Project Team

Gene Tan, PhD: Assistant professor at the J. Craig Venter Institute working in the Infectious Disease group

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

Terri Gelbart, Research Associate

Project lead Dr. Gene Tan

Project summary:

The project will determine if suboptimal antiviral immune activity is associated with SARS-CoV-2 persistence, viral reactivation, and increased gut permeability in Long COVID. Blood samples from 250 Long COVID patients and healthy controls are being analyzed. Specifically, the team is:

  1. Defining the viral antibody response in Long COVID blood: They are performing an in-depth analysis of the SARS-CoV-2 antibody response by evaluating binding, neutralizing capacity and Fc region glycosylation patterns/affinity properties. This can provide a more qualitative study of the humoral adaptive response that contributes to disease trajectory.
  2. Detecting viral antigens in Long COVID blood: Altered antibody responses may facilitate viral persistence or reactivation. To test this possibility, the team has innovated a single molecule array platform that can detect small amounts of pathogen proteins in blood. These include SARS-CoV-2 spike protein and proteins created by other pathogens such as Epstein-Barr virus (EBV) and human herpesvirus 6 (HHV-6). The team is also isolating exosomes from Long COVID samples. Exosomes are membrane-bound vesicles that can harbor viral proteins or RNA, potentially facilitating their transport from tissue viral reservoir sites into the blood.
  3. Evaluating virus-induced intestinal permeability: A chronic inflammatory state may perturb the intestinal lining, resulting in microbial composition changes and translocation of organisms into the bloodstream. To measure these potential alterations the team is i) evaluating the host innate immune response to bacterial species in circulation, ii) evaluating changes in short chain fatty acid (SCFA) concentration and iii) measuring antibody response to dietary antigens, all of which can reflect the structural integrity or permeability of the gastrointestinal lining.

Project background:

Long COVID is increasingly tied to SARS-CoV-2 persistence, viral reactivation, microbiome changes, and/or altered gut permeability. However, mechanisms underlying development of these issues in some people and not others after SARS-CoV-2 infection remain unclear. Differences in the immune response and the activity of a specific person’s antibodies may impact how they manage SARS-CoV-2 infection and its chronic consequences. The current study is designed to probe how differences in antibody neutralization, and glycosylation patterns, and past infectious history impact Long COVID development.

Studies – including those by the project team – suggest that suboptimal antiviral host responses typified by early induction of non-neutralizing antibodies and post-translational modification of the Fc can predict the progression of mild COVID-19 to more severe forms of disease. This suboptimal antiviral activity may also contribute to Long COVID, potentially facilitating SARS-CoV-2 persistence, viral reactivation, or microbiome changes. To test this hypothesis, the team is performing an in- depth analysis of the antibody response to SARS-CoV-2 viral proteins. This involves using immunology assays to measure antibody binding efficiency and high throughput pseudoparticle-based neutralization to evaluate neutralizing activity against different variants of concern and other human coronaviruses.

Previous infections can also modulate how the immune system responds to infection by a new pathogen such as SARS-CoV-2. The team is consequently using system serological and virological approaches to provide a broad survey of past and present infections. In parallel they are using tools capable of detecting tiny amounts of viral proteins and RNA (including those potentially hidden inside exosomes) in patient blood. Data generated from the experiments should provide a platform by which the team can detect very low levels of viral products in persistently infected patients as well as the biological mechanism by which they are disseminated into circulation.

Viral infection can lead to host microbial perturbation that is tightly linked to inflammation. The gastrointestinal tract contains the largest and richest source of the human microbiome in the human body. Inflammation-induced microbial perturbations can negatively impact the intestinal epithelial lining and drive a loss of gut lining structural integrity. This leads to a microbial translocation process whereby commensal and opportunistic bacteria normally found in the gut “leak” into general blood circulation and cause chronic pathological responses. To capture these effects, the project team is measuring gut permeability biomarkers such as zonulin, fatty acid binding protein 2, and SCFAs in samples from all study participants.