When you wake up with a fever, sore throat, and body aches, it’s hard to tell if it’s the flu or COVID-19. Both hit fast, both spread easily, and both can land you in the hospital. But in 2025, something unexpected happened: influenza caused more deaths and hospitalizations than COVID-19 for the first time since the pandemic began. That shift changed everything - from how doctors test you to how long you need to stay home. Here’s what you actually need to know right now.
Testing: Why One Test Isn’t Enough Anymore
In 2024-2025, hospitals across the U.S. started running multiplex PCR tests that check for flu, COVID-19, and RSV all at once. Why? Because symptoms overlap too much. A runny nose, cough, and fatigue could be either - and guessing leads to mistakes. A survey of 1,200 clinicians found that nearly one in five patients got the wrong diagnosis in outpatient settings.
Fast antigen tests still exist, but their accuracy varies. For flu, they catch about 75-85% of cases. For COVID-19, they’re better - around 80-90% - but only if you test during the peak viral load. That’s why timing matters. Flu symptoms usually show up 1-4 days after exposure. COVID-19? It can take 2-14 days. If you test too early, you might get a false negative. The CDC now recommends testing within the first 48 hours of symptoms for both.
And here’s the kicker: many people still rely on single-pathogen tests. But with over 78% of U.S. hospitals using combined panels, waiting for separate tests means losing 48 hours of critical treatment time. If you’re sick and your doctor only tests for flu, ask if they can also check for SARS-CoV-2. It’s now standard.
Treatment: Antivirals Are Time-Sensitive
For flu, oseltamivir (Tamiflu) is still the go-to. But it only works if taken within 48 hours of symptoms. The CDC says early use cuts hospitalization risk by 70%. Yet, in 2025, only 63% of hospitalized flu patients got it on time. Why? Many waited too long - or didn’t realize they needed it.
For COVID-19, Paxlovid (nirmatrelvir/ritonavir) is the gold standard. It reduces hospitalization by 89% when taken within five days. But here’s the problem: in 2025, only 41% of hospitalized COVID-19 patients received it. Why? Some were too sick to take pills. Others had drug interactions - Paxlovid can clash with common meds for blood pressure, cholesterol, or heart conditions.
There’s also a new player: a zanamivir prodrug approved in January 2025. It’s 92% effective against the dominant H1N1 pdm09 strain and works for people who can’t swallow pills. It’s not everywhere yet, but it’s starting to show up in ERs.
Antibiotics? Don’t take them unless you have a bacterial infection. Flu patients are more likely to get them - 38% of hospitalized flu cases had mixed bacterial pneumonia. COVID-19 patients? Only 22%. That’s because pure viral pneumonia is more common with COVID-19. Antibiotics won’t help that.
Isolation: The 5-Day Rule Isn’t the Same for Both
The CDC says isolate for 5 days for both illnesses. Sounds simple, right? But the rules underneath are totally different.
For flu: You can stop isolating after 24 hours without fever (and no fever-reducing meds). You don’t need a test. That’s because flu virus shedding drops sharply after day 5. Kids? They can spread it for up to 14 days, so schools often keep them home longer.
For COVID-19: You must test negative on an antigen test on day 5 before ending isolation. Why? The XEC subvariant sticks around longer. Studies show people can still shed infectious virus for 8-10 days. Some immunocompromised people shed it for weeks. That’s why hospitals still require negative tests before letting patients leave isolation rooms.
And here’s what most people don’t know: masks still matter. After day 5, the CDC recommends wearing a mask around others for another 5 days - especially indoors. This applies to both illnesses. Why? You might still be contagious, even if you feel fine.
Healthcare workers follow even stricter rules. Ninety-two percent of hospitals require N95 masks for staff caring for COVID-19 patients. For flu? Only 68%. That’s because SARS-CoV-2 spreads more easily in close quarters - and causes more hospital-acquired pneumonia.
Who’s at Higher Risk? The Real Differences
It’s not just about symptoms. The people most likely to get seriously sick are different.
Flu hits harder in people with no underlying conditions. In 2025, 42% of hospitalized flu patients had no chronic illnesses. That’s unusual - most think flu only hurts the elderly or asthmatics. But this season, healthy adults and young parents were flooding ERs. Why? The H1N1 pdm09 strain is aggressive, and vaccination rates dipped below 53%.
COVID-19 still targets those with weakened immune systems. People with kidney disease, cancer, autoimmune disorders, or those on immunosuppressants were far more likely to be hospitalized with COVID-19 than flu. In fact, 71% of severe COVID-19 cases had at least one major risk factor.
Loss of taste or smell? That’s still a red flag for COVID-19. It happens in 40-80% of cases. For flu? Only 5-10%. If you lose your sense of taste, assume it’s COVID-19 until proven otherwise.
What’s Changed in 2026?
The CDC’s 2025-2026 outlook says we’re entering a new phase. Flu and COVID-19 are now treated as co-circulating threats - not separate epidemics. The “unified respiratory guidance” means one set of clinical protocols, but still separate rules for isolation and antiviral use.
Vaccines? Coverage is up. Flu shots hit 52.6% of the U.S. population in 2025. Updated COVID-19 vaccines? 48.3%. That small gap helped flip the mortality numbers. But if a new variant emerges - say, one that dodges immunity - hospitalizations could spike again by late 2026.
Testing is getting easier. BinaxNOW’s combined flu/COVID test, approved in late 2024, is now sold in pharmacies. It’s 89% accurate for both. At-home tests are cheaper, faster, and more reliable than ever. If you’re unsure what you have, buy the combo test. It costs less than a doctor’s copay.
Insurance coverage? Still uneven. Eighty-seven percent of people with private insurance got full coverage for flu antivirals. Only 63% got the same for Paxlovid. If you’re denied, appeal. The FDA’s expanded EUA now covers mild cases with risk factors - and many insurers are catching up.
What to Do If You’re Sick Right Now
- Take a combined flu/COVID test as soon as symptoms start.
- If positive for flu, call your doctor within 24 hours to get Tamiflu or the new zanamivir prodrug.
- If positive for COVID-19, ask if Paxlovid is right for you - especially if you’re over 50, have diabetes, or are immunocompromised.
- Stay home for 5 days. No exceptions. Even if you feel better.
- On day 5, take an antigen test. If negative, you can end isolation. If positive, keep isolating until day 7 or until you test negative.
- Wear a mask around others for 5 more days.
- Don’t take antibiotics unless your doctor says you have a bacterial infection.
And remember: this isn’t 2020 anymore. We have tools. We have data. We know how to handle this. But only if we treat flu and COVID-19 for what they are - similar, but not the same.
Can I get flu and COVID-19 at the same time?
Yes. Co-infections happened in about 12% of hospitalized patients during the 2024-2025 season. Symptoms can be worse, and recovery takes longer. Testing for both at the same time is the only way to know.
Do I need to isolate if I’m vaccinated?
Yes. Vaccines reduce severity, but they don’t stop transmission. You can still carry and spread both viruses, even if you feel fine. Isolation rules apply to everyone - vaccinated or not.
Why is Paxlovid harder to get than Tamiflu?
Paxlovid has more drug interactions - it can’t be taken with many common medications. That means doctors need to check your full list of prescriptions before prescribing it. Tamiflu has fewer restrictions. Also, insurance coverage for Paxlovid is still catching up in some states.
Is the new flu antiviral available at my pharmacy?
Not yet everywhere. It’s being rolled out to hospitals and major clinics first. By mid-2026, it should be in most pharmacies. Ask your pharmacist if they’ve received shipments. If not, they can order it - the FDA has approved it for widespread use.
Should I get tested if I only have a sore throat and no fever?
Yes. Both flu and COVID-19 can start with just a sore throat or cough. Fever isn’t required. The CDC says testing is recommended for anyone with respiratory symptoms during peak season - even mild ones.
Next Steps: What to Do Today
- Check your medicine cabinet. Do you have a combined flu/COVID test? If not, buy one now.
- Review your vaccination records. If you haven’t had a flu shot this season, get one. If you’re eligible for the updated COVID-19 vaccine, schedule it.
- Talk to your doctor. Ask if you’re a candidate for Paxlovid or the new flu antiviral - especially if you’re over 50 or have chronic conditions.
- Keep masks on hand. N95s or KN95s are still the best option for crowded places.
- Don’t panic. But don’t ignore symptoms. Both illnesses are manageable - if you act fast.
