J Craig Venter Institute

Department of health and human services: two million people in the u.s. are diagnosed annually with life-threatening infections caused by antibiotic resistant bacteria that are responsible for 35,000 deaths each year with an economic impact estimated to be as much as $20 billion a year in direct healthcare costs. Due to the spread of antibiotic resistance, very few drugs remain that can treat these infections. Led by derrick fouts, phd, (jcvi) and funded by the centers for disease control and prevention (cdc), the J. Craig Venter Institute and cleveland va prevention and intervention epicenter are developing novel interventions that will prevent the colonization and spread of antibiotic resistant (ar) bacteria that cause hospital acquired infections (hai), and to develop diagnostics and interventions to combat the colonization by the rapidly emerging fungal pathogen candida auris. Richard scheuermann, phd, 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 the sars-cov-2 virus during the early stages of the outbreak to ensure data and tools are accessible to frontline researchers worldwide. Additionally, in collaboration with investigators from la jolla Institute for immunology, dr. scheuermann and his team provided machine learning methods to help complete the first analysis that identified potential targets for human immune responses to sars-cov-2 infection. This information is crucial to the design and evaluation of diagnostics and vaccine candidates.

Department of defense: wound microbiome project - chronic wounds are wounds that fail to heal after 3 months under standard of care wound management. Derrick fouds leads a study to gain a better understanding of the different classes of microbes that could be present in human chronic wounds (i.e. The wound microbiome), and ask whether specific microbes or microbial communities are associated with non-healing wounds. Led by derrick fouts, phd, next generation sequencing is being used to identify and catalog the microbial species of bacteria, fungi, and viruses that are present in chronic wound specimens. Computational and bioinformatics analyses of the microbial community dna sequences will be carried out to characterize the presence any pathogenic, virulence, and antimicrobial resistance-related genes and pathways. The eventual goal is to identify any pathogenic species or features that are associated with non-healing wounds, and could be used as diagnostic and treatment targets of chronic wounds. Through an iarpa-funded collaboration with investigators at harvard wyss Institute, john glass, phd, 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.

Department of energy: jcvi is the recipient of a large collaborative assistance award from the us department of energy. Awarded to the value of $10.7m. Led by andrew allen, phd, the jcvi and its collaborators, Colorado state university, vanderbilt university and the university of California, san diego, seek to leverage significant recent advances in diatom genome engineering and metabolic modeling; including the ability to introduce chromosome-like expression platforms, which substantially advance possibilities for high-throughput generation and screening of genetically engineered diatoms. Research proposed here will result in dramatic improvements in the predicative capacity of existing genome scale metabolic models of diatom metabolism. For the first time on a large scale, fluxomics, which is compound specific incorporation of an isotopically-labeled feedstock, will be used to provide better first step constraints on co2 assimilation of in diatoms. State-of-the-art high throughput in vitro examinations of nearly all 200 diatom transcription factors will be conducted to better understand regulatory architecture underlying diatom metabolism as well as serve as a source for new tools for genome engineering. Taken together, research proposed here will address currently limiting bottlenecks through fostering state-of-the-art integration of genome-scale modeling with genome engineering to optimize energy and metabolte flux through subcellular compartments to promote efficient production of high value and fuel-related metabolites.

Other: as part of their inaugural grant cycle, the conrad prebys foundation funded the institutes research work in both coronary artery disease and sars-cov-2. Heart disease is the leading cause of death in the us and coronary artery disease (cad) is the most common type of heart disease, killing ~366,000 people annually in the us. About 6.7% (18.2 million) us adults have cad and ~20% of deaths from cad occur before age 65. A list of genetic factors linked to cad has been found over the last few decades. But they only explain a small portion of the heritability in cad. To better understand the genetics and etiology of cad at genomic level, more rare genetic variants need to be investigated. Led by weizhong li, this project, analyzed the whole genome deep sequence data of a large cohort of ~1000 cad patients. Using the cloud-based genome analysis pipeline, hundreds of terabytes of sequence data were processed and millions of various types of genetic variants were identified. A list of variants are found to be associated with cad and the extent of disease in cad. By using machine learning approaches, we built very accurate predictive models for the prediction of cad risks and disease severity. Early warning system for sars-cov-2 immune escape project. Neutralizing antibodies elicited against the severe acute respiratory syndrome coronavirus (sars-cov-2) spike protein is widely accepted as the main correlate of protection. To better understand the role of antibodies in neutralization and protection, jcvi, led by richard scheuermann, phd, and gene tan, phd, is constructing a panel of chimeric pseudoviruses (based on the vesicular stomatitis virus platform) that we hypothesize can reveal the immunological dominant and subdominant antigenic regions of the spike protein. Notably, our approach can identify subdominant regions within the spike that are highly conserved even amongst sars-cov-2 variants of concern (vocs). Covid19 continues to impact global health, highlighting the need to develop novel therapeutics. Marcelo freire, phd, and his laboratory discovered that saliva is a biofluid important for measuring the virus but also the immune response presenting diverse immune cell populations. Whitin saliva, we find various antiviral, anti-inflammatory and anti-bacterial functions. Different from blood, salivary immune cells are in direct contact with the live virus. In this proposal we investigated (i) the composition of antiviral immune cells, (ii) the protein sequence of antiviral molecules derived from innate immune cells, and (iii) their mechanism of action. The freire lab have successfully collected samples from covid-19 and healthy control samples and initiated sequencing of saliva cells in health and in covid-19. In addition, we also recruited samples longitudinally at jcvi to evaluate healthy versus disease. To date, we completed immunoglobulin immunoassays of all our samples including investigations to custom elisa assays for sars-cov-2 antigens (rbd, s1, s2, np proteins). We have identified that salivary immunoglobulin iga as highly significant compared to blood plasma levels. Several markers from igg and iga responses were found in saliva as well as plasma. Simple linear regression model verified significant correlations between saliva and plasma antibody responses, specifically for the iga (p=0.001), igg (p=0.037), and igm (p=0.0054) specific to the sars-cov-2 receptor binding site (rbd). These are antiviral molecules that have potential to block viral activity. To test this further from our assays, jcvi performed a neutralization assay and comparative analysis to understand if these molecules have a functional response. Despite that saliva contained robust iga response to the sars-cov-2, which was even higher than plasma, most of saliva samples demonstrated level of neutralization of vesicular stomatitis virus (vsv) pseudoviruses bearing s of sars-cov-2 (rvsv-gfpg*spike). It was contrasted with that the plasma displayed a significant level of neutralizing activity even from healthy individuals. These results suggest that the oral mucosal immune components cooperate with systemic immune response in response to the sars-cov-2 infection. Saliva and plasma samples contained significantly higher levels of sars-cov-2 specific antibodies than healthy and we discovered multiple peptides present a role against viral particles. Ultimately, this project aims to map the salivary molecular content when exposed to the virus. We aim provide to the scientific community a new layer of immune response composition and function related to mucosal lining when facing viral attack. This will then guide new clinical approaches with the formation of the therapeutics that emulate how and why the mucosal tissues keep disease in check. Sanjay vashee, phd, collaborating with investigators at the university of Maryland to use synthetic genomics to develop a sars-cov-2 infectious clone. They are pairing this with a rapid, modular reverse genetic system to assess genomic variants identified in the wealth of global sequencing data, develop and test vaccine candidates, and generate needed reagents, including fluorescent and tagged virus strains. Marcelo freire, phd, is leading efforts in the development of a salivary serological and immune testing. Monitoring saliva immunity provides non-invasive molecular information, essential for diagnostics, and response to therapy during the pandemic. His laboratory is comparing covid-19 patients' blood and salivary immunoglobulins levels to find better ways to evaluate immune response to sars-cov-2.