Differentiating between respiratory pathogens can be challenging for primary care providers. It can be very difficult to distinguish SARS-CoV-2 and influenza infections, and these viruses can co-infect a patient.15 COVID-19 also has an extremely variable presentation. All providers will need to have a high clinical suspicion for both illnesses during the flu season this fall.

Patients with influenza typically present with acute onset of fever, cough, headache, muscle and joint pain, severe malaise, fatigue, sore throat, and runny nose.16 The incubation period typically is 2 days but ranges from 1 to 4 days.16 Children with influenza may have vomiting and/or diarrhea.17

Patients with COVID-19 most commonly experience fever, dry cough, and fatigue;  they may also have body aches, sore throat, diarrhea, conjunctivitis, headache, loss of taste or smell, rash on skin, or discoloration of fingers or toes.18 COVID-19 tends to have a more gradual onset, with a mean incubation period of 5 days and a range of 1 to 14 days.19

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Studies have shown that both patients with influenza and those with COVID-19 present with fever, cough, and dyspnea.20 Fever tends to be more severe in patients with influenza, and some patients with COVID-19 do not develop fevers, even when their illness has advanced to pneumonia.21,22 Gastrointestinal symptoms have been found to be much more prevalent in patients with COVID-19 compared with those with influenza.20-22 Another potential differentiating factor is that fatigue tends to be more severe in patients with COVID-19 (Table 1).20,22

Patients infected with SARS-CoV-2 can be co-infected with other respiratory pathogens, such as influenza. A study by Kim et al demonstrated that 20.7% of SARS-CoV-2–positive patients also were positive for 1 or more additional respiratory pathogens.15 Therefore, diagnosis of 1 respiratory pathogen does not rule out an infection with another. Although general testing for respiratory pathogens in addition to COVID-19 may not be beneficial because it does not rule out the coronavirus, testing for influenza is indicated because this could affect the treatment plan.15