus in their system.

“But a negative antigen test doesn’t necessarily mean you aren’t contagious. If someone has COVID-19, but hasn’t yet reached the test’s threshold of viral particles, they may still test negative with an antigen test but positive on a PCR.”

PCR tests, which amplify the genetic material, are mostly carried out at hospitals and other testing facilities. “They’re able to detect smaller quantities of the virus and detect them sooner (and for more time) than antigen tests,” Landon added.

And then there is the elephant in the room, as outlined in a small and, thus far, non-peer reviewed study published this month , which compared rapid antigen tests with those more sensitive PCR tests.

The research looked at 30 fully vaccinated workers in Los Angeles, New York, and San Francisco who were tested daily last month, using both nasal antigen and saliva PCR tests. A high, but unspecified number, had booster shots.

The results were concerning, particularly as millions of people rely on at-home antigen tests. “Most omicron cases were infectious for several days before being detectable by rapid antigen tests,” the researchers concluded. 

In fact, it took approximately three days from the first positive PCR test to detect the virus that causes COVID-19 with a standard antigen test. As a result, four participants spread the virus before discovering they were positive. 

Isolate and test with symptoms. But when do you exit isolation?

How do you interpret those rapid tests? One red line is negative, while two red lines means positive. A stronger second red line likely means you’re at your most infectious. A lighter red line means you’re at the beginning or end of your infection.

When and how you exit isolation has just gotten trickier. The CDC is maintaining its positio n on its isolation policy, instructing people who had symptoms and who have access to a test to take one before exiting isolation. But it does not require it.

Even if you are less contagious after your symptoms have alleviated, the CDC’s critics argue that this creates another gray area of confusion, and puts the onus on the individual to make decisions that are best left up to public-health officials.

The CDC’s explanation : “The majority of SARS-CoV-2 transmission occurs early in the course of illness, generally in the 1-2 days prior to onset of symptoms and the 2-3 days after.” That, however, was before omicron spread like wildfire.

This stance has divided public opinion, and frustrated some epidemiologists. Mina called the CDC guidelines “reckless.” Many public-health advocates say it’s safer to get that negative antigen test before going out to a social occasion.

Related: A critical question hovers over SCOTUS decision on COVID-19 vaccine mandate: What if unvaccinated workers can’t find tests?

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