CORONAVIRUS VARIANTS RAPID RESPONSE NETWORK

CoVaRR-Net: Publications

PROJECT OVERVIEW

CoVaRR-Net (Coronavirus Variants Rapid Response Network)’s goal? Rapidly answer critical and immediate questions regarding variants, such as their increased transmissibility, likelihood to cause severe cases of COVID-19, and resistance to vaccines.

We are a network of interdisciplinary researchers from institutions across the country created to assist in the Government of Canada’s overall strategy to address the potential threat of emerging SARS-CoV-2 variants. Our mandate is to coordinate, facilitate and accelerate rapid response research throughout Canada.

We aim to create mechanisms, such as a national biobank, a data sharing platform, and material sharing agreements to allow researchers to share physical research resources, data and knowledge, making it easier and faster for researchers to get what they need to study variants in Canada.

Our network continuously monitors Canadian and international virus sequencing efforts, making it a critical element of the Canadian ecosystem for the surveillance of variants of concern (VOCs). We work collaboratively with the Public Health Agency of Canada’s National Microbiology Laboratory (NML), the Canadian COVID-19 Genomics Network (CanCOGeN), provincial and territorial public health labs, and other national and international bodies.

Our network’s findings inform the Public Health Agency of Canada (PHAC), and federal, provincial, territorial, and regional public health decision makers, helping to guide their response in an effort to reduce virus transmission and keep Canadians safe.

CoVaRR-Net was created with a $9 million investment at the end of March 2021 as part of the Government of Canada’s Variants of Concern Strategy.

Wastewater-based epidemiology has emerged as a promising tool to monitor pathogens in a population, particularly when clinical diagnostic capacities become overwhelmed. During the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), several jurisdictions have tracked viral concentrations in wastewater to inform public health authorities. While some studies have also sequenced SARS-CoV-2 genomes from wastewater, there have been relatively few direct comparisons between viral genetic diversity in wastewater and matched clinical samples from the same region and time period. Here we report sequencing and inference of SARS-CoV-2 mutations and variant lineages (including variants of concern) in 936 wastewater samples and thousands of matched clinical sequences collected between March 2020 and July 2021 in the cities of Montreal, Quebec City, and Laval, representing almost half the population of the Canadian province of Quebec. We benchmarked our sequencing and variant-calling methods on known viral genome sequences to establish thresholds for inferring variants in wastewater with confidence. We found that variant frequency estimates in wastewater and clinical samples are correlated over time in each city, with similar dates of first detection. Across all variant lineages, wastewater detection is more concordant with targeted outbreak sequencing than with semi-random clinical swab sampling. Most variants were first observed in clinical and outbreak data due to higher sequencing rate. However, wastewater sequencing is highly efficient, detecting more variants for a given sampling effort. This shows the potential for wastewater sequencing to provide useful public health data, especially at places or times when sufficient clinical sampling is infrequent or infeasible.

COLLABORATORS

Robert Delatolla PhD - University of Ottawa

Caroline Quach PhD - University of Montreal

Terrance P. Snutch PhD- University of British Columbia

Jeff Wrana PhD - University of Toronto

Extensive list of collaborators found here.

OUR TEAM

Anthony Bayega PhD

Sarah Reiling PhD

Ju-Ling "Linda" Liu, PhD