Throughout the COVID-19 pandemic, wastewater surveillance became a powerful strategy for monitoring SARS-CoV-2 levels in the population and predicting the emergence of new variants. Now, as we move into the next levels of surveillance, University of Waterloo scientists Dr. Trevor Charles and Dr. Andrew Doxey have been granted $1.57M in research funds to fulfill their part of a larger multi-institute team looking to change the game in wastewater analysis.

As part of the HI3 Hub (University of Toronto), Dr. Charles and Dr. Doxey are working on a project that received CBRF-BRIF funding this week. The project, entitled INSPIRE: Integrated Network for the Surveillance of Pathogens: Increasing Resilience and capacity in Canada's pandemic response brings together experts in this area from across Ontario. The goal of INSPIRE is to create a rapid and flexible early warning system that expands and integrates existing wastewater and saliva-based pathogen surveillance capabilities at strategic land border crossings and airports to coordinate with health system data networks and supply networks.

During the pandemic, analysis of wastewater was originally done using qRT-PCR methods to analyze influent samples from local, municipal wastewater treatment plants. While PCR-based methods are effective for detecting known viruses, they also want to develop methods to detect all pathogens that might be present. Additionally, the ability to retroactively go back and trace the emergence of novel pathogens in the data isn’t something they had access to before but is something that can be done using metagenomic sequencing.

By using high-throughput metagenomic sequencing, Dr. Charles and his team will detect existing, new, and emerging pathogens and antimicrobial resistance, building on all the work done in Waterloo research labs tracking SARS-CoV-2 and its variants, as well as with other viruses like influenza and RSV.

“This same technology also has potential for application in agriculture and food production, with implications for human, animal and crop health,” Dr. Charles says. “A recent example is the emergence of avian influenza in cattle.”

Luckily, the University is well-equipped for this type of sequencing work through its recently developed Waterloo Genomic Surveillance Centre, making it possible for Dr. Charles and his lab team to sequence the data in-house.

Analyzing the enormous amount of sequenced data generated by this process is no small feat, but Dr. Doxey and the Applied Bioinformatics Lab have developed a computational platform, AlignDx, that allows them to tackle this challenge. Using AlignDx lets researchers explore hundreds of potential pathogens of interest in sequencing data and monitoring their abundance over time. They have also developed visualization tools for exploring the genomes and the genes that make them pathogenic.

“A big advantage of this approach is that, through sequencing, we can query the historical wastewater data and identify when and where a pathogen first appeared,” Dr. Doxey says. "Collecting and analyzing this data is crucial for monitoring the ongoing evolution of pathogens and the potential emergence of new ones.”

In addition to the INSPIRE project, Waterloo researcher Dr. Valerie Ward, Canada Research Chair in Microalgae Biomanufacturing, is supporting the BioHubNet project – a talent development program that integrates new and existing infrastructure to train more than 500 personnel in the biomanufacturing and life sciences ecosystem. Alongside colleagues at the HI3 Hub, Ward’s work will deliver the talent critical to ensuring Canada is prepared for future pandemics and other health emergencies.

Waterloo scientists continue to be at the forefront of groundbreaking research in public health. This grant will allow Waterloo researchers to continue to build upon the work done at the University and collaborating institutions to develop new bioinformatics and metagenomics approaches for improving the detection and analysis of known and emerging pathogens, and to training the experts who are critical to protecting the health of Canadians.