How wastewater surveillance in Manitoba is helping the fight against COVID-19

What is flowing in our sewers could offer important insights into COVID-19 in Manitoba.

Wastewater surveillance is a tool that does not care about testing limitations, and with the potential for data gaps from changes to provincial COVID-19 testing policies and diagnostic processing backlogs researchers say information learned from what goes down the toilet can be valuable.

“Sampling the wastewater is a decent brute force way to get an overall picture of large populations,” said Kevin Coombs, a professor and virus researcher in the Rady Faculty of Sciences at the University of Manitoba. “It cannot tell you at an individual level or at a block or street level necessarily, but it can provide a rapid way at looking at large populations.”

The National Microbiology Lab began wastewater surveillance for COVID-19 in September 2020, with samples taken from five cities: Vancouver, Montreal, Toronto Edmonton, and Halifax.

The program expanded to include about 60 different water treatment plants or sewer sheds including some First Nations. The lab is also working with Correctional Services Canada to monitor for outbreaks at some institutions.

In Winnipeg, the lab has been monitoring wastewater from three Winnipeg water treatment plants. Samples are tested to determine COVID-19 levels and are sequenced to determine their viral RNA, enabling the detection of variants.

“With wastewater, we might start seeing different sequences for different variants of the virus so we have different techniques and algorithms to pull that information out,” said Michael Mulvey, the chief of antimicrobial resistance and nosocomial infections at the National Microbiology Lab.

In December, Mulvey said Omicron was discovered in some Winnipeg samples.

Provincial health officials have warned daily reported COVID-19 case counts are an underestimate of actual transmission rates in the province due to a testing backlog.

It is also probable COVID-19 metrics like test positivity rates have been affected by the province handing out rapid test kits and limiting access to PCR tests.

“When testing becomes difficult, you can maybe rely more heavily on the wastewater trends going up or down to help you determine what’s going on in the community in general,” said Mulvey.

Another use for wastewater testing is the early detection of viruses or outbreaks.

Mulvey said testing in the Northwest Territories discovered a COVID-19 outbreak before public health officials were aware the virus was in a community.

An added benefit is that wastewater testing is cost-effective.

“A wastewater plant in Edmonton services about a million people so one sample of that wastewater and one PCR test we can sort of look at what’s happening with a million people,” said Mulvey.

However, the information gained is limited because it is unknown how the number of copies of the virus found in a wastewater sample relates to the number of cases in a community.

There can also be environmental factors affecting samples because wastewater includes more than what goes down the toilet.

FUTURE APPLICATIONS

Wastewater testing is not new, with Coombs saying some of the more famous historic examples involved polio.

“It came down to the fact that one was looking at large neighbourhoods and so that actually became important to monitor that polio was being eradicated during all of the vaccine efforts,” Coombs said.

In addition to polio and COVID-19, Mulvey said it’s possible surveillance could find traces of any disease that is evident in the stool or urine. It could also offer insight into things like antimicrobial resistance, the spread of influenza, and even drug use in a community.

“There’s lots of unexplored potential for this and very excited about this whole area moving forward and the whole COVID-19 has put wastewater epidemiology on the map,” Mulvey said.