Abstract SARS-CoV-2, the cause of COVID-19, continues to cause widespread infection and morbidity, but death rates have decreased as most of the world has either been infected or vaccinated or both. However, at the same time, it has become clear that many patients have developed long term sequelae. These sequelae, called PASC (Post Acute Sequelae of COVID-19), affect many organ systems even though virus is found at autopsy in nearly all studies only in the respiratory and gastrointestinal tracts. One common symptom of acute COVID-19 is anosmia. Recovery of olfactory function is often incomplete in patients. However, only supporting (sustentacular) cells and not olfactory sensory neurons are infected in patients, raising the question of how infection of a supporting cell could have such profound effects on olfaction. In addition, neurological disease is also present in many patients with PASC. Many of these manifestations reflect ongoing inflammation (usually observed on autopsy), but the basis of these inflammatory changes is unclear since virus cannot be detected. We have isolated a mouse- adapted virus that causes severe acute respiratory disease in infected mice, as well as persistent signs of disease is the lungs and brains months after the acute infection has resolved. Infected mice develop anosmia, as well as long term behavioral abnormalities and defects in neurotransmitter expression, but virus is not present in the brain. Our central hypothesis is that ongoing inflammation is a major contributory factor in the observed dysfunction in the olfactory and neurological systems. This hypothesis will be addressed in the following specific aims: Specific Aim 1: To understand the relationship between sustentacular cell infection and olfactory dysfunction and to understand the basis of chronic changes in the brains of SARS-CoV-2-infected mice. Acute and chronic changes in olfactory pathways will be probed using electrophysiological and olfactory measurements. These changes will be related to sustentacular function and gene expression. Parts of the brain, such as the substantia nigra, which are affected in neurodegenerative diseases such as Parkinson’s disease will be studied. Our preliminary results show changes in neurotransmitter expression in the substantia nigra several months after infection, supporting this hypothesis. Specific Aim 2: To examine the role of viral macromolecular products and infiltrating inflammatory cells in the brains of mice infected with SARS-CoV-2 in the development of PASC. Using molecular and immunological approaches, we will assess whether inflammation results from extrapulmonary SARS-CoV-2 infection and rapid clearance within the first days of infection (‘hit and run’). Using a mouse in which infiltrating myeloid cells can be readily identified, we will analyze localization, function and gene expression of these infiltrating myeloid cells, as well as of T cells that infect the brain chronically. The ultimate goal is to relate these changes in inflammation to the neurological/olfactory dysfunction that we characterize in Aim 1.

Narrative Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes substantial morbidity and mortality in humans. It has become apparent that, even as most people have developed an immune response to the virus either from infection or vaccination, long term sequelae of the infection will be a burden on human health for years to come. This project will examine long term effects of the infection in the olfactory system and brain, with the ultimate goal of identifying novel therapeutic targets.