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N.S. gains COVID early warning system via wastewater sampling

Dr. Crystal Sweeney, Dalhousie University-based Project Manager for the Nova Scotia-wide wastewater surveillance project.

Nova Scotia’s low incidence of COVID-19 has endowed a short-term, province-wide wastewater surveillance project with the ability to act as an early warning system for clinical caseload surges.

That capability sets the Nova Scotia program apart from other wastewater sampling initiatives across the country, monitoring for the virus that causes the disease, according to Dr. Graham Gagnon, who co-leads the surveillance project with Dr. Amina Stoddart, both from Dalhousie University’s Faculty of Engineering.

Dr. Gagnon, who is also the University Research Professor and Director of the Centre for Water Resources Studies, explained, “in regions of high caseloads, the viral signal is expected to be seen in the wastewater and can be monitored for increasing or decreasing trends.

“What’s interesting about our program is that while we expect the viral signal in wastewater to be low when cases are few, a notable increase in the signal could indicate the presence of the virus before new cases are reported.

“When used in this way, our research has the potential to provide us with an early warning signal for the re-occurrence of COVID-19 in our communities.”

As talk of a third pandemic wave grows, advance warning could give Nova Scotia Public Health officials a distinct advantage to take mitigating measures ahead of a viral outbreak and reduce its potential impact.

“Another notable feature of our program,” said Dr. Gagnon, “is that in addition to wastewater testing, we are incorporating primary solids testing, as well as passive sampling in targeted locations for a more comprehensive monitoring strategy.”

Wastewater surveillance exploits a quirk of SARS-CoV-2, the virus that causes COVID-19. Its genetic material survives longer in the gastrointestinal tract than in the respiratory system where it causes most of its havoc. That factor makes it possible to detect the virus, via its RNA, when excreted in human waste by individuals who may be asymptomatic, pre-symptomatic or symptomatic.

With the mass vaccination program against COVID-19 under way, Public Health worries have shifted to the infiltration of variants of concern and their potential to show resistance to the antibodies generated by the new vaccines and the natural immunity acquired from having had COVID-19. In some cases, variants first detected in the U.K., Brazil and South Africa seem to be more transmissible and, to cause more serious disease, than the wild form of the virus – the non-mutated form we are more familiar with.

Responding to these developments, Project Manager, Dr. Crystal Sweeney, noted the Nova Scotia team’s detection method targets the N2 gene on the viral RNA to identify the presence of SARS-CoV-2 in wastewater samples.

“Since the mutations identified in the variants of concern do not involve the N2 gene,” she said, “our method is able to detect the variants, if present, but we cannot identify whether the viral signal is from the wild-type SARS-CoV-2 or a variant.

“However, we are working with a laboratory here at Dalhousie University to sequence RNA extracted from our wastewater samples to determine whether variants of concern are present in the environmental samples.”

Dr. Sweeney is confident RNA fragments from SARS-CoV-2 cannot easily elude the sensitivity of the team’s testing method. “Through strategic and targeted monitoring, along with innovative method advances, we have demonstrated the ability to detect the viral signal in wastewater when there were only nine active cases in the entire province,” she said.

Data collection and assembly have been organized for fast, accurate retrieval and distribution, with a dashboard that displays the latest sample collection and analysis data. Dr. Sweeney said, “We have also prepared consolidated reports for wastewater testing results at each sampling site so that a complete sampling and data history can be provided for any site at any time.”

Wastewater sampling for pathogens is not new to public health. It was widely used in the past to uncover Poliovirus 1, for instance.  Many countries, most of them in the context of research, are using wastewater sampling for SARS-CoV-2 detection, and Dr. Gagnon said, “We view our work as a research program that builds upon the active body of research that is happening in the field of wastewater surveillance across the globe.”

The current Dalhousie-led project is the successor to a Genome Atlantic-funded pilot in which Dr. Gagnon’s team succeeded in finding evidence of SARS-CoV-2 in Wolfville’s municipal wastewater system, last year. The province’s Public Health officials responded by expanding capacity at the town’s primary COVID-19 assessment centre and opening pop-up rapid testing sites in the community. It was a demonstration of how wastewater surveillance and Public Health officials can work together to mitigate the spread of COVID-19.

Dr. Gagnon recounted, “Genome Atlantic’s support allowed us to get some small laboratory equipment and to bridge a research assistant into this much larger project.” The funding helped finalize some lab testing and demonstrated the potential of the wastewater sampling method on environmental specimens.

The current $852,000 wastewater surveillance project, sponsored by Research Nova Scotia, has more than 15 wastewater sampling sites around the province. Weekly sentinel sampling for sustained monitoring in vulnerable locations is done at wastewater treatment facilities in the Halifax Regional Municipality, Sydney, Antigonish and Wolfville. Specimens are also collected up to three times a week from targeted sewersheds in surrounding areas designated for intense and frequent monitoring.  

The research team’s affiliation with a wastewater research program initiated with Halifax Water and NSERC, said Dr. Gagnon, facilitated sample collection, access to sewersheds and the ability to build the sampling programs critical to the project.

Samples are analysed by the 18-member project team within three to four hours of arrival at a lab. The team uses the new internationally deployed rapid and direct SARS-CoV-2 RNA extraction method, recently developed by Dr. Gagnon and his research group, in partnership with LuminUltra Technologies, an international biotech company based in Fredericton, N.B.  

The company is a key partner in the program along with Halifax Water, which is a co-investigator in the project along with Acadia University, Cape Breton University and St. Francis Xavier University.

It is worth pointing out that although detection of the SARS-CoV-2 signal involves the amplification of RNA fragments, Dr. Sweeney said, “the virus itself may not be in the infectious state.” She added, “although no cases of transmission through contact with sewage or contaminated water have been reported to our knowledge, and studies conducted with these matrices have not detected infectious viruses, it is important to apply the precautionary principle when handling samples.”

The surveillance program is expected to continue until July, with a final report due in November.

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