Validation of a naturally-occurring animal model for SARS-CoV-2 infection

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The overall objective of this project is to validate mechanisms of viral fitness and immunopathogenesis during SARS-CoV-2 infection in domestic cats to establish baselines for downstream translational studies. Major goals (specific aims) for this project are as follows: Aim 1. Evaluate in vivo infection kinetics and viral fitness of SARS-CoV-2 in the domestic cat. We will use droplet digital PCR (ddPCR) to quantify absolute copy numbers of SARS-CoV-2 RNA in blood, nasal swabs, and respiratory tissues in order to characterize viral replication kinetics during acute infection in domestic cats, and compare these changes with co-expression of viral antigen and ACE2 receptors in respiratory tissues (IHC). We will also use virus amplicon sequencing assembly to evaluate the potential for genetic divergence in the feline host (i.e. does the virus evolve during infection in domestic cats). Hypotheses: SARS-CoV-2 infects ACE2-expressing feline respiratory cells, resulting in progressive replication of genetically conserved virus elements and lesions analogous to human COVID-19 Aim 2. Identify key factors of immune dysfunction contributing to COVID-19 disease progression. We will use scRNASeq, flow cytometry, and multiplex immunoassays to define shifts in the immune profile during acute SARS-CoV-2 infection. We will compare changes in immunological parameters with viral replication kinetics (Aim 1) and clinical disease progression in order to (i) define how perturbations of immune function impact clinical disease progression and (ii) identify novel immunomodulatory targets to guide more effective therapies or vaccine candidates. Hypothesis: Progression of severe COVID-19 in cats is analogous to human disease and correlated with (i) CD4+ and CD8+ T cell deficiencies and (ii) pro-inflammatory cytokine expression (IL-6, IL-1β, TNFα,)