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An illustration of a person wearing a mask with two stickers on their arms. On the left is a sticker that says "I got my COVID-19 vaccine." On the right is a sticker that says "I got my flu shot."
Credit: Tatiana Ayazo

With all the recent discussion about COVID-19 vaccine third doses and booster shots, it can almost be easy to forget that flu season is upon us in the northern hemisphere. In the United States, flu activity typically begins to increase in October and peaks between December and February, lasting as late as May, according to the U.S. Centers for Disease Control and Prevention (CDC).

If you’re immunocompromised because you take immunosuppressant medication for an inflammatory or autoimmune condition, you’ve likely already talked to your doctor about how to best time COVID-19 vaccine doses with your treatment. But the approval of the third COVID-19 dose for people at risk for severe COVID-19 and now the arrival of flu shots may affect your medication schedule again.

Remember: It’s incredibly important to get an additional dose of the COVID-19 vaccine and the flu shot if you are immunocompromised.

“Whether it’s COVID-19, the flu, or any virus or bacterial infection, you are just that much more susceptible to getting sick faster than someone who’s immunocompetent,” says Geeta Nayyar, MD, MBA, Associate Professor of Medicine at the University of Miami. “It’s so important to get the COVID-19 vaccine, the booster, and the flu shot because you want the first line of defense to be really strong.”

Here’s everything you need to know about timing your third COVID-19 dose with the flu shot if you’re immunocompromised.

Can You Get a COVID-19 Vaccine and Flu Vaccine at the Same Time?

Although data is still limited on giving COVID-19 vaccines with other vaccines like the flu vaccines, the body generally develops protection and possible side effects similarly whether vaccines are given alone or with other vaccines, according to the CDC.

The agency says you can get a COVID-19 vaccine and flu vaccine at the same time — though you should still follow the recommended schedule for either vaccine (so don’t delay one just to get them together).

Recently, Anthony Fauci, MD, one of the nation’s top infectious disease experts, added to this, noting that getting the flu shot and the booster shot as soon as possible is what’s most important. “Get it as soon as you can and in the most expeditious manner,” Dr. Fauci told CNN Health in an interview. “If that means going in and getting the flu shot in one arm, the COVID shot in the other, that’s perfectly fine.”

However, a booster COVID-19 shot and an “additional third dose” of the COVID-19 vaccine for at-risk individuals are slightly different in terms of what they’re used for — and you may have additional factors to consider with your doctor based on your immunocompromised status.

Booster COVID-19 Vaccine

The Pfizer booster shot has been approved for certain groups of people, including those who are 65 years of age or older and those who are at high risk of severe COVID-19 because of underlying medical conditions, such diabetes, heart disease, or obesity.

This booster shot is an extra dose of the vaccine administered six months after your primary series to help increase immunity because of waning antibody levels over time.

Third Dose of the COVID-19 Vaccine for Immunocompromised Patients

A third dose of the Pfizer and Moderna vaccines has been approved for certain immunocompromised individuals, who may receive it at least 28 days after the second dose of the primary vaccine series. In this case, the extra shot is meant to give you additional initial protection if your immune system may not bolster a large response to just two shots (because you take immunosuppressant medication or have medical conditions that weaken the immune system).

Timing Your Immunosuppressive Medication with the COVID-19 Vaccine

You may have worked with your doctor to time your immunosuppressant medication (such as methotrexate, JAK inhibitors, rituximab, and abatacept) around your first two doses of the COVID-19 vaccine. However, if you’re off your medication for all three doses of the vaccine, you may be off it for a long period of time. The risks of this could outweigh the benefits of pausing your medication for certain patients.

“The circumstance differs by the individual patient — if somebody is thinking about starting an immunosuppressant or restarting an immunosuppressant, it’s generally advisable to wait two weeks until after the vaccination to restart that medication,” says Paul J. Maglione, MD, PhD, Assistant Professor of Medicine at Boston University School of Medicine and a pulmonary physician at Boston Medical Center. “For those who are already on an immunosuppressant, this is a challenging question and it really should be individualized between the patient and the doctor.”

Certain immunosuppressive medications can reduce the efficacy of the vaccine, which is a major reason why the third vaccine dose has been recommended for those who are on significant immunosuppressive medications. However, just because you’re on immunosuppressive medications doesn’t mean that the vaccine isn’t going to work. You may simply need that third dose for adequate protection.

In August, the American College of Rheumatology (ACR) released clinical guidance around the timing of third COVID-19 vaccine doses with immunomodulatory drugs. Its key recommendations included that providers should counsel patients to hold certain immunomodulatory or immunosuppressive medications for one to two weeks after booster vaccination if disease activity allows — with exceptions for glucocorticoids and anti-cytokine therapies, which includes most biologics.

The ACR task force didn’t come to a consensus on whether anti-cytokine medications like tumor necrosis factor (TNF) inhibitors and others such as IL-17, IL-12/23, IL-23, IL-1R, and IL-6R antagonists impair vaccine response in a way to warrant pausing them. Because of that, no recommendation was made on whether or not to hold or continue these treatments for the third dose until additional evidence is available. So its up to patients and their doctors to decide whether they should stay on these medications or temporarily pause them.

Meanwhile, patients on rituximab or other anti-CD20 medications should discuss the best timing with their rheumatology provider before receiving a third dose. Some doctors measure levels of B cells to help determine the timing of a booster and subsequent rituximab dosing. But for those who don’t have or want to use that information, the general recommendation is to provide the third dose two to four weeks before the next anticipated rituximab dose (so at month 5 or 5.5 for patients who receive rituximab every six months).

“Most studies have shown that there may be a diminished response, but nonetheless a response, for those who are on these immunosuppressive medicines,” says Dr. Maglione. “That’s why that third dose is key to get to that response that would normally be achieved with two doses in those who are not on immunosuppressive medications.”

Of course, the definition of “immunocompromised” can vary widely, and your doctor will have insight on timing of medications and vaccines for your particular condition.

Timing Your Immunosuppressive Medication with the Flu Vaccine

Although it may have been less commonly discussed before COVID-19, the timing of immunosuppressive medications can also have an effect on the effectiveness of the flu shot.

“We should always be having these conversations because the idea is the same that if you’re on immunosuppressive medication, it could impact the efficacy of the vaccine for the same reasons,” says Dr. Maglione. “I do think that COVID has raised our awareness and mindfulness of this in a way that maybe people will be discussing it more this year than ever.”

Some doctors have recommended that patients on methotrexate, a disease-modifying drug commonly used for rheumatoid arthritis and other inflammatory conditions, stop taking it for up to two weeks after the flu shot to help increase its effectiveness, for example.

Holding other immunosuppressant medications after getting the flu shot is not generally recommended, but you can ask your doctor about your specific situation. If you get the flu vaccine and a COVID-19 vaccine dose at the same time, however — and withhold medication as a result — it stands to reason you may also help boost the efficacy of the flu shot along with that of the COVID-19 vaccine.

Read more here about getting the flu shot during the COVID-19 pandemic when you have inflammatory arthritis.

Potential Risks of Combining the Flu and COVID-19 Vaccines

Common side effects of the COVID-19 vaccine include pain, redness, and swelling in the arm where you received the shot. Throughout the rest of your body, you might experience tiredness, headache, muscle pain, chills, fever, and nausea, per the CDC.

These are similar to side effects you may experience with the flu shot.

“These vaccines can trigger some flu-like symptoms or discomfort afterward,” says Dr. Maglione. “That could theoretically be worsened by getting two at once. But I think overall, those concerns are outweighed by the benefit that is getting the vaccines and getting them at the right time.”

In other words, if it’s easiest for you to get a third dose or booster dose of the COVID-19 vaccine at the same time as your flu shot, getting both simultaneously could help you avoid delaying your vaccines — and keep you safer as a result.

“In our patients, we now know that side effects do occur but severe side effects are rare and disease flare isn’t as high as we were concerned with at first,” says rheumatologist Jiha Lee, MD, a Clinical Assistant Professor at Michigan Medicine. “I think because of the opportunity we have to deliver both vaccines in a timely and convenient manner, even immunocompromised patients can get both COVID-19 and the flu vaccine at the same time — provided that they have not had a severe reaction to their prior series or prior flu vaccine.”

However, if you haven’t been vaccinated for COVID-19 yet and you’re concerned about potential side effects or disease flare-ups, your doctor may advise you to get the COVID-19 shot and flu shot separately.

“I think for their first primary series, I may shy away from doing the flu vaccine and COVID-19 vaccine together because they have not been able to experience and delineate what their side effects are or how they react to it,” says Dr. Lee. “If they’ve done well enough with the first COVID-19 vaccine dose, I think even with the second dose it would be okay for them to get the flu vaccine at the same time — as with the third additional dose.”

Additional Ways to Protect Yourself from COVID-19 and Flu

In addition to getting vaccinated, how you protect yourself from the flu and from COVID-19 are very similar: Avoid close contact with people who are sick, cover your mouth and nose with a tissue when coughing or sneezing, wash your hands, and avoid touching your eyes, nose, or mouth.

“COVID-19 and the flu are two different viruses, but the same things we’re following for COVID-19 will actually help prevent the flu as well,” says Dr. Nayyar.

Following general hygiene habits will help you avoid getting sick and needing to visit the hospital, which may be crowded with COVID-19 and flu patients this winter.

“The best line of defense for immunocompromised patients is not to get sick in the first place,” adds Dr. Nayyar.

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COVID-19 Vaccine Clinical Guidance Summary for Patients with Rheumatic and Musculoskeletal Diseases. American College of Rheumatology. August 19, 2021. https://www.rheumatology.org/Portals/0/Files/COVID-19-Vaccine-Clinical-Guidance-Rheumatic-Diseases-Summary.pdf.

Flu Season. Influenza (Flu). U.S. Centers for Disease Control and Prevention. September 28, 2021. https://www.cdc.gov/flu/about/season/flu-season.htm.

How should you time your flu and Covid-19 shots? Dr. Fauci explains. CNN Health. Accessed October 5, 2021. https://www.cnn.com/videos/health/2021/09/27/covid-19-vaccine-booster-flu-shot-timing-dr-fauci-sot-tsr-vpx.cnn/video/playlists/coronavirus/.

Interview with Geeta Nayyar, MD, MBA, Associate Professor of Medicine at the University of Miami

Interview with rheumatologist Jiha Lee, MD, a Clinical Assistant Professor at Michigan Medicine

Interview with Paul J. Maglione, MD, PhD, assistant professor medicine at Boston University School of Medicine and a pulmonary physician at Boston Medical Center

Possible Side Effects After Getting a COVID-19 Vaccine. COVID-19. U.S. Centers for Disease Control and Prevention. September 30, 2021. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/expect/after.html.