SARS-CoV-2 and influenza co-infection: A cross-sectional study in central Missouri during the 2021–2022 influenza season

As SARS-CoV-2 and influenza viruses co-circulate, co-infections with these viruses generate an increasing concern to public health. To evaluate the prevalence and clinical impacts of SARS-CoV-2 and influenza A virus co-infections during the 2021–2022 influenza season, SARS-CoV-2-positive samples from 462 individuals were collected from October 2021 to January 2022. Of these individuals, 152 tested positive for influenza, and the monthly co-infection rate ranged from 7.1% to 48%. Compared to the Delta variant, individuals infected with Omicron were less likely to be co-infected and hospitalized, and individuals who received influenza vaccines were less likely to become co-infected. Three individuals had two samples collected on different dates, and all three developed a co-infection after their initial SARS-CoV-2 infection. This study demonstrates high prevalence of co-infections in central Missouri during the 2021–2022 influenza season, differences in co-infection prevalence between the Delta and the Omicron waves, and the importance of influenza vaccinations against co-infections. •SARS-CoV-2 and influenza A virus co-infections were high in central Missouri during the 2021–2022 influenza season.•The prevalence of co-infections differs between the Delta and Omicron variant waves.•Influenza vaccinations provide protection against SARS-CoV-2 and influenza co-infections.