Using single cell spatial and transcriptional analysis to understand early host response to RNA virus infections

Abstract The innate immune system serves as the first line of defense against pathogens. One innate defense mechanism is the RIG-I like receptor pathway (RLR) which signals through the mitochondrial anti-viral signaling protein (MAVS) which plays a role in initiating the interferon (IFN) response to RNA viruses such as vesicular stomatitis virus (VSV). To investigate the mechanisms the MAVS-dependent pathway has on early viral control following VSV infection in vivo, we used a combination of two approaches: single cell RNA sequencing and multiplex imaging. These two techniques allow us to assess the individual cellular response to VSV in whole lymph node tissue. After intradermal inoculation, skin draining lymph nodes were assessed using single cell sequencing. Macrophages and plasmacytoid dendritic cells (pDCs) showed significantly elevated IFN stimulated gene (ISG) detection in C57Bl/6J (B6) mice compared to the MAVS−/− animals at 8 hours post infection (hpi), yet there was no detectable viral reads. This early initiation of ISG expression played a role in detection of viral RNA at 24 hpi which saw significantly elevated viral RNA in the MAVS−/− animals compared to the B6 animals. Interestingly, the virus replication in both conditions was contained to the macrophage populations suggesting that without the MAVS pathway active, the virus was still contained. Combining this information along with the observed spatial organization through multiplex tissue imaging, we aim to develop a model illustrating the role of the MAVS-dependent pathway in controlling early virus replication. Animal experiments were done in accordance with the guidelines of the NIAID/NIH Institutional ACUC. This research was supported by the IRP of NIH/NIAID.