COVID-19 Therapeutic and Vaccine Development

COVID-19 Disease Therapeutic and Vaccine Development

Understanding immune response and disease immunopathology can help refine development of treatments and vaccines for better disease management.

Fluidigm platforms for both microfluidics and CyTOF® technology, which powers mass cytometry and Imaging Mass Cytometry™, are enabling immune response studies in COVID-19 patients. These platforms are designed to identify prognostic and mechanistic biomarkers that can be used to guide the development of effective vaccines and direct treatment of COVID-19 disease.

Learn how we can support COVID-19 disease research in different ways

  COVID-19 Disease Therapeutic Intervention Research
  COVID-19 Disease Vaccine Development and Testing
COVID-19 Disease Therapeutic Intervention Research

Fluidigm technology is being used in three National Clinical Trial (NCT) COVID-19 studies:

IMPACC Clinical Study

The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) clinical study (NCT04378777) is a prospective observational cohort surveillance study of up to 2,000 adult participants hospitalized with known or presumptive COVID-19. Detailed analysis of the immunophenotypic and genomic data collected will be used to identify key features of COVID-19 disease susceptibility and/or progression.

The primary goals of this study are to generate hypotheses for effective therapeutic interventions, to aid in prioritizing proposals for these interventions and to optimize the timing for administration of therapeutics.

High-parameter mass cytometry panels will be used to analyze immune cell frequencies and activation states in both peripheral whole blood and endotracheal aspirate samples over time (see recorded webinar by Ruth Montgomery, Yale University).

Two key advantages make mass cytometry ideal for gathering this data: the ability to stain, freeze and ship samples processed with the Maxpar® Direct™ Immune Profiling Assay™ to a centralized location for processing on a mass cytometer and the ability to analyze small sample sizes, such as endotracheal aspirates.

In addition, circulating immune mediators in the plasma of cohort subjects will be assessed by an Olink® protein biomarker panel performed using Fluidigm microfluidics on the Biomark™ HD.

COntAGIouS Trial

The COntAGIouS trial (COvid-19 Advanced Genetic and Immunologic Sampling) is designed as an in-depth characterization of the dynamic host immune response to coronavirus SARS-CoV-2. It proposes a transdisciplinary approach to identify host factors that result in hypersusceptibility to SARS-CoV-2 infection. Identifying these factors is urgently needed for directed medical interventions.

Real-time CyTOF analysis will be performed as screening, along with in-depth immunophenotyping using the Maxpar Direct Immune Profiling Assay.

Prospective Natural History Study of Smoking, Immune Cell Profiles, Epigenetics and COVID-19 (NCT04403386)

This study is a prospective, longitudinal, observational study to collect samples and data that will enable explorations of the interaction between smoking, immune system characteristics and coronavirus disease 2019 (COVID-19). Early evidence in the COVID-19 pandemic suggests that smokers have higher risk for morbidity and mortality associated with COVID-19 infection. We have identified smoking-associated altered epigenetics, transcription and changes in immune cell profiles. Smoking exposure drives loss of naive CD8+ T cells and increases in senescent CD8+ T cells, and these effects are signs of immune system dysfunction. We propose that the immune system senescence associated with prior smoking is a susceptibility factor in COVID-19 morbidity.

This study will establish a bank of cryopreserved peripheral blood mononuclear cells (PBMC) from before and after COVID-19 exposure from smokers and nonsmokers and use mass cytometry (CyTOF) to analyze detailed immune profiles, and test if the frequency of senescent CD8 T cells is higher among smokers who develop COVID-19 (antibody positivity) relative to those who do not develop COVID-19 positivity.

Therapeutic Interventions Webinar

Profiling of COVID-19 Patient Immune Responses


Ruth Montgomery, PhD
Professor of Internal Medicine
Director, Yale CyTOF Facility
Associate Dean for Scientific Affairs

Montgomery describes her team’s work using mass cytometry in infectious disease studies and how her team will be contributing to the IMPACC study by analyzing endotracheal aspirates from participants.

“Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures.” Zhao, Y. et al. PLOS Neglected Tropical Diseases 14 (2020): e0008112.

Therapeutic Interventions Publications

COVID-19 Disease Vaccine Development and Testing

Mass cytometry has been used to monitor immune responses during vaccine development and testing for years, and it will be useful in SARS-CoV-2 vaccine development as well. Here we spotlight reference materials that outline the current use of CyTOF technology in this area.

Multiple research groups around the world employ mass cytometry to investigate many aspects of vaccine development and efficacy. Two reviews1,2 provide excellent background on this topic. The Brodin1 article emphasizes the importance of a systems immunology approach to monitoring vaccine responses, especially when sample volume is limited, as in pediatric samples. In Reeves et al.2, the potential of mass cytometry to capture the complex and often unanticipated immune cell interactions and responses to candidate vaccines is highlighted by review of multiple publications and comparison to other technologies.

Other publications show how mass cytometry has helped researchers investigate the impact of vaccine schedule on immune response3,4, including deep profiling of specific immune cell populations5,6, use of immune profiles to predict vaccine response7 and identification and deep profiling of antigen-specific T cells using metal-labeled HLA tetramers8,9. Of key importance in vaccine research are papers on high-dimensional data analytic approaches10–12 (read the article).

In addition, mass cytometry is being used as a readout in five ongoing clinical trials of vaccine response as well as in one additional completed trial (Table 1).

Spotlight Article

Machine learning and infectious disease: how we can better understand vaccine efficacy at the patient level


Adriana Tomic, PhD,
University of Oxford

In one of the 20 most-read papers in the Journal of Immunology in 2019, Stanford University and University of Oxford researchers reported developing an automated machine learning system, Sequential Iterative Modeling “OverNight” (SIMON), that compares high-dimensional datasets from heterogeneous clinical studies focusing on vaccine response. The aim of the project is to build more accurate predictive models and accelerate analysis and discovery.
Clinical Trial Name Sponsor/ Collaborator Start Date Phase NCT Number
CVD 38000: Study of Responses to Vaccination with Typhoid and/or Cholera University of Maryland 2018 4 03705585
Blood Donor CVD 5000 University of Maryland 2004 4 03971669
CVD 37000: Immunity and Microbiome Studies at Intestinal and Systemic Sites in Ty21a Vaccinated Adults University of Maryland 2013 4 03970304
Study of a New MVA Vaccine for Hepatitis C Virus ReiThera Srl/ University of Oxford, Oxford University Hospitals, University Hospital Birmingham 2010 1 01296451
High Dose Flu Vaccine in Treating Children Who Have Undergone Donor Stem Cell Transplant Vanderbilt-Ingram Cancer Center/ National Cancer Institute 2016 2 02860039

Table 1. Clinical trials using mass cytometry to study vaccine response as of May 8, 2020. Source:


  1. Brodin, P. “Technologies for assessing vaccine responses in the very young.” Current Opinion in Immunology 65 (2020):28–31.
  2. Reeves, P.M. et al. “Application and utility of mass cytometry in vaccine development.” FASEB Journal 32: (2018): 5–15.
  3. Palgen, J-L. et al. “Innate and secondary humoral responses are improved by increasing the time between MVA vaccine immunizations.” npj Vaccines (2020): 24.
  4. Palgen, J-L. et al. “Prime and boost vaccination elicit a distinct innate myeloid cell immune response.” Scientific Reports 8 (2018): 3,087.
  5. Palgen, J-L. et al. “NK cell immune responses differ after prime and boost vaccination.” Journal of Leukocyte Biology (2019): 1,055–1,073.
  6. Rudolph, M.E. et al. “Diversity of Salmonella Typhi-responsive CD4 and CD8 T cells before and after Ty21a typhoid vaccination in children and adults.” International Immunology (2019): 315–333.
  7. Lingblom, C.M.D. et al. “Baseline immune profile by CyTOF® can predict response to an investigational adjuvanted vaccine in elderly adults.” Journal of Translational Medicine 16 (2018): 153.
  8. Chng, M.H.Y. et al. “Large-scale HLA tetramer tracking of T cells during dengue infection reveals broad acute activation and differentiation into two memory cell fates.” Immunity 51 (2019): 1,119–1,135.
  9. Newell E.W. et al. “Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization.” Nature Biotechnology 31 (2013):623–629.
  10. Tomic, A. et al. “SIMON, an automated machine learning system, reveals immune signatures of influenza vaccine responses.” The Journal of Immunology 1203 (2019): 749–759.
  11. Tomic, A. et al. “The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system.” Scientific Data 6 (2019): 214.
  12. Lucchesi, S. et al. “From bivariate to multivariate analysis of cytometric data: overview of computational methods and their application in vaccination studies.” Vaccines 8 (2020): 138.
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