Share on Pinterest
Experts say when symptoms and side effects show up is important. Raquel Arocena Torres/Getty Images
  • The side effects from a COVID-19 vaccine can be similar to allergies, the flu, or even COVID-19 symptoms themselves.
  • Experts say the vaccine can bring on muscle pain, fatigue, fever, and chills, but probably not loss of taste or smell, runny nose, or sore throat.
  • Experts also note that most side effects occur within 2 weeks of a vaccination.

All data and statistics are based on publicly available data at the time of publication. Some information may be out of date. Visit our coronavirus hub and follow our live updates page for the most recent information on the COVID-19 pandemic.

You wake up in the morning with a cough, a headache, and fatigue.

Do you have COVID-19? Allergies? The flu? Or is it just the side effects of getting a COVID-19 vaccination?

All can have similar symptoms.

“There’s a huge amount of overlap,” Dr. David Cutler, a family medicine physician at Providence Saint John’s Health Center in Santa Monica, California, told Healthline.

But there are a few clues that can help you accurately determine what ails you.

If you’ve recently had your first or second dose of a COVID-19 vaccine — Pfizer, Moderna, or the single shot Johnson & Johnson — you might experience an immune reaction that resembles symptoms of COVID-19.

“Anybody who gets a COVID-19 vaccine can expect to have some symptoms, which are associated with an inflammatory response to the vaccine,” Dr. Sanjeev Jain, a board certified allergist and immunologist at Columbia Allergy, told Healthline.

“That’s how the body develops antibodies to the virus,” Jain said. “That’s a positive thing and expected.”

In addition to pain, redness, and soreness at the injection site, vaccine side effects may include fatigue, headache, muscle pain, chills, fever, and nausea, according to the Centers for Disease Control and Prevention (CDC).

That sounds a lot like the symptoms of COVID-19.

But not exactly.

For example, if you’re not experiencing a new loss of taste or smell, sore throat, congestion and runny nose, or diarrhea, chances are you’re having a reaction to the vaccine, not COVID-19.

Breathing problems and a feeling of pressure on the chest also can occur with COVID-19, according to the CDC, but aren’t associated with reactions to the vaccine.

When you start feeling sick is an important indicator, too.

“If it’s been 2 weeks or more after vaccination, it’s very unlikely that you’re experiencing the side effects of the vaccine, and unlikely that it’s COVID-19 either,” said Cutler. “If it’s under 2 weeks, then everything is in the mix.”

Most side effects of COVID-19 vaccines appear to resolve within 3 or 4 days of vaccination.

“They tend not to last long or be severe,” Cutler said.

Cases of COVID-19 have been reported within 2 weeks of the first vaccination shot because recipients let their guard down, he noted.

“If they had held out just a little longer, they would have been fully protected,” he said.

“Nobody gets COVID-19 from the vaccine itself, but you can get unlucky and get infected around the time you get the vaccine,” added Jain. “If you’re concerned, you can get a nasal swab (COVID-19 test) to determine whether you have COVID-19 or not.”

Both COVID-19 and vaccine side effects can also be similar to the symptoms of the seasonal flu. But, as Cutler noted, influenza has been virtually nonexistent this season.

“This year, the flu would be a very unusual disease to have,” he said.

But what about seasonal allergies and asthma?

Like COVID-19, allergies and asthma can cause breathing problems. Allergies may also trigger sneezing, congestion, and runny nose.

Less commonly, allergy symptoms may include headache, wheezing, and coughing.

Allergies, however, rarely cause fever, chills, muscle pain, fatigue, or nausea like COVID-19 or a COVID-19 vaccine can.

Cutler said that proper diagnosis requires taking a detailed medical history to determine whether people have a history of allergies and asthma and if these conditions have been well controlled.

“If you have well controlled asthma it’s very unlikely that a new cough is asthma,” he said.

Likewise, said Jain, “In allergy season it’s not uncommon for people to have a cough or runny nose. If that’s similar to what you typically get during spring, it’s probably just your allergies.”

However, Jain noted that some people have an allergic reaction to the COVID-19 vaccine that can have symptoms resembling allergies, such as itchiness and hives.

Allergic reactions are commonly mild, but in rare cases can be severe, even life threatening, Jain said.