SARS-CoV-2 and Autophagy

PROJECT SUMMARY/ABSTRACTCoronaviruses are major causes of disease worldwide, from the common cold to outbreaks of strains causingsevere and sometimes lethal respiratory distress, including SARS, MERS, and the current outbreak of COVID-19 caused by SARS-CoV-2. It has been observed over the last two decades that multiple coronavirusesinteract with components of the autophagy pathway to rearrange cellular membranes and generate sites forRNA replication. In this application, we propose to test the interactions of SARS-CoV-2 with the autophagypathway. We will rapidly assess whether SARS-CoV-2 has similar interactions with the autophagy pathway asother coronaviruses, then extend the field by identifying how these interactions interfere with viral replication,providing novel therapeutic targets. We will carry this strategy out through three Aims: In the first, we willidentify requirements from the early autophagy pathway for SARS-CoV-2 replication. Data from coronavirusstudies suggest that the autophagy protein LC3 is recruited to generate double membraned vesicles for virusgenomic RNA replication. Other data suggest LC3 is utilized through the ER-associated degradation (ERAD)machinery to generate replication vesicles. We will determine which, if either, of these two pathways is used bySARS-CoV-2. In the second aim, we will determine the role of vesicle acidification in SARS-CoV-2 replication.There is strong evidence that acidification of vesicles plays a role in multiple steps of CoV replication, and wewill identify the role of vesicle acidification in SARS-CoV-2 replication. In the third aim, we will identify thespecific roles of SARS-CoV-2 non-structural proteins in induction of the autophagic machinery. We haveidentified previous studies of expression of non-structural proteins in coronavirus and will use this to guide ourstudy of SARS-CoV-2 proteins. These Aims complement existing studies of autophagy in RNA viral life cyclesby the Jackson Lab while leveraging the existing expertise of the Frieman Lab in studying cell biology ofcoronavirus infections. By completing these Aims, we will understand whether SARS-CoV-2 interacts with theautophagy pathway in a similar or unique fashion compared to other coronaviruses, and extend thecoronavirus field by identifying specific host-virus interactions that may be targeted for COVID-19 therapies.