COVID-19 and flu pose similar long-term risks, except for severe cases

Researchers tracking nearly 75,000 COVID-19 cases and almost 19,000 influenza cases through Kaiser Permanente's Southern California health system have found something that challenges a widespread assumption: the long-term health complications that follow COVID-19 are not dramatically different from those that follow the flu.

The study, published in PLOS Medicine in October 2025, examined what happens in the months after people recover from their acute illness. Between September 2022 and December 2023, the researchers followed patients across the full spectrum of care—from those who saw a doctor by video call to those hospitalized with severe respiratory disease. Within 31 to 90 days after infection, COVID-19 patients had only a 4 percent higher risk of developing post-acute sequelae, the medical term for lingering complications. By the time six months had passed, that difference had nearly vanished. The risk of any post-acute condition was essentially the same for both groups.

But there is a crucial exception. When the researchers looked specifically at severe complications requiring hospital admission, the picture shifted. COVID-19 patients who had been hospitalized during their initial illness faced 31 to 49 percent higher risk of needing inpatient care again for post-acute problems compared to influenza patients who had also been hospitalized. This gap persisted through the entire six-month follow-up period. Among patients whose initial infection was mild enough to treat at home or in an emergency department, no meaningful difference emerged between COVID-19 and influenza in terms of severe post-acute complications.

The study included 74,738 COVID-19 cases and 18,790 influenza cases, with nearly all participants retained through at least three months of follow-up. Overall, 45 percent of COVID-19 patients and 39 percent of influenza patients developed post-acute conditions requiring medical care within the first three months. By six months, those figures rose to 53 percent and 44 percent respectively. Heart and lung problems dominated the list of complications for both groups, followed by conditions affecting the nervous system, muscles, kidneys, and mental health.

Two factors appeared to narrow the gap between COVID-19 and influenza outcomes. Patients who received antiviral medications during their acute illness showed reduced risk of severe post-acute complications. Similarly, people whose vaccination status was current at the time of infection—three or more COVID-19 vaccine doses for COVID patients, or a recent flu shot for influenza patients—showed no meaningful difference in severe post-acute risk compared to the other group. This suggests that preventing severe acute illness in the first place may be the most effective way to avoid long-term complications.

The researchers acknowledge important limitations. Their analysis captured only complications serious enough to require a healthcare visit, missing patient-reported symptoms and quality-of-life impacts that might not show up in medical records. The study also did not include children, and it was restricted to people who received a diagnosis of acute respiratory illness, meaning asymptomatic infections were not tracked. Testing practices differed during the study period—COVID-19 testing was more widespread than influenza testing—which could have skewed the comparison if milder flu cases went undetected.

The findings suggest that the long-term burden of influenza may have been historically underestimated. While post-COVID conditions have received substantial medical and public attention, similar complications following influenza have been documented in medical literature for over a century but have not generated equivalent clinical focus or research investment. The study points toward a more nuanced understanding: both viruses carry substantial risk of long-term health consequences, but the nature of that risk differs. For most people, the two infections pose comparable threats. For those sick enough to require hospitalization, COVID-19 appears to carry a higher risk of severe post-acute illness—a distinction that may reflect the greater severity of COVID-19 among hospitalized patients rather than something unique to the virus itself.