The Impact of SARS-CoV-2 Accessory Proteins and Non-Spike Mutations on Viral Pathogenesis

Abstract

In December of 2019, a viral pneumonia emerged in Wuhan, Hubei Province, China. This disease, known as COVID-19, would continue to spread rapidly. The causative agent of this pneumonia was later found to be a novel coronavirus designated SARS-CoV-2. To date, this virus is responsible for over 750 million cases and nearly 7 million deaths. Due to the massive impact this virus had on the population, efforts to manufacture a vaccine based on the immunodominant spike antigen were both swift and successful. Despite this development, the virus continues to spread, and additional characterization of SARS-CoV-2 is needed to assist in the development of therapeutics and preparedness for significant resurgence. We were specifically interested in the accessory proteins located at the 3′ end of the viral genome. Coronaviral accessory proteins have previously been shown to impact viral replication and pathogenesis, although they are not necessary for the virus to cause disease. To assess the impact of the accessory proteins of SARS-CoV-2 on viral replication and pathogenesis, we synthesized novel infectious clones of this virus that lacked one or more of these accessory proteins and examined their replicative fitness and impact on pathogenesis in a mouse model. Soon after we began our work with these accessory proteins, viral variants of SARS-CoV-2 emerged and began to dominate over the wildtype strain. We noticed a significant number of mutations in the accessory protein region of these genomes and aimed to characterize their impact on pathogenesis through the synthesis of novel infectious clones possessing the variant spike protein in the wildtype background to allow for determination of the effect of non-spike mutations on variant pathogenesis. Our work with these deletion viruses and variant spike viruses led us to determine that the accessory protein ORF8 of SARS-CoV-2, which differs significantly from that of SARS-CoV-1, contributes significantly to the modulation of inflammation in the lungs during infection and the variants of SARS-CoV-2 have evolved to lose this function.