Abstract Despite being the most widely consumed meat worldwide, the pig industry faces economic challenges from respiratory viruses including influenza. Pigs are also used as a reliable translational model for human respiratory disorders due to their similar respiratory tracts. However, limited pig-specific reagents have hindered understanding the pig’s immune system. Hence, here we used single cell RNA sequencing (scRNAseq) for unbiased transcriptional profiling of pig immune responses during influenza infection and oseltamivir antiviral therapy. Fourteen six-week-old mixed-breed pigs were intratracheally infected with pandemic 2009 H1N1 influenza virus. Seven of these pigs were treated for 5 days with oseltamivir. A control group was mock-infected. Lung samples were taken 5 days post-infection for scRNAseq, histopathology, and virus titers. We identified 24 pig leukocytes populations which were integrated with previously published human and mouse lung cells. Influenza virus infection/oseltamivir treatment altered the cellular composition, transcriptional networks, and cell-cell interactions in the lung. γδ T cells that are unique to pigs and abundant in the lung responded strongly to infection. Oseltamivir reduced antiviral and inflammatory responses. Our data provide a resource to better understand the pulmonary immune responses of pigs and advances using swine as a model for studying human pulmonary immune responses.
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