Single-cell analysis of Mucosal Associated Invariant T cells in influenza A virus infection

<bold>Introduction:</bold> We previously demonstrated TCR-independent MAIT cell protection against severe influenza A virus (IAV) infection in vivo in mice, mediated, at least partially, via IFN-γ. To understand how MAIT cells regulate the immune response during virus infection, we performed single cell analysis and spectral flow cytometry on whole lungs from wild-type (wt) C57BL/6 and MAIT deficient (MR1-/-) mice post IAV infection. <bold>Methods:</bold> MR1-/- and wt mice were infected i.n. with 100 PFU of IAV PR8, and lung tissues analysed at days 0, 3, 5, 7 post-infection by 3' Chromium 10X. 71,762 cells were sequenced, and analysed by CellRanger mapping to an integrated reference genome including both virus and mouse genome enabling assessment of infected and bystander cells and analysed by pseudobulk expression (Muscat), differential gene expression, GSEA, KEGG pathways, Reactome pathways, and the MSigDB Hallmark gene sets, and NicheNet for cell-cell communication. <bold>Results:</bold> Virus was detected by genome mapping predominantly in myeloid cells. A specific subtype of neutrophil emerges during viral infection. Gene expression differed between infected and bystander cells within the same cell type. MAIT cell deficient mice exhibited altered microenvironment and immune responses. In MAIT cells the main pathways upregulated were related to antiviral response, response to interferon γ/β, and cytokine-mediated signalling. Despite absence of riboflavin-synthesising microbes, infection also induced a tissue repair signature peaking at day 3. <bold>Conclusions:</bold> MAIT cells are activated by viral infection and contribute to type-1 IFN-mediated antiviral responses <italic>in vivo</italic> and to a tissue repair programme.