Q&A: Researchers search Sask. wastewater for potential COVID sub-variants

When researchers at the University of Saskatchewan began to find bits of COVID-19 they couldn't identify earlier this month, they began to get curious.

According to readings released on May 8, samples taken from Saskatoon's wastewater showed that 3.2 per cent were listed as "other lineages" and were not identified as the BA.2 variant of Omicron, which made up the vast majority of samples being taken (96.8 per cent).

As a result, the researchers decided to send the mystery samples from Saskatoon and Prince Albert to the National Microbiology Laboratory (NML) in Winnipeg for whole-genome sequencing.

Researchers at the University of Saskatchewan want to know if the samples are a new sub-variant of Omicron, like BA.3, BA.4 or BA.5, which have not been officially spotted in the province. Some of the new sub-variants are more transmissible than BA.2.

To find out more, CBC talked to NML scientist Chrystal Landgraff about how the process works and why it's important to search for these new variants.

The following has been edited for clarity and length.

David Shield: How difficult is it to search for these variants when you're getting information from wastewater samples? It certainly isn't like doing a nasal swab.

Chrystal Landgraff:  You start with the collection of a sample from a lagoon or a municipal wastewater treatment plant. Once the sample arrives here, if it's destined for sequencing, it comes to our lab and we first have to actually pull the virus out of the samples. So, you can think of it like a big jar of trail mix, where the jar is your wastewater sample. And then you're really looking to pull, say, just the Smarties out away from the crackers and pretzels. So, that's the first step. So we do a lab test to pull the virus out of the samples. 

Then, we have to isolate the genomic materials and then we amplify all of the pieces of the virus. They're in pieces because, of course, this is wastewater. We are pulling out pieces of the virus that were shed by many different people in the community. So we make many, many copies of those pieces that were each shed by different members of the community using a very, very specialized type of PCR test. And then we throw all those pieces that we've made, millions of copies, onto a sequencing instrument. That's the first step. So it is more complicated than just a simple diagnostic plus or minus test, like a rapid antigen test that quickly gives you results. 

And then the next part of it is just as complicated, which is the analysis. 

So now we're working with specialized computer programs. Wastewater data is a mess of different sequences from different people. So we need to be able to really tease things apart at a much deeper level than is necessary for clinical sequencing. Once we have all the pieces teased apart, and we use specialized computer programs to do that, then we can really rapidly say, OK, I'm interested in determining if Omicron is present in my sample. So we have scripts that we can just change a little bit each time that are readily adaptable to any new variant or any new type of SARS-CoV-2 virus that comes out, which we call the lineage. And so Omicron, for example, is a lineage. And then we are able to really tell you do you have Omicron? Do you have a mix of maybe Omicron and some Deltas, etc.

DS: How important is it for this work to happen? This continual search for the presence of new variants? 

CL: The virus has changed continuously or evolved over the course of the pandemic. We have seen some variants or some lineages that are perhaps associated with increased rates of transmission in a population. What the wastewater testing is allowing us to do is to continue monitoring at a community level which variants are present in a community and allows us to monitor their spread. It provides information on the relative amounts of the variants in the wastewater. 

We're not just telling you that you have SARS-CoV-2 in the wastewater. We are producing information for public consumption that informs the Canadian public about which variants are in their community. It really allows them to do a personalized risk assessment every day. Am I going to go to that concert and not wear a mask, for example, or that hockey game? Which variant is currently circulating in my community and how concerned should I be? 

DS: Are there any particular variants that you're searching for? Is there anything in particular you're keeping a close eye on? 

CL: In some ways, yes. We are living in a BA.2 world right now and that is really the dominant variant at this time. But we have also seen that this virus is constantly changing. So it's constantly acquiring small changes in its genome that lead to these variants, such as BA.1, BA.3, BA.2. So, the tools that we use allow us to look for as many or as few of these variants that we're interested in looking for. We would just list out a bunch of these changes in a text file and then we feed it into one of our computer programs and it looks through all the data and then spits out a report at the end that tells us whether or not it detected these different variants. 

So we are, of course, remaining up to date on the literature, on the global picture. We utilize a very, very useful website to do that, and that provides information on the breakdown of different variants in multiple countries. There's lots and lots of data out there, including the canada.ca website that publishes up to date information on which variant lineages are present in Canada. So we incorporate all of that information into our scans of the data. So currently we are definitely looking for all of these Omicron lineages, BA.1, 2, 3, 4 and 5 and just really continue to monitor the international picture and the Canadian picture to help us determine that we are directing our scans of the data in the right direction.