Enhanced interferon-stimulated gene signatures in B cells following influenza B virus infection compared to influenza vaccination

Despite influenza vaccination, some individuals succumb to life-threatening influenza or even death. Yet our understanding of differential immune features generated by vaccination versus infection by influenza A and influenza B viruses (IAVs, IBVs) is limited. We sought to define molecular signatures of influenza-specific B cells elicited following influenza virus infection or vaccination towards both IAV and IBV subtypes. Using barcoded fluorescently-labelled haemagglutinin (HA)-specific probes, we performed single-cell RNA sequencing of influenza-specific B cells on day 0, 7 and 28 following influenza inactivated vaccination, in comparison to hospitalized patients during acute IAVor IBV as well as at 1-month convalescence. Comparing B cell responses elicited by infection and vaccination, the most striking findings stemmed from increased interferon-stimulated gene signatures, especially IF44L, IFITM1 and XAF1, in total B cells during acute IBV infection, which decreased at 1 month following patients’ recovery. These interferon-stimulated genes were not observed in B cells following influenza vaccination encompassing both IAV and IBV components or IAV infection in our patients. For HA-specific B cells, transcriptomic analysis revealed phenotypic differentiation and isotype class-switching following vaccination, with evidence of clonal sharing between memory and atypical B cell phenotypes. In in vitro influenza virus infection experiments, IBVs showed higher infectivity of human peripheral blood mononuclear cells, including B cells, in comparison to IAVs. Additional co-culture of infected PBMCs with plasma obtained from patients hospitalized with IAV, IBV, COVID-19 and RSV increased the infectivity of immune cells by both IBV and IAV, suggesting that B cell infectivity we observed might also be driven by plasma mediators. IBV infection also resulted in reduced B cell proliferation compared to IAV, potentially associated with the antiproliferative effect of IFITM1. Our findings comparing and contrasting influenza-specific B cell responses elicited following acute influenza virus infection versus vaccination provide key insights into understanding B cell immunity towards IBV versus IAV infections, in contrast to vaccination responses, to inform rational vaccine design and therapeutic targets.