Why we’re seeing a rise in COVID-19 this fall and the roles of booster doses & continued tracking

Need to know which vaccines are available in your part of the country, where to go, how to make an appointment, and the masking policy?

This CoVaRR-Net summary gives you the answers, taken from the websites of governments across the country.

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“We need to be prepared for the perfect storm of three respiratory viruses – Omicron subvariants, RSV (respiratory syncytial virus), and influenza – circulating at the same time later this fall. That’s what people in Australia experienced during their fall/winter season and it’s rare that we don’t see similar patterns here,” says Dr. Nathalie Grandvaux, CoVaRR-Net’s Antiviral Strategies and Antiviral Therapeutics Pillar Deputy, Professor at Université de Montréal, and Principal Investigator, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM).

Being prepared starts with recognizing that SARS-CoV-2, the virus that causes COVID-19, continues to evolve with mutations that frequently make the virus more transmissible and better able to evade our immune systems. “We saw COVID-19 cases rise rapidly in early fall, reaching numbers in September that we have not seen in Canada since March 2023,” says Dr. Sally Otto, Co-Lead of CoVaRR-Net’s CAMEO (Computational Analysis, Modelling and Evolutionary Outcomes) Pillar, Killam Professor and Tier 1 Canada Research Chair at the University of British Columbia. “Why was there an upsurge in cases long before the normal fall respiratory season? Immunity from vaccines and previous infections has certainly waned in Canada, but is there a variant driving the upsurge?”

“At CoVaRR-Net, we’ve been tracking lineages as they arise and spread, both globally and in Canada. The upsurge in early fall coincided with the spread of EG.5.1 and descendant variants, including HV.1 and HK.3. These are all in the broader group of Omicron XBB viruses.  Two striking features highlight why Canadians need to take precautions now: the genetic changes carried by these variants increase the virus’s ability to infect cells and hide from our immune system,” adds Dr. Otto. “While case numbers are now stabilizing, we’re seeing even more distinct variants emerge, like BA.2.86.”

New COVID-19 vaccine formulations are timely

Health Canada approved new reformulated versions of Moderna’s Spikevax and Pfizer-BioNTech’s Comirnaty COVID-19 vaccines – targeting the Omicron sublineage XBB.1.5 – in September, making these readily available to Canadians this fall and winter. “The reformulated COVID-19 vaccines couldn’t have come at a better time given that the vaccines this fall are targeting the variant that had spawned the currently circulating highly infectious variants and that for most Canadians it has been more than six months since they have had the last dose of COVID-19 vaccine,” says Dr. Nazeem Muhajarine, Co-Lead of CoVaRR-Net’s Public Health, Health Systems and Social Policy Impact Pillar and Professor of Community Health and Epidemiology at the University of Saskatchewan.

“At the population level, our collective immunity has eroded a bit, and the virus is always mutating, so people are more susceptible to infection and for some, that means serious disease. If you haven’t had a vaccine dose for COVID-19 or been infected in the past six months, you need to get the updated vaccine. We now need to think of this updated COVID vaccine as any other vaccine we get in regular intervals, such as the flu vaccine every fall,” advises Dr. Muhajarine.

The new vaccine formulations target XBB specifically and will help train our immune systems to better recognize the main variants circulating today. “The new vaccine formulations have enough similarity to currently circulating variants and their immune-evasive mutations that they can provide more effective protection than the previous bivalent vaccines,” explains Dr. Fiona Brinkman, with CoVaRR-Net’s CAMEO Pillar and Distinguished Professor in Bioinformatics and Genomics at Simon Fraser University. “The updated vaccines can reduce your chance of getting infected and the severity of any symptoms you get, providing a helpful immune boost through the fall and winter respiratory virus seasons and ahead of holiday gatherings.”

CoVaRR-Net’s CAMEO team is also tracking other emerging variants with additional immune-evasive properties. “It’s still an evolving situation, where we do have other emerging variants, carrying what are referred to as “FLIP” mutations, which have an even greater ability to evade our immune system than EG.5.1. We don’t expect COVID-19 cases to drop down to low levels, with HV.1 and new variants like BA.2.86 on the rise with additional mutations that confer an advantage, so getting an updated vaccine is wise,” adds Dr. Brinkman.

Dual shots for flu and COVID-19 protection

CoVaRR-Net experts suggest that eligible Canadians should get a reformulated COVID-19 dose and a flu shot as soon as available to them. “Getting vaccinated for COVID-19 and the flu will not only help protect you from severe symptoms, but it will also reduce the chances of infecting those around you,” says Dr. Grandvaux. So far, most people getting both shots at the same time have not been experiencing issues. “Getting COVID-19 and flu shots together is also important for people eligible to get the RSV vaccine – particularly the elderly who are vulnerable to all three viruses — since they need to wait two weeks after those shots, and RSV cases have started to rise now,” adds Dr. Brinkman.

Better tools to help guide public health responses and recommendations

Through innovative research conducted during the pandemic, CoVaRR-Net has developed and expanded the tools available to track and predict changes in SARS-CoV-2 and other viruses, such as the flu and RSV. These tools, and the associated modelling of the data, aid a collective early-warning system public health officials can use to rapidly adjust their recommendations when there are changes in the viruses circulating.

“Through CAMEO, we’re modelling future impacts for respiratory viruses. We’re taking what we learned from COVID-19 and applying it to other infectious diseases, such as RSV and the flu,” says Dr. Brinkman. “What we want to do is really benefit from all we’ve learned from the COVID-19 pandemic, developing tools that help us be more ready for what’s next.”