Project Team

Marcelo Freire, DDS, PhD, DMedSc, Associate professor in the Genomic Medicine and Infectious Disease Department, the J. Craig Venter Institute 

Christopher Dupont, PhD, Professor in Genomic Medicine, Environment & Sustainability, and Synthetic Biology, the J. Craig Venter Institute

Gene S. Tan PhD, Assistant Professor in the Infectious Disease Group, the J. Craig Venter Institute

Project summary:

Project lead and oral surgeon Dr. Marcelo Freire

To determine the degree to which the oral cavity can serve as a window into the identification LongCOVID immune, clotting, microbiome, and viral protein biomarkers. The team is using shotgun proteomics to identify persistent innate immune and clotting dysfunction in saliva collected from LongCOVID patients and matched controls. Data is being entered into the Human Salivary Proteome to facilitate integration with additional measurements of microbiome activity, inflammatory cytokine levels, and viral proteins in samples collected from the same participants. Similar analyses are also being performed on patient blood to determine the degree to which LongCOVID saliva biomarkers mirror those in the systemic circulation.

Project background:

Saliva is an important biofluid that helps protect oral, esophageal, and gastrointestinal tissues, and provides immune functions against pathogens. Saliva also has systemic functions as it enhances mucosal immunity, production of antibodies and antimicrobial proteins. Because of these functions, saliva has long been investigated for its biological potential and as a diagnostic medium for both oral and systemic diseases. Compared to blood and other body fluids, saliva can be easily and non-invasively collected, making it ideal for diagnostic development.

The project team recently used shotgun proteomics to identify persistent inflammatory patterns including dysfunction of salivary neutrophil markers and clotting factors (e.g., fibrinogen) in plasma  from post-COVID patients. Saliva samples were characterized by higher concentrations of IgA, and proteomics showed altered myeloid-derived pathways that correlated positively with SARS-CoV-2 IgA levels in severe subjects, suggesting IgA regulation of innate immune cells such as neutrophils. The current study builds on these findings to measure inflammatory, microbiome, viral and coagulation-related sequelae in saliva and blood collected from a larger group of Long COVID patients. Data is being integrated into The Human Salivary Proteome Wiki – a public data portal for searching and retrieving custom-curated information about the proteome and transcriptome of human saliva. The HSP database is led by project lead Dr. Marcelo Freire’s laboratory at the J Craig Venter Institute and is the biggest collection of datasets in saliva and blood globally.