Interference between SARS-CoV-2 and influenza B virus during coinfection is mediated by induction of specific interferon responses in the lung epithelium

Coinfections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus have represented a major health concern since the beginning of the COVID-19 pandemic. The continued spread and constant emergence of new SARS-CoV-2 variants mean that cocirculation and coinfection with seasonal respiratory viruses will continue. Despite the considerable contribution of influenza B virus (IBV) infections to global disease burdens, its interactions with SARS-CoV-2 remain largely unstudied. In this study, we sequentially coinfected lung epithelial cells with representative SARS-CoV-2 variants and IBV strains. We found that prior infection with IBV impaired SARS-CoV-2 D614G, Delta and Omicron BA.1 replication, but did not affect replication of the more recent Omicron EG.5.1 variant. We additionally show that pre-infection with SARS-CoV-2 reduces live attenuated influenza vaccine (LAIV) replication, suggesting vaccine effectiveness in children carrying SARS-CoV-2 pre-infections can be negatively impacted in coinfection. Both SARS-CoV-2 and IBV induced strong type III interferon (IFN) responses, whereas SARS-CoV-2 drove type I IFN production not seen in IBV infection, suggesting viral interference through specific IFN responses. Treatment with innate immune response inhibitors BX795 and Ruxolitinib abrogated viral interference between IBV and SARS-CoV-2 in coinfection, demonstrating that IFN-stimulated gene (ISG) responses play a vital role in viral interference. More specifically, we show that the magnitude and timing of ISG expression, triggered by the primary infecting virus in sequential coinfection, facilitates viral interference between IBV and SARS-CoV-2.