SARS-CoV-2 continues to circulate in Canada while the watch is on for highly pathogenic avian influenza

SARS-CoV-2 and its resulting disease, COVID-19, have not gone away. Wastewater tracking indicates that SARS-CoV-2 levels in Canada are now at 10 to 15 per cent of peak levels during the height of the pandemic. While encouraging that they are much lower than at the peak, these levels still represent a significant community viral load and in turn a significant incidence of disease across the country. Currently there is also an uptick in cases in many regions.

“KP.3 is the most dominant variant in Canada now, but other variants with notable immune evasive mutations are also growing, providing a selection of viral variants that people may be susceptible to,” says Dr. Fiona Brinkman, Deputy in CoVaRR-Net’s CAMEO Pillar and Distinguished Professor in Bioinformatics and Genomics at Simon Fraser University. “These are all descendants of the JN.1 variant. What’s notable about the current wave of variants is that most are increasingly immune evasive.” That means prior immunity due to an infection or vaccination with another variant is not as effective in warding off infection.

“While there is no significant concern at this time, Canadians are encouraged to keep up to date with vaccinations when they are eligible, especially those such as the elderly who are more susceptible to this virus, since vaccination could reduce the severity of the disease,” states Dr. Brinkman. The National Advisory Committee on Immunization (NACI) recently updated its recommendations, advising that Canadians receive a booster of the most updated COVID-19 vaccine formulation this fall, if it’s been three to six months since the previous COVID-19 vaccination or an infection.

Watching out for ‘bird flu’ in Canada

In the meantime, experts, including many at CoVaRR-Net, are aiding analyses that help track a subtype of bird flu, or H5N1, also known as highly pathogenic avian influenza (HPAI).

A surprising outbreak of H5N1 in U.S. cattle was first reported on March 25, 2024. Genomic analyses, including a rapidly released study involving CoVaRR-Net members, indicated that this virus jumped into cows likely as a single introduction, probably sometime toward the end of 2023. It has since spread to more than 100 dairy cow herds across at least 12 U.S. states including some that border Canada. Sporadic cases of dairy farm workers have been reported, and cases have also been identified in multiple other animals, including birds and mammals who have contracted this particular viral subtype from this cow outbreak.

“In Canada, there is currently no report of H5N1 in cattle, which is good news,” says Dr. Brinkman. “Although we’re in a good position now, public health working with researchers and others in the community need to be prepared and vigilant in surveillance, working closely with those that could be most impacted – including economically.”

“A key concern at this time is that this virus is newly jumping from cows into multiple other mammalian species – and in some cases is causing very severe disease with a high fatality rate of around 50 per cent,” cautions Dr. Brinkman.

“As public health emphasizes, the risk to people is currently low. But the jump from birds to multiple mammals via cows is concerning, because each time the virus jumps from one species to another, there is more selective pressure for the virus to acquire certain adaptive mutations that could allow transmission between mammals, including humans, of a severe form of the disease,” she adds. “We simply cannot have a repeat of a pandemic like COVID-19 and must protect our agriculture industry which has been struggling already. With strong surveillance we can more quickly react – in ways that lessen impact on people, other animals, industries, and our economy.”

Wastewater surveillance: a cross-country smoke alarm for human bird flu

CoVaRR-Net’s Dr. Robert Delatolla agrees that vigilance is essential to prevent or reduce the risk of bird flu outbreaks in humans. “Now is the time for us to be prepared for the improbable happening, where bird flu in cattle adapts and jumps to humans, and spreads between humans,” says Dr. Delatolla, Director of CoVaRR-Net’s Wastewater Surveillance Research Group, Viral Genomics & Sequencing Pillar Deputy, and Professor, Department of Civil Engineering, University of Ottawa. “I’m concerned that the improbable is becoming more probable as H5N1 jumps back and forth across more mammalian species and continues to evolve. Before the pandemic, it seemed improbable that SARS-CoV-2 would jump from animals to humans.”

Delatolla and some colleagues across the country are now using wastewater surveillance to look for early signs of bird flu infecting humans. In the U.S., wastewater monitoring in Texas picked up an early signal of a bird flu outbreak in cattle three weeks before the U.S. Department of Agriculture reported infected cattle for the first time. “There is a substantial network of 100 to 200 sites across Canada actively doing wastewater surveillance for different pathogens. Because we are in the off season for people getting seasonal flu, it would be unusual to see influenza A levels go up in wastewater in the spring and summer. That would be an indicator of possible bird flu in a community that needs more investigation,” explains Delatolla, noting that U.S. wastewater systems in some states include both human waste and animal byproduct waste.

Canada’s wastewater surveillance system focuses on human waste, an important advantage in accurately determining whether humans are the source of any H5N1 virus detected. “We have the exact monitoring capability across Canada needed to pick up probable or possible signs of H5N1 using a general influenza A probe. We can then do a subtyping test to confirm whether the influenza A virus detected is H5N1. Through a coordinated national wastewater surveillance effort working with public health, we would have the ability to sound an alarm across the country for any emerging cases of bird flu in humans,” he says.

Tracking bird flu’s evolution to assess the changing risks to humans

Dr. Brinkman says ongoing surveillance and analysis of how H5N1 is evolving and moving across (and within) different mammalian species is essential to rapidly and effectively assess the changing risks to humans. “We can really learn from water and wastewater. My interest is in helping to coordinate different efforts being undertaken by researchers across Canada who are studying the evolution of H5N1 and other pathogens, and integrate data in ways that support researchers, communities, and public health to develop appropriate, community-sensitive measures that will help to control disease threats,” she says.

As a member of Canada’s VirusSeq Data Portal development team, Dr. Brinkman is working with Mélanie Courtot (Ontario Institute for Cancer Research), Emma Griffiths (Simon Fraser University), Guillaume Bourque (McGill) and others to expand this open-source and open-access national database to support analyses and visualization of pathogen wastewater data from across the country. “We can include in this data platform additional data not present in other databases and develop this with an approach that facilitates research-public health collaboration and innovation, and factors in Canada’s needs, such as data sovereignty for Indigenous Peoples,” says Dr. Brinkman. The team received some funding from CoVaRR-Net to help support the expansion.

“Having a Canadian data platform enables researchers, community members, public health officials, and policymakers to look at what’s happening in real time and over time with pathogens, such as those causing COVID-19, RSV, and flu – across the country and within each region,” Dr. Delatolla adds. “This will improve our response to new disease outbreaks, nipping it in the bud so there’s less impact on people, industries, and our economy.”

CoVaRR-Net is extremely concerned and strongly disagrees with Ontario defunding and shutting down its wastewater surveillance program.

This unfortunate news comes as there is a High-Consequence pathogen, namely the highly pathogenic avian influenza H5N1, that is currently infecting dairy cows just south of our border. Wastewater surveillance is a highly effective and low cost method to monitor the prevalence and spread of harmful pathogens in the population. It is the first line of surveillance to quickly identify if any outbreaks occur and help mitigate the spread of a pathogen. This decision by Ontario will deal a devastating blow to national surveillance efforts as 58 testing sites will be shut down across Ontario and highly qualified personnel who are experts in wastewater surveillance will likely begin transitioning away from this area of research and surveillance. As of this moment, we are unaware of any other provincial or federal initiatives to compensate for this loss in national surveillance capacity.