As Ontario enters phase 2 of reopening, there are significant hurdles that remain to be overcome. Despite the many unknowns surrounding this pandemic, one thing has remained clear: widespread testing is crucial to restore any sense of normalcy to our lives. Over the past couple of months, Public Health Ontario has made significant progress in ramping up testing efforts, reducing time required to process test samples, and increasing the number of tests performed each day. To date, Ontario has conducted over 1.5 million tests, on average performing ~25,000 tests each day over the past month. Despite screening approximately 10% of Ontarians, COVID-19 remains a moving target and population-scale testing will be essential for the safe return to our everyday lives.

          One approach, discussed at the most recent PRiME COVID-19 mini symposium on June 23rd, is to harness the power of next generation sequencing (NGS) to enhance diagnostic capabilities. Researchers in the group of Dr. Jeff Wrana, a Senior Investigator at the Lunenfeld-Tanenbaum Research Institute, have adapted a multi-plex RT-PCR technique called SPAR-Seq, previously used to monitor splicing events in stem cells. COVID-19-SPAR-Seq utilizes a pooled barcoded NGS approach to increase the throughput of SARS-CoV-2 diagnostics. This platform performs well across both purified RNA and patient Nasopharyngeal swabs with the potential to sequence ~50,000-100,000/cycle for a single NGS run. This promising approach has the potential to be applicable across diverse respiratory pathogens, an important feature in the early detection of novel viruses in the population.

          While detection of the virus tells us how many Canadians currently have COVID-19, antibody tests provide important insight into how many of us have previously been infected. Testing positive for COVID-19 antibodies may mean that this person has immunity against the virus, however, the extent and duration of this immunity is still unknown. Nevertheless, serology testing is a powerful tool that has the potential to inform public health and government decisions surrounding emergency measures. Dr. Anne-Claude Gingras and her colleagues have established a direct ELISA assay to quantify antibody levels in patient serum using a set of presumed positives, negatives, and test samples from patients across the Toronto hospital network. To test antibody functionality, her group has also developed protein-based neutralization assays to determine the ability of these antibodies to disrupt viral-host receptor interactions. These assays represent a “made-in-Canada” approach to gain insights into viral prevalence and immunity in our communities.

          In addition to serology, therapeutic antibodies may provide a promising avenue for treatment of COVID-19. In collaboration with Dr. Sachdev Sidhu, Dr. James Rini is working to develop neutralizing antibodies that exploit the coronavirus S-protein-receptor interaction to block viral entry into host cells. Structural insights from other human coronaviruses, including HCoV-229E, have revealed that neutralizing antibodies produced by the immune system bind to key receptor binding loops in the S-protein of coronaviruses. Because of this, viral immune evasion has driven mutational changes that lead to these loops being the most significantly variable regions in the viral genome. Studies from the Rini lab and others have found that neutralizing antibodies functionally mimic that virus’ receptor and promote the formation of a destabilized S-protein conformation preventing viral binding and entry into human cells. This research contributes to a growing body of work that characterizes this important interaction and paves the way for the development of novel therapeutic strategies against human coronaviruses.

          This transformative work is made possible by the University of Toronto’s combined containment level 3 unit, which has enabled research with Risk Group 3 pathogens, such as Mycobacterium tuberculosis, HIV, and SARS-CoV, for more than 20 years. As of late, this facility has been expanded to include a Virology Core Facility and integrated BioBank to support new SARS-CoV-2 research initiatives and facilitate the cataloguing and storage of clinical specimens. This C-CL3 unit is outfitted to support both in vitro and in vivo research including cell culture capability for cell toxicity and infection assays and animal facilities for the development of relevant SARS-CoV-2 models. Unique animal models such as ferrets are being explored for transmission studies as they can both be infected with SARS-COV-2 and pass the infection on to other members of the same species. These resources have been essential in supporting the ongoing research at the University of Toronto and play an important role in helping Ontario move forward through this pandemic.