Abstract Over the past three months, COVID-19 has emerged as a major pandemic with over ~ 1.9 million productive infections and ~100,000 deaths due to infection with the novel Coronavirus SARS-CoV-2, a viral pathogen which is highly infectious and pathogenic. This is particularly true in the elderly and people with immunocompromising conditions who are exhibiting acute respiratory distress syndrome at a greater frequency. Unfortunately, no known cures and vaccines exist. Worse, there were no well-characterized animal models of SARS-CoV-2 infection and COVID-19 disease till recently. With the limited information on host innate immune responses, early reports implicate a role for inflammation in mediating COVID-19 disease. As an logical extension of ongoing work on innate immune responses in the lung on the parent grant, we hypothesize that similar to tuberculosis (TB), control of SARS-CoV2 will correlate with accumulation of innate lymphoid cells including NK cells in the lung, while inflammation and increased disease will be associated with myeloid cell accumulation. To test this hypothesis, we will utilize recently acquired banked lung samples from a novel rhesus macaque model of SARS-CoV-2 infection/COVID-19 disease developed at the SouthWest National Primate Research Center (in collaboration with Deepak Kaushal Lab, Co-I on parent grant). These new results from the NHP model indicate that rhesus macaques develop signs of human COVID-19 disease including pyrexia, dysregulation of complete blood cell counts indicative of viral infection, acute stress markers, and experience cough and weight-loss. This is accompanied by high viral loads in bronchoalveolar lavage (BAL) and lungs, and pneumonia is detected by CT scan as well as grossly at necropsy. Single cell RNA sequencing (scRNA-seq) is just beginning to be applied to the immune system in animal models and humans in both healthy and diseased states. The application of scRNA-seq to COVID-19 samples from macaques is particularly well-suited, as the immune cells infiltrating the lung that may play roles in the disease are diverse, including virtually all types of lymphocytes (ILCs, CD4+ T cells, CD8+ T cells, γδ T cells, NK cells, B cells) and several myeloid cell types (monocytes, macrophages and potentially dendritic cells (DCs) and neutrophils (PMNs)). Within each of these subtypes, further heterogeneity exists in terms of cytokine production and transcription factor expression, such that each subtype may demonstrate further heterogeneity. Because scRNA-seq can define the transcriptomic heterogeneity of a complex community of cells and assign unbiased identity classifications to cell populations, it is optimally suited for application to the study of complex inflammatory disease such as TB and COVID-19. The data obtained and its computational analysis will delineate the nature of inflammation, especially the role of innate cells such as NK cells and ILCs in COVID-19 mediated inflammation. These ...