Characterizing the broad antibody response to HIV superinfection

The greatest hope for an end to the COVID19 pandemic caused by SARS-CoV-2 is a vaccine and/orantibody therapy. At this point, we know little about protective immunity to SARS-CoV-2, including whichepitopes are the major target of the antibody response to this virus and whether antibodies to specific epitopesimpact outcome. Advancing our understanding of SARS-CoV-2 immunity is critical not only for informingvaccine design, but also for understanding the epidemiology and spread of SARS-CoV-2, including amongasymptomatic individuals. There is considerable focus on targeting the region of the Spike protein that interactswith the receptor, which has also been a focus of HIV vaccine efforts for more than three decades with limitedsuccess to-date. Thus, given the urgency due to this pandemic, multiple approaches are warranted tocomplement this approach. We propose comprehensive profiling of the antibody response to SARS-CoV-2,which has the potential to detect both neutralizing and non-neutralizing antibody responses to all the proteinsin the virus. For this purpose, we will develop novel methods based on creating custom Coronavirus (CoV)phage display peptide libraries and using immunoprecipitation and deep sequencing to comprehensivelyexamine the antibody response to SARS-CoV-2 in a high-throughput manner. Using this platform, we willdevelop and test custom libraries that encode all seven CoV clades, including genetic circulating variants andpeptides spanning all viral proteins. This method will allow us to simultaneously detect antibodies to all CoVs ina person's plasma, enabling the detection of the specific responses to SARS CoV-2 infection as well asproviding insights on any interactions between common CoV and SARS-CoV-2 infections, be they protective orenhancing. We will also develop libraries of SARS-CoV-2 proteins that have mutations to all possible aminoacids at every possible amino acid using an approach we pioneered called Phage-DMS. We have validatedPhage-DMS as a tool to define key amino acids residues of epitopes and pathways of escape from antibodies.We propose to collect and compare convalescent plasma from verified cases of SARS-CoV-2, including thosewith severe symptoms, moderate symptoms and very mild symptoms as well as uninfected controls. Theinformation gained from these studies will help identify the peptide sequences that define the epitopes targetedby antibodies in response to SARS-CoV-2 infection and those that distinguish SARS-CoV-2 infection fromother CoV infections. We also hope to identify the antibody responses across the entire CoV genomes thatcorrelate with outcome, including specific responses to SARS-CoV-2 as well as any interacting effects ofresponses to other CoVs.