UC San Diego

The Severe Acute Respiratory Virus 2 (SARS-CoV-2) virus is responsible for the Coronavirus Disease 2019 (COVID-19) pandemic that continues to plague present-day society as new variants with increased virulence emerge. Viral infection may only occur once the host cell’s angiotensin-converting enzyme 2 (ACE2) receptor binds to an exposed viral spike glycoprotein’s Receptor Binding Domain (RBD) in its “up” state. Over the years as new variants emerged, an increase in infectivity has been observed. We hypothesize that mutations observed in later variants contribute to RBD instability, resulting in a greater likelihood of an RBD up spike. To elucidate the relationship between RBD dynamics and increased virulence amongst SARS-CoV-2 Wuhan 2019/Wild-type (WT), Delta, and Omicron variants, the MS-based protein footprinting method fast photochemical oxidation of proteins (FPOP) was performed using GenNext® Technologies’ Flash Oxidation (FOX®) system. As glycans are preferentially labeled, this instrument simultaneously allows for sufficient glycoprotein labeling via UV-based radical dosimetry and ensures user safety by generating hydroxyl radicals via lamp-based photolysis of hydrogen peroxide. Preliminary results show the FOX® system may be utilized to perform in vitro FPOP studies on the SARS-CoV-2 spike glycoprotein, however, further optimization is needed for more accurate comparison across conditions to discuss virulence in relation to spike structure.