PROJECT SUMMARY As the COVID-19 pandemic continues, managing post COVID-19 long-haul symptoms have become the next level challenge. Persistent skeletal muscle aches (myalgia) and fatigue are among the most common symptoms reported by COVID-19 long haulers who have symptoms beyond 20 weeks. The myalgia associated with COVID-19 often responds poorly to pain medications. The long-COVID symptoms, especially myalgia, fatigue, dyspnea, and brain fog, significantly affect the quality of life and employment status of COVID-19 long haulers. Although myalgia and fatigue are common during acute respiratory viral infection, the muscle symptoms caused by SARS-CoV-2 often last much longer than other respiratory viral infections including influenza. The pathogenic mechanisms underlying the development and persistence of myalgia and fatigue associated with COVID-19, however, is largely unknown, which makes the treatment difficult. We thus propose this R21 study to explore the mechanisms. There are four potential mechanisms, including direct viral invasion to skeletal muscle, ischemic muscle injury from microthrombi and cardiopulmonary dysfunction, immune- mediated muscle damage caused by an exuberant systemic inflammatory response, and altered muscle energy homeostasis. We propose to address these mechanisms by conducting an exploratory longitudinal study to characterize the skeletal muscle response to respiratory SARS-CoV-2 infection to determine how skeletal muscle is affected at the histopathological level and transcriptional level during and after acute infection, and whether the muscle responses to SARS-CoV-2 and influenza A (IAV) viral infections are different. By using muscle tissues collected from SARS-CoV-2-infected golden hamsters, one of the best small animal models for COVID-19, our preliminary study found no detectable SARS-CoV-2 nucleocapsid protein or inflammation to suggest direct viral invasion to muscle. There were no microthrombi either. These findings lead to our central hypothesis that myalgia and fatigue associated with COVID-19 are likely caused by altered muscle energy metabolism due to a systemic inflammatory response and hypoxia during acute SARS-CoV-2 infection, followed by a prolonged recovery course. This hypothesis will be addressed by two specific aims. Aim 1 will identify muscle histopathological changes at different stages after SARS-CoV-2 infection and compare with IAV infection. Aim 2 will characterize the muscle transcriptional response to SARS-CoV-2 infection and the dynamic transcriptional changes with time. We will also compare SARS-CoV-2 infection with IAV infection to address whether the recovery of the initial skeletal muscle response to SARS-CoV-2 infection is slower. Our study will likely identify histopathological features and transcriptional signatures that may underlie myalgia and fatigue associated with COVID-19. The mechanisms uncovered will help guide therapies.