CITF-funded findings on breakthroughs in laboratory and in research infrastructure

Multiple platforms and novel technologies have been created over the past three years to aid Canadian clinical and research efforts in monitoring immune responses to SARS-CoV-2. These breakthroughs in laboratory and research infrastructure have been crucial to ensuring Canadian researchers have the necessary tools, infrastructure, resources, and procedural pipelines to enable rapid responses to this pandemic and any future one. Here, we elaborate on some of these breakthroughs and summarize research results from the five presentations given during the breakout session “Breakthroughs in laboratory and research infrastructure,” at the CITF Scientific Meeting in Vancouver, March 8-10, 2023.

1. Presenter and CITF PI Dr. Angela Crawley: CoVaRR-Net Biobank support of CITF projects established framework for pandemic preparedness biobanking

The CoVaRR-Net Biobank is a multidisciplinary initiative that aims to facilitate rapid research by coordinating access to resources across multiple Canadian sites. Its goal is to meet the needs of the COVID-19 pandemic emergency and build upon this initiative for the future.

• The CoVaRR-Net Biobank has collected samples, which include blood, plasma, serum, saliva, and dried blood spots from more than 2,000 participants, and participated in significant distribution of them. It offers inventory management using SLIMS (Agilent), a state-of-the-art management system that cost over $130K to develop, which is one of the first in Canada to handle various sample types and study designs.
• The CoVaRR-Net Biobank is developing a federated model of biobanks to share material and data through the Canadian COVID-19 Biobank and Data Alliance. The CoVaRR-Net Biobank facilitates open, fair, and rapid exchange between researchers. In the federated model, each partner can maintain autonomy and retain custody over the materials and data they collect and store. A strict de-identified process is used to honour privacy. Adequate quality assurance is ensured through standardized operating procedures, sample quality control, sample and data auditing, and distribution follow-up.
• CoVaRR-Net is working on a ready to use research ethics protocol to avoid delays to research. Starting with the Clinical Trials Ontario Protocol model, a provincial and multi-jurisdictional model was developed and became a revised tCPS2 protocol. This protocol, which allows data sharing with a single ethics review for minimal risk research across Canada, is a major achievement helping to overcome significant  hurdles to biobanking and data sharing across Canada.
• The CoVaRR-Net Biobank developed a Universal Data and Biological Material Transfer Agreement (UDBMTA) that was signed and fully executed by over 30 institutions by April 2022.
• The CoVaRR-Net Biobank is continuing baseline operations, with plans to evolve into post-pandemic activities to monitor the health of Canadians. These would include collecting longitudinal samples and data and developing the capacity for targeted sampling and prioritization of testing to handle a surge of cases in the event of a future pandemic.

2. Presenter Danielle Dewar-Darch and CITF PI Dr. Marc-André Langlois: The University of Ottawa serology and diagnostics high-throughput facility

A dedicated fully automated high-throughput facility was developed with the capacity to handle multiple infectious sample types.

• The facility has two Hamilton micro lab liquid handlers for serum, plasma, DBS, saliva, amniotic fluid, and breast milk samples. The system is fully automated and integrated with a plate washer and reader.
• The facility has the capability to handle antigens such as SARS-CoV-2 S, RBD, and N proteins. It can conduct neutralization assays such as the snELISA, which is automatable in a high-throughput fashion.
• It can run up to 800K samples per year and is able to increase capacity, with a focus on data quality and standardization across studies.
  • The facility has worked with its partners to show that batch-to-batch variability can be minimal.
  • It has conducted inter-lab assay validations to demonstrate comparability across labs, successfully harmonizing the methodology for data collection.
• The facility is currently collaborating on over 30 Canadian research studies with researchers and other partners, including Statistics Canada and the National Microbiology Laboratory (NML), for assay validation. The current infrastructure is a valuable resource that is ready and prepared to respond to future challenges.

3. Presenter and CITF PI Dr. Andrei Drabovich: Rational design and development of SARS-CoV-2 serological diagnostics by immunoaffinity proteomics

This study team leveraged the proteomics technique, Mass Spectrometry (MS), for a diagnostic assay that involves direct measurements with lower non-specific binding, high selectivity, and low cross-reactivity. This assay could be used as a “gold standard” assay, which could enable inter-hospital standardization (ng/mL) using stable quantifiable synthetic peptide standards. It could be used as a high-throughput assay to assess ~700 samples/week for engagement in precision immunology and comprehensive investigation of immune responses.

Using this assay the researchers found:

• Each subclass of antibodies has a unique signature that can be detected by mass spectrometry. The RBD-IgG1 combination had the highest diagnostic performance and lowest non-specific binding.
• Using 400 ng/mL IgG1 as the cut-off provides 99.3% specificity at 88% sensitivity.
• Multiplexing IgG1/IgM/IgA1 antibodies in a multiple assay provides ~100% specificity at 96.3% sensitivity.
• IgG1 levels in COVID-19 convalescent plasma may reach ~5,000 ng/mL.

4. Presenter Ms. Freda Qi and CITF PI Dr. Anne-Claude Gingras:  Optimizing the dilution factors for an in-house chemiluminescent ELISA assay to expand the linear range of quantified IgG antibodies to SARS-CoV-2 in vaccinated and infected individuals

The study team developed an in-house luminescence ELISA assay in March 2020. Within three years of the start of the pandemic, they had processed over 185,000 unique samples. Currently, they are expanding the range of quantification of SARS-CoV-2 serology assays.

• The serology assay is dynamic and is being improved continuously, having been tested using three recombinant antigens.
• The team calibrated its assays to World Health Organization (WHO) international standards.
  • The assay is within the 0.5-2-fold range of the geometric mean reported in the WHO document, based on results compared from 51 labs using these standardized controls. This gave the team confidence that their BAU/mL calculation was accurate.
  • The issue with this assay was the identification of an appropriate dilution for calculating concentration. The original concentrations of 1:160 and 1:2560 led to issues where the assay was saturated and unable to give a raw value in BAU/mL.
  • To help collaborators who are increasingly looking for quantitative results, the team has added an additional concentration of 1:40960 to expand the dynamic range of its assays calculating a BAU/mL.
  • Using this assay, antibody levels can be quantified up to 24013 BAU/mL for S, 71263 BAU/mL for RBD, and 85000 BAU/mL for N.

5. Presenter and CITF PI Dr. Madeleine Durand and CITF PI Dr. Simon Rousseau: Characteristics of participants obtained from the data visualization tools of the Biobanque québécoise de la COVID-19: A powerful open science tool to advance COVID-19 research

The Biobanque québécoise de la COVID-19 (BQC19) was launched in March 2020 and has collected 6,000 samples from hospitalized and community participants.

• The mean number of samples is 2.4 per participant, but some individuals have contributed samples at 6 to 8 time points, providing a great opportunity to evaluate long-term responses.
• An interesting observation from this cohort was that only half of the samples were from vaccinated individuals since participants were recruited early in the pandemic when vaccination rates were low. This also allows for unvaccinated controls and observation of increases in immune responses over time.
• BQC19 has developed a software called BENTO-BQC19, which allows analysis of collected samples through a dashboard. It provides an overview of the key clinical variables in the datasets of samples in the biobank and shows aggregate measures and summary statistics. BENTO-BQC19 allows users to select the variables to create a personalized dashboard.