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Harnessing the power of wastewater testing to detect COVID-19 outbreaks

Scientists at the Public Health Agency of Canada (PHAC) are expanding the frontiers of public health surveillance using advanced techniques to detect COVID-19 in communities across Canada through wastewater analysis.

In the early days of the pandemic, Drs. Mike Mulvey of the National Microbiology Laboratory (NML) and James Brooks of the Centre for Communicable Diseases and Infection Control developed wastewater surveillance approaches to generate an "early-warning" indicator for detection of COVID-19.

NML scientists Drs. Chand Mangat and Chrystal Landgraff quickly pivoted attention from their usual research to focus on how wastewater surveillance could be applied to detect the virus that causes COVID-19 and help protect the health of Canadians.

Wastewater - a clear window into the community

Dr. Mangat describes wastewater as a "clear window into the community" as it provides insight to public health officials on the types of infectious diseases circulating locally. Wastewater surveillance is also efficient because it provides the same information as collecting and testing individual samples.

"Wastewater samples are much more informative than anyone would have believed when we first started," says Dr. Landgraff. "One of the chief advantages of wastewater testing for COVID-19 is that it can serve as an early warning system."

People infected with the virus can take up to 14 days to show symptoms, or they can be asymptomatic or mildly symptomatic, meaning many infected individuals may not get tested and know they are potentially spreading the virus to others. Regardless, they still shed the virus through their urine and feces. Testing wastewater can pick up on positive cases at least a week before people show symptoms and spur increased testing and public health interventions to stop further spread.

Becoming experts in real time

For PHAC scientists, 2020-21 represented a flurry of activity to establish complex wastewater laboratory tests and a national surveillance program. They are testing wastewater in two different ways: the traditional laboratory test that detects active infections known as the polymerase chain reaction (PCR) testing, and metagenomics - an advanced form of genetic sequencing. Their data is being used by colleagues Drs. Aamir Fazil and David Champredon to develop models to predict the course of COVID-19 outbreaks.

Dr. Mangat and his team are focusing on PCR testing. His job involves setting up surveillance networks, supplying laboratory supplies and providing technical expertise. The team even developed an illustrated sampling guide so people without specialized knowledge can collect, package and send samples. He is working closely with other federal agencies, such as Statistics Canada, Environment and Climate Change Canada, Indigenous Services Canada and Correctional Services Canada, as well as several provincial and academic partners to combine resources and expertise.

"We became experts on wastewater analysis as we went," says Dr. Mangat. "We've been moving at a breakneck pace and there's a lot of really cool science going on. We've learnt a lot about adapting our laboratory tests for this specialized process."

Dr. Landgraff's focus is metagenomics, an advanced form of genetic sequencing. Metagenomics differs from traditional genomic sequencing in that it pulls out all of the genetic information, looking for every possible infectious disease that is present – like a soup where scientists are able to identify all the ingredients, including spices. Traditional genomic sequencing focuses on finding an individual virus or bacteria and looks for just one specific ingredient.

"While some PCR tests can screen if there is a variant, metagenomic sequencing can help communities find which and how much of the variants of concern are present. This is where the real power of sequencing comes in to play because we get the whole genome," says Dr. Landgraff.

Finding success in early detection

The wastewater surveillance program has grown substantially and has successfully been used to stop outbreaks and detect variants of concern. The scientists continue to expand the network and their testing activity, receiving samples from various locations across Canada.

Dr. Mangat illustrates an example of the effectiveness of using wastewater testing as an early intervention in the Northwest Territories. The first indication it was working came when an individual was quarantined in Yellowknife and they detected COVID-19 in the city's wastewater. Through continued surveillance, they picked up more positive samples, suggesting other cases were present in the community. Public health issued a press release asking quarantining community members to present for testing and identified additional cases, preventing a potential outbreak by taking action.

Tracking and preventing future outbreaks

Wastewater surveillance has applications far beyond testing for COVID-19. It is just the start of a surveillance system that can be used to protect the health of Canadians from a variety of different infectious diseases. This approach can be used to detect antimicrobial resistant "superbugs" and food-borne diseases like E. coli or Listeria.

The most advantageous application of wastewater surveillance is in smaller communities, since the smaller the population, the more it can be used to guide public health action. There is a clear public health benefit when it is utilized in northern, remote and isolated communities.

Canada is a geographically vast country and wastewater offers a window into communities in order to understand and use resources efficiently to protect the health of residents.


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