Spotlight on CoVaRR-Net’s Pillar 5 Viral Genomics and Sequencing: The Team’s High-Tech Tools Tracked and Traced with Precision the Trajectory of Successive COVID-19 Variants

In February 2020, a month before the World Health Organization (WHO) characterized the spread of COVID-19 as a pandemic on March 11, Dr. Jiannis Ragoussis and his team at the McGill Genome Centre started work on sequencing samples of the entire genome of the SARS-CoV-2 virus using next generation sequencing (NGS) technologies. These technologies enable rapid and detailed genetic analysis of a virus as it evolves into different strains.

“Given that RNA viruses have a very high mutation rate, we suspected the SARS-CoV-2 virus would mutate rapidly, leading to strains that could be more virulent or more immune evasive, and potentially cause more severe symptoms. The only way to identify all the mutations or small differences in sequences in samples as the virus evolves is by sequencing the whole genome,” explains Dr. Ragoussis, Lead of CoVaRR-Net’s Viral Genomics & Sequencing Pillar 5, member of the Network’s Wastewater Surveillance Research Group (WWSRG), and Professor at McGill University.

Pillar 5’s innovations in genomic sequencing of variants gave Canada an edge

In April 2020, he began applying cutting-edge techniques to sequence the entire genomes of clinical SARS-CoV-2 samples from Quebec patients, in partnership with the Quebec government and its public health laboratories.

“The whole genome sequencing methods we developed and adapted were very important to identify and track variants of concern (VOCs) with precision. These tools allowed us to better understand the transmission and evolution of the virus in Quebec and, as of 2021 once CoVaRR-Net was formed, across Canada in collaboration with other CoVaRR-Net scientists and public health authorities through different pandemic phases,” says Dr. Ragoussis.

Key to wastewater surveillance

Pillar 5 scientists were also extensively involved in wastewater testing.

“We recognized early on that clinical sampling alone, which is costly and can underestimate the proportion of the population infected, was not sustainable over time. When CoVaRR-Net was launched, our immediate priority was to sequence SARS-CoV-2 genomes from both clinical and wastewater samples and show the benefits of systematically combining data from these two complementary screening approaches,” says Dr. Ragoussis.

Pillar 5 scientists developed and tested a wide range of high sensitivity sequencing assays to optimize detection of VOCs in both clinical and wastewater samples. For example, to improve detection and characterization of SARS-CoV-2 variants in wastewater samples, the researchers developed a novel approach that combined short- and long-read genomic sequencing technologies.

Pillar 5 Developed a Novel Approach to Sequence Wastewater Data Using Short- and Long-Read Technologies

“Combining the two technologies was especially important for identifying variants of concern with precision in wastewater screening, since wastewater has so many types of pathogenic viruses,” he explains.

The team then helped show that wastewater surveillance is effective and is an early warning system by matching wastewater samples to clinical samples.

For example, Pillar 5 member Dr. Jeff Wrana at Toronto’s Sinai Health led and contributed to rapid, high-throughput screening studies that mapped how the different SARS-CoV-2 variants evolved and spread in the Greater Toronto Area (GTA) from 2020 to 2023. He showed the value of integrating data from clinical and wastewater sampling. “Dr. Wrana’s deep, detailed genomic sequencing of variants in the GTA also enabled detection of quasi-species of the virus, or minor variants, that emerged within immunocompromised individuals who were exposed to the virus for a long time,” explains Dr. Ragoussis.

“We demonstrated that combining and integrating data from these two complementary screening approaches was feasible, useful and could enhance public health surveillance of SARS-CoV-2 variants in many ways locally, regionally, and nationally,” says Dr. Ragoussis, who along with Pillar 6 Co-Lead Dr. Jesse Shapiro and WWSRG member Dr. Peter Vanrolleghem became members of CentrEau. This organization performed extensive genomic wastewater surveillance in Quebec and ultimately transferred its innovative technology and methodologies to the provincial health laboratories.

The work of Pillar 5 provided a unique Canadian model for monitoring the trajectory of the COVID-19 pandemic. It was also instrumental in establishing wastewater genomic surveillance networks that Pillar 5 members led or co-led in Ontario, Quebec, Alberta, and British Columbia and in forming CoVaRR-Net’s Wastewater Surveillance Research Group (WWSRG) in 2022.

Fruitful collaborations across the Network

Pillar 5 also provided expert genomics support to other CoVaRR-Net units and actively collaborated on numerous projects with Pillars 1 (Immunology & Vaccine Protection), 3 (Virology), 4 (Functional Genomics & Structure-Function of VOCs), 6 (Computational Analysis, Modelling and Evolutionary Outcomes  or CAMEO), the WWSRG and Biobank, Data Platform and Bioethics Major Initiatives, and CUBE (Coronavirus in the Built Environment).

Pillar 5’s ongoing collaboration with Pillar 6/CAMEO, for example, provided them with a steady stream of viral genomic sequencing data from clinical and wastewater samples. CAMEO researchers used that data to analyze and track the prevalence and rise of variant lineages in the Canadian population, model the genetic evolution of the virus, and assess rates of spread, immune evasive characteristics, and pathogenicity.

Working with CUBE, Pillar 5 researchers helped develop new sequencing methods to improve the sensitivity of SARS-CoV-2 detection from viral traces on environmental surfaces, such as floors, which supported CUBE’s innovative SARS-CoV-2 screening studies in hospitals and long-term care homes. “We proved that you could produce whole genome sequencing data and identify variants of concern from surfaces in long-term care homes, hospitals, schools, daycare facilities, and other buildings,” says Dr. Ragoussis.

Preparing for future pathogens and health emergencies

As a result of their CoVaRR-Net-funded work, Pillar 5 researchers are applying and adapting their new genomic sequencing methods to enable rapid detection and analysis of more pathogens, including other respiratory viruses and bacterial threats. “The Public Health Agency of Canada is providing significant funds for Pillar 5 members to expand these kinds of studies to other pathogens. This includes a project to detect Campylobacter pathogens, which cause food poisoning, and their related antimicrobial resistance genes (ARGS), using metagenomic tools for wastewater-based surveillance,” explains Dr. Ragoussis.

“CoVaRR-Net brought together scientists from many different disciplines to solve a common health problem. It was very satisfying to be able to work with groups of researchers I wouldn’t have had an opportunity to work with otherwise and most importantly, to have an impact on Canada’s success in fighting against the pandemic,” he says. “Genomics-based surveillance was instrumental to that success, and I believe the interdisciplinary work we did together will help to ensure that Canada is better prepared for future pandemics and public health crises.”