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Canada is entering a period of relative calm as the Omicron-driven fifth wave subsides across much of the country. But our ability to track new and existing variants is in jeopardy with testing access still heavily restricted — leaving us vulnerable to pandemic whiplash.
Dr. Theresa Tam, Canada’s chief public health officer, said Friday that COVID-19 levels have continued to decline in most of Canada, with weekly case counts down 26 per cent and hospitalizations and ICU admissions down 20 per cent compared to the previous week.
“Nevertheless, as the virus is still circulating widely, some jurisdictions are reporting weekly increases in case counts and others could see additional bumps in the weeks ahead,” she said.
“At the same time, there is a continued high volume of PCR testing being performed and ongoing genetic sequencing of circulating virus variants.”
But the level of COVID-19 testing in Canada has actually dropped off dramatically since the start of the Omicron wave — with more than 100,000 daily tests being performed in early December, about 150,000 in early January, down to just over 50,000 as of Friday.
That makes it nearly impossible to get a clear sense of what the true number of COVID-19 cases are in Canada, and severely limits the number of testing samples that can undergo genomic sequencing to detect for the presence of variants.
World ‘cannot abandon’ testing amid threat of variants
The World Health Organization’s leading coronavirus expert Maria Van Kerkhove said this week that while there has been a 20 per cent drop in COVID-19 levels globally in the past week compared to the previous week, the decline “may not be real” due to a lack of testing.
“We are very concerned about a reduction in testing around the world,” she said Tuesday.
“We need to be smart about this, we need to be strategic about this, but we cannot abandon it — and what we do not want to see is the dismantling of these surveillance systems that have been put in place for COVID-19.”
Van Kerkhove said widespread COVID-19 testing is “absolutely critical” to detecting new variants and understanding how the virus is evolving, because you can’t sequence testing samples for the presence of variants if people aren’t actually being tested.
She added the virus will evolve over time because the more it circulates, the more opportunities it has to change — but while more variants can emerge with “concerning” properties, they won’t become a public health threat unless they spread.
“About the only thing I am certain about is that there will be a new variant,” said Angela Rasmussen, a virologist at the Vaccine and Infectious Disease Organization (VIDO) at the University of Saskatchewan.
“With three billion worldwide unvaccinated, coupled with relaxed precautions intended to reduce transmission, I feel pretty confident saying that the next variant is not a question of if, but when.”
Rasmussen said while it’s very difficult to determine exactly what the next variant will look like, the emergence of Omicron should give us pause because it “caught us by surprise” due to its “uncertain origins.”
“Unlike Alpha, Beta, Gamma, and Delta, Omicron did not arise from widespread transmission in unvaccinated populations,” she said.
“I’m very concerned about another variant coming ‘out of nowhere’ — emerging from an unexpected source, such as a persistently infected patient or from spillback into animals.”
Canada needs ‘advance warning systems’ for variants
If widespread PCR testing isn’t coming back to Canada anytime soon, or at all, experts say we need to build up other COVID-19 surveillance systems.
“Current levels of PCR testing are very unlikely to be capturing the true extent of spread,” said Dr. David Naylor, who led the federal inquiry into Canada’s response to the 2003 SARS epidemic and now co-chairs the federal government’s COVID-19 Immunity Task Force.
“As Omicron showed, it’s difficult to forecast the downstream effectiveness of vaccines and previous infections at preventing spread and, more importantly, averting serious disease. That’s why we need advance warning systems.”
Naylor said there are two key advance warning systems to build up now that access to testing has been dramatically restricted — bolstering national wastewater surveillance and creating a national PCR testing program using random sampling of tests to track the virus.
Marc-André Langlois, a molecular virologist at the University of Ottawa who heads the Coronavirus Variants Rapid Response Network (CoVaRR-Net), says wastewater surveillance is one of the last reliable ways to track and sequence variants with testing scaled back.
“Where do we capture variants? Where can we monitor this in a systematic manner? Well, everyone goes to the toilet, right?” he said.
“If we capture what’s happening in our wastewater, for one thing, we get around all of the privacy issues, because it’s an amalgam of a population, and second of all, we now have technologies that are better than just PCR.”
Langlois said scientists now have the ability to sequence variants directly from wastewater samples, allowing them to determine the prevalence of a certain variant in a given population as well as the overall level of virus in the community better than PCR testing.
Wastewater surveillance is also way more cost effective, allowing researchers to test thousands of samples at once — compared to the astronomical cost of administering, processing and sequencing the more than 58 million tests performed in Canada to date.
“I can test one wastewater site for the same cost almost that it costs to do a PCR test on one patient and I get information on 100,000 people,” said Eric Arts, Canada Research Chair in viral control and professor of microbiology and immunology at Western University.
“If you think about it, you can add $150 to every test that we’ve performed across the country that reported on an individual case — it’s unbelievable the cost.”
Arts says he fully believes in individual testing when someone has to be hospitalized with severe COVID-19 and needs confirmed results in order to access treatment, but it “doesn’t make sense” for those who don’t develop serious symptoms and recover at home.
“It’s not perfect,” he said. “But I would say it’s more accurate in the long run than individual testing because not everybody’s going to get tested.”
Canada lacks a national strategy for wastewater testing and much of the data isn’t publicly available across the country, something Langlois and Arts both said need to be invested in and standardized across the country.
Langlois said if national wastewater surveillance data was publicly available across the country, Canadians could use it to make individual decisions to protect themselves if their community saw a sudden uptick in COVID-19 or the emergence of a variant in the future.
“There should be some sort of dashboard telling the population ‘Well, the incidence is going up, I’m due for my booster shot, maybe it’s a good time that I get my booster shot,” he said.
“And with additional government funding, it could grow into its own entity where there’s a general wastewater surveillance for other common pathogens — like influenza.”