Pillar 6
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)

The ongoing pandemic wave caused by the Omicron variant of SARS-CoV-2 has overwhelmed PCR testing capacity in many parts of the world, including Canada. As a result, it has become hard or impossible to accurately count COVID-19 cases in a given community ­– and also to identify new mutations or variants (combinations of mutations) that might be evolving and spreading.

When clinical samples are lacking, wastewater provides an alternative way to track the amount and types of virus in a community. When people are infected with SARS-CoV-2, they excrete it in their poop and it can be detected in wastewater. In this work, we showed that we are able to sequence SARS-CoV-2 genomes from wastewater and identify mutations characteristic of different variant lineages such as Alpha or Omicron. Wastewater contains a mixture of viruses shed by many different people, so we are able to detect many different variants from a single sample. We found that the variants detected in wastewater were generally similar to those found in clinical sequences from nasal swabs collected in the same city and time period. In the current context of very limited clinical testing, wastewater provides a time- and cost-effective way to keep monitoring coronavirus variants circulating in the community.

In some other studies, researchers have found wastewater to be a “leading indicator” of pandemic waves, meaning that concentrations of coronavirus start increasing in wastewater before a spike of clinical cases is seen. However, in our sampling of cities in Quebec, we found that variants were not usually detected in wastewater before they were sequenced from clinical samples. For example, we detected the Omicron variant in Montreal on December 4, 2021 – just a few days later than it was first sequenced from a nasal swab in the province of Quebec. This means that ­– so far anyway ­– clinical testing in Quebec has been doing an excellent job of picking up variants in a timely fashion. But as clinical testing capacity gets scaled down going forward, wastewater provides a cost-effective way to keep track of variants.

Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada. Arnaud N’Guessan, Alexandra Tsitouras, Fernando Sanchez-Quere, Eyerusalem Goitom, Sarah J. Reiling, Jose Hector Galvez, Thanh Luan Nguyen, Ha Thanh Loan Nguyen, Flavia Visentin, Mounia Hachad, Kateryna Krylova, Sara Matthews, Susanne A. Kraemer, Paul Stretenowich, Mathieu Bourgey, Haig Djambazian, Shu-Huang Chen, Anne-Marie Roy, Brent Brookes, Sally Lee, Marie-Michelle Simon, Thomas Maere, Peter A. Vanrolleghem, Marc-Andre Labelle, Sandrine Moreira, Inés Levade, Guillaume Bourque, Jiannis Ragoussis, Sarah Dorner, Dominic Frigon, B. Jesse Shapiro. medRxiv.2022.02.01.22270171; https://www.medrxiv.org/content/10.1101/2022.02.01.22270170v1