Tracking viruses down the drain

Replacing frequent screening tests with monitoring for the presence of the virus in city sewage? There are still pitfalls before we get there, but the pandemic will have highlighted this once marginal method.

Mid-March 2021. The second wave of COVID-19 appears to be over and the Quebec government has just announced an easing of health measures in several regions. In Quebec City, there are about 50 new cases per day, which is a quarter of what we saw in previous months.

However, a third creeping wave is already underway, even if the screening tests haven’t shown it yet. Everything happens underground… “We detected the first increases in viral particles in Quebec’s streams in mid-March,” explains Dominique Fregon, a researcher at McGill University and coordinator of the Center for Scientific Research in Quebec (CentrEau). Each week, public health authorities can be told that cases detected by screening will increase in the following week. “

As in fact, on March 31, the number of new patients is approaching 300 per day at Capital National. That day, at the press conference, the government announced that the city and its region had moved to the “dark red” area.

This predictability is the result of the hard work of a group of ten researchers across Quebec. Their project is part of a global movement that has the potential to change the way we practice epidemiology: tracking the evolution of pathogens in wastewater discharges.

Since January 2021, researchers have been measuring the abundance of SARS-CoV-2 at 40 sewage collection sites across the province, mainly in the cities of Quebec, Montreal and Laval, as well as various municipalities in the Maurice Center of Quebec and Bass-Saint-Laurent.

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Although it is a respiratory virus, SARS-CoV-2 ends up in our faeces and then in our sewers. The more sick people are in the city, the more sewage will spread in it. “The virus can infect many cells in the body, including cells in the intestine,” explains Dominique Fregon. Once the virus leaves the body in the stool, its lipid membrane rapidly degrades, but its genetic material is protected by proteins called nucleocapsid plug. This part of the virus is highly resistant in the environment, which is what makes it possible to detect certain viral sequences in the sewers. “

How is a city diagnosed?

Le monitorage des eaux usées n’est pas nouveau : on l’a utilisé de façon anecdotique au cours des dernières années pour détecter le virus de la poliïélite dans certain villages ou mesurer l’utilisation de drogues, commeca les ou big cities.

But the technological leap required to move from these first severe tests to monitoring a pandemic virus on a scale of tens of millions of people is enormous.

“For polio, it’s simple,” explains Dominique Fregon. We are looking to see if the virus can be detected in water. In the case of COVID-19, we know the virus is there. What we want to monitor is the variance in its presence in order to make public health decisions. It’s much more complicated. “

“Until then, we had never sampled coronavirus in sewers and the entire methodology had to be developed,” explains Peter Vanrolleghem, Professor of Water Engineering at Université Laval and Director of the CentrEau Network.

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To monitor the presence of the virus in city waters, researchers take samples from strategic locations in the network or even directly from institutions where screening tests are difficult to conduct, such as health centers, residences or prisons.

RNA in murky water

However, sewers are a tough environment for RNA, which can be degraded by anything that passes through them. Measurements can be affected by several factors. “On heavy rainy days, runoff can weaken RNA by a factor of 3,” Peter Vanrolleghem explains. Wastewater may also contain substances that interfere with the test. Finally, the amount of virus excreted in the stool varies a lot from person to person. We need ways to normalize that. “

To achieve this, researchers use control viruses. “We first add to our sample a bovine virus whose envelope is very similar to that of SARS-CoV-2 and simultaneously measure its presence with the virus of interest,” explains Professor Frigon. This ensures that the water does not contain chemicals that degrade RNA which would distort our results. “

Researchers also measure the level of chili pepper peel virus, which is present in the human digestive system through the vegetables we eat. It is increasingly used as a fecal marker. “This virus is our foundation,” adds Professor Vanrolegim. As its expression remains relatively stable in the population, this provides a point of comparison to check whether the expression of SARS-CoV-2 increases or decreases, even if the water volume varies in sewers. “

Although the method has proven successful in Quebec City, conditions on the ground are still challenging.

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“The ideal would be to take samples that represent the wastewater of about 100,000 people at one time,” says Dominique Fregon. The samples at the end of the grid are very large; They combine the rejection of millions of people, which significantly reduces our sensitivity. In contrast, the samples at the beginning of the network, which collect wastewater from one neighborhood, contain discharges from too few people to be representative of a large city. It will therefore now be necessary to plan the sampling systems to be installed in strategic locations in order to obtain the best data. This should be done over several years in anticipation of a coming epidemic, rather than trying to implement it in an emergency. “

For researchers, the wastewater monitoring project has great potential. Dominique Fregon continues: “It will take 2-3 years to vaccinate the rest of the planet, and in the meantime, we must continue to measure the presence of the virus. This method can also be applied to assess antibiotic resistance or identify influenza strains. Wastewater is an incredible source of information.” “

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