Director, La Jolla Campus
Craig Venter Institute
What are you and your institution currently working on regarding SARS-CoV-2?
Dr. Scheuermann is leading a team of investigators at JCVI in response to the COVID-19 outbreak. Through his NIH-sponsored Bioinformatics Resource Center project, his team released a dedicated public web portal for data about the SARS-CoV-2 virus during the early stages of the outbreak, and collaborated with investigators at the La Jolla Institute for Immunology to apply machine learning methods to predict the likely immune epitopes targeted by the immune response to SARS-CoV-2 infection. Gene Tan, at the JCVI’s La Jolla campus, is leading efforts to develop SARS-CoV-2 spike glycoprotein pseudotyped viruses for receptor binding and antibody neutralization assays. Through an IARPA-funded collaboration with investigators at Harvard Wyss Institute, John Glass is using in vitro cell culture systems to assess the capacity of SARS-CoV-2 proteins to inhibit antiviral mechanisms of the human innate immune system that would otherwise prevent viral replication in those cells. Lauren Oldfield and Sanjay Vashee, at JCVI’s Rockville campus, are collaborating with investigators at the University of Maryland to use synthetic genomics to develop a SARS-CoV-2 infectious clone paired with a rapid, modular reverse genetic system to assess genomic variants from the wealth of global sequencing data, develop and test vaccine candidates, and generate needed tools, including fluorescent and tagged virus strains.
What efforts are you making on COVID-19 serology, and how would you assess the progress of current testing?
JCVI is developing critical resources for the evaluation of antibody reactivity for serology testing. From an informatics perspective, the use of comparative genomics methods and predictive machine learning algorithms are being used to identify the key determinants for immune system recognition and to monitor the impact of virus evolution in immune system evasion. The bioinformatics analyses will aid in developing critical resources for the evaluation of antibody reactivity for serology testing. In the laboratory, viral surface proteins are being generated for use as ELISA antigens, pseudotyped recombinant viruses are being constructed for neutralizing assays, and candidate vaccine constructs are being synthetized to define the immunogenicity of the viral proteins and to understand the basis of immune response and protection against SARS-CoV-2.
Richard H. Scheuermann is Director of JCVI’s La Jolla Campus and an adjunct professor of pathology at U.C. San Diego. He received a BS in Life Sciences from the Massachusetts Institute of Technology, and a PhD in Molecular Biology from the University of California, Berkeley.
Dr. Scheuermann has applied his deep knowledge in molecular immunology and infectious disease toward the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, novel methods for the analysis of gene expression, protein network and flow cytometry data, and novel comparative genomics methods. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database, the Virus Pathogen Resource, and the Immunology Database and Analysis Portal supported by the U.S. National Institutes of Health.
Overview of J. Craig Venter Institute and GVN
The J. Craig Venter Institute (JCVI), which has campuses in both Rockville, MD, and La Jolla, CA, has become a major center in virology research. The thread that runs through all JCVI research is genomics, i.e. analysis of the genetic material of populations of organisms, cells, and viruses. The virology program at JCVI conducts research focused primarily on genomics, evolution, pathogenesis, and vaccine development. The JCVI virology community is composed of representatives from every group in the institute: infectious diseases, human genomics, bioinformatics, synthetic biology, and environmental genomics. JCVI virology may be best known for sequencing thousands of complete influenza virus genomes, and the viral genomics program also has expertise in sequencing, assembly, and annotation of many other virus families. Thus, the ability of JCVI to rapidly isolate, sequence, analyze, and synthesize virus genomes through a fully integrated workflow infrastructure makes JCVI unique as a possible rapid response center and therefore a valuable partner in the GVN.