Scientists advance wastewater testing to detect new COVID-19 variants

As more infectious COVID-19 variants take hold in Ontario, scientists are looking at wastewater testing in Ottawa to keep track of variants like B.1.617, which was first identified in India and also known as Delta.

Researchers have been using wastewater to test for SARS-CoV-2 in the city since April 2020. In February, they started tracking the variant first identified in the United Kingdom, also known as Alpha. 

Now, new funding of more than $338,000 from Genome Canada, Ontario Genomics and Illumina means researchers can develop tests for newer variants like Delta and the P1 COVID-19 variant, first seen in Brazil. 

• Wastewater data shows shutdown may be improving COVID-19 numbers
• Wastewater is a COVID-19 'early warning system,' Ontario spends $12M to test sewage

Tyson Graber, a cell biologist and research associate at the Children's Hospital of Eastern Ontario Research Institute who's working on the project with others from CHEO, the University of Ottawa and the University of Guelph, told CBC Radio's Ottawa Morning that tweaking the test to detect variants can be challenging. 

He said new tests are designed on a computer, but when it's finally tested on wastewater, "usually there's issues" that take time to fix. "This is biology, this is real world science." 

A more complete picture

Researchers are also developing another test that could work in tandem with variant-specific testing, Graber said. This second test, called metagenomic sequencing, would monitor wastewater and identify all COVID-19 variants present in a mixed sample.

Genomic sequencing of COVID-19 is already happening in a fraction of patient tests that come back positive, Graber said. When you go for your nasal swab, some of those tests are sent to a special site in Toronto for sequencing. "So they know the entire alphabet of that virus that's infecting you."

The same concept can be applied to wastewater, where different sequencing from different people would make up a "community genome." Graber said this metagenomic sequencing is what scientists are now analyzing for more data on the presence of variants in Ottawa.

Since mid-April, they've collected and analyzed two points of data. "We can more or less confidently say that Ottawa is quite good, quite clean, in the sense that it's mostly all Alpha variant that's out there," Graber said.

'It will be here'

The latest data is from May 10, and Graber said he hasn't seen much of the Delta variant yet, but he is anticipating a spike. Researchers can identify the novel coronavirus in wastewater several days before it shows up through clinical testing. 

Last week, Peel Region's Medical Officer of Health Dr. Lawrence Loh said his region has the highest proportion of the Delta variant in the province. The Ontario COVID-19 Science Advisory Table estimates that about 27 per cent of new cases are linked to the Delta variant. 

• Delta variant prompts calls for Ontario to prioritize Peel for 2nd COVID-19 vaccine doses
• Race between vaccines and variants is back on as B.1.617 takes hold in Canada

Evidence suggests that one dose of a COVID-19 vaccine was found to be less effective against the Delta variant, compared with two doses.

While the race is on to fully vaccinate vulnerable populations, Graber said scientists are also racing to develop a wastewater test to identify B.1.617, because while Ottawa's cases of the variant are low and its population is partially immunized, things can change quickly. 

"It's still coming, and it will be here," Graber said.