As flu season picks up over the next few months, it’s going to get harder for public health officials to rely on trends in the number of people with coughs and fevers to monitor the COVD-19 pandemic. Starting next month, people coming into the emergency room with flu-like symptoms could just have the flu. 

“The symptoms overlap,” says Edward Belongia, an infectious disease epidemiologist at the Marshfield Clinic Research Institute in Wisconsin. Experts will have to lean on other methods, like lab testing, to distinguish COVID-19 from influenza. 

The Centers for Disease Control and Prevention (CDC) tracks illnesses that look like the flu (referred to as influenza-like illness) through a network of thousands of healthcare providers around the country. They publish data showing the baseline levels of influenza-like illness in different areas during a flu season, which typically runs from around October to February. 

The COVID-19 pandemic started accelerating in parts of the United States in March, just as the flu was dying down. Reports of influenza-like illness started to climb. Normally, the illness reports track pretty closely with the amount of flu cases confirmed by lab testing. But that wasn’t happening anymore: instead, in states like New York, illness reports went up while the amount of flu caught by labs went down. Researchers were able to use the gap to get a picture of how much coronavirus was circulating. 

That type of rough measure is useful for new, relatively mysterious diseases like COVID-19, says John Brownstein, an infectious disease epidemiologist and chief innovation officer at Boston Children’s Hospital. Early on, doctors didn’t have a good grasp of what, specifically, cases of COVID-19 looked like. “That’s when you look for aberrations in data, and spikes beyond what you’d expect from historical data on flu and other respiratory viruses,” he says.  

Distinguishing the two illnesses was easier in March and April when flu was on the way down — any spikes or departures from the usual baseline levels of influenza-like illness were more apparent. Doctors could also more comfortably predict that someone sick with flu-like symptoms didn’t actually have the flu. 

Over the past few months, doctors and researchers have also refined the criteria for illnesses that are likely to be COVID-19. It’s an ongoing process, and there are still overlaps between COVID-19 and the flu — fever, shortness of breath, cough — but some of the features specific to coronavirus infection, such as a loss of taste or smell, are a bit clearer. 

North Carolina has already been able to break down their symptom surveillance into two data streams: influenza-like illness and COVID-19-like illness. Its division of public health pulls in information from emergency departments around the state, and an algorithm goes through and looks for patients who meet their definitions for each illness, says Zack Moore, a state epidemiologist in North Carolina. If someone says they lost their sense of taste, that would get flagged as COVID-19-like illness rather than something resembling the flu. 

Symptom surveillance isn’t the only way public health officials monitor the pandemic, though. They also track metrics like the number of positive tests, which show how many people are actually infected with the coronavirus. Combining multiple data sources helps experts get a fuller picture of the pandemic than they’d be able to get with just one measure. 

Lab data will help public health officials make sense of the messier symptom surveillance they could see during flu season. Testing for COVID-19 will be much more widespread this flu season than it was in February and March. If officials see increases in influenza-like illness, they’ll be able to analyze it in the context of test results. North Carolina, for example, gets information on testing results for flu, COVID-19, and other viruses from a network of hospitals. “We will be leaning very heavily on the information about what respiratory viruses are being detected on the laboratory side to help us understand the symptom surveillance data,” Moore says. 

It always takes context to properly interpret flu-like symptom surveillance data, even without the urgency of a pandemic. Moore says they often see slight jumps in influenza-like illness reports just before Christmas, for example, but it doesn’t usually mean there’s more flu. Typically, it’s another type of respiratory illness.

The stakes are high. Figuring out how many of the people who get sick this fall and winter actually have COVID-19 versus the flu is critical to managing and tracking the pandemic. Brownstein thinks that the push to successfully measure the signals from two, simultaneous viruses could help refine disease tracking overall. “The hope would be that COVID-19 is forcing us to do a better job around general surveillance,” he says.