Continuing evolution of SARS-CoV-2 variants and other viruses poses ongoing threat & requires regular monitoring: CAMEO

Every week, CoVaRR-Net’s CAMEO (Computational Analysis, Modelling and Evolutionary Outcomes) Pillar produces a new, up-to-date snapshot, situational report, and analyses of what’s happening with SARS-CoV-2 variants in Canada through its interactive, web-based Duotang notebook. In collaboration with a global team of variant hunters, Duotang also reports on new variants of note in other countries.

Current CAMEO modelling shows that JN.1 and its descendent viruses (subvariants) comprise more than 90% of new cases in Canada. “This lineage is a highly immune evasive Omicron variant in the BA.2.86 group,” explains Dr. Sally Otto, Co-Lead of CoVaRR-Net’s CAMEO Pillar, Killam University Professor and Canada Research Chair at the University of British Columbia. “JN.1 has been spreading rapidly, doubling every 10 days relative to the previously dominant XBB lineage. This spread of JN.1 contributed to the recent peak in cases across the country. Fortunately, the JN.1 peak appears to be subsiding as spring approaches. While we don’t see any significant new variant of concern, waning immunity and new immune evasive subvariants are expected to keep COVID at moderate levels.”

COVID-19 may be endemic, but monitoring is still necessary

“Working together as a team, we’ve made it possible with Duotang to stay on top of the diversity of SARS-CoV-2 lineages that keep evolving – including more than 400 named lineages in Canada over the last four months alone,” says Dr. Otto. “We have automated analyses of viral sequences to scan for variants that are spreading unusually fast or that have unusual mutational characteristics. Our team then pores over the results to determine what this means,” adds Dr. Otto. “Together, we’re acting as a COVID-19 weather station, helping the public and government know how the virus is evolving and how that is expected to impact cases.” 

CAMEO experts see SARS-CoV-2 as being in an endemic phase, where the rapid, continuing evolution of the virus poses an ongoing threat that requires vigilance and regular monitoring. “It’s an endemic situation, more of a steady state, with smaller waves that can last for six months as immunity wanes in the population. The virus is still evolving, with new mutations that evade immunity, and we will need new vaccines for effective protection,” suggests Dr. Jesse Shapiro, Co-Lead, CoVaRR-Net’s CAMEO Pillar, Member of CoVaRR-Net’s Wastewater Surveillance Research Group, and Associate Professor, McGill University & McGill Genome Centre.

“A very novel variant could also emerge that drives a big, unexpected spike in cases, similar to when Omicron first appeared, and people would have much less immunity to that,” he cautions.

CAMEO researchers use data compiled from the Canadian VirusSeq Data Portal for their analyses. This open-source and open-access portal enables rapid data-sharing for all Canadian SARS-CoV-2 genome sequences and associated metadata used to detect, diagnose, and anticipate the spread of new variants. It is the key database for analyses by Duotang and other tools to aid investigations, such as SARS-CoV-2 variant risk assessment. The VirusSeq Data Portal team has received $346,505 in funding from CoVaRR-Net and is being expanded to support analyses and visualization of SARS-CoV-2 wastewater data from across the country and potentially data for other national priority viral pathogens.

CAMEO also works closely with CoVaRR-Net’s Host-Pathogen Interactions Pillar to track and analyze SARS-CoV-2 evolution and mutations in animal reservoirs. “It’s plausible that the next variant of concern or other viral pathogen could evolve in animals and jump to humans. We’re analyzing 2,000 SARS-CoV-2 genome sequences of animal origin and looking at their relationships with matched human sequences using public health data,” says Dr. Shapiro.

He has been collaborating with CoVaRR-Net’s Wastewater Surveillance Research Group as well to develop, apply, and benchmark methods to track SARS-CoV-2 variants and mutations in the built environment and wastewater. “For example, for sequencing of wastewater samples, we’re helping to determine how much sequencing needs to be done to get meaningful and reliable results in a cost-effective way,” explains Dr. Shapiro.

Adapting Duotang to other pathogens

CAMEO is now adapting its modelling capabilities to track and rapidly analyze the spread and evolution of other viral pathogens too. An expanded capability could be useful going forward for rapid monitoring, modelling, and analysis of different respiratory viruses circulating at the same time and new or emerging viruses of concern. 

“All the tools we’ve developed as part of Duotang and VIRUS-MVP [an interactive heat-map visualization tool for SARS-CoV-2] are in the process of being adapted for influenza, including seasonal human flu, bird flu, and swine flu, as well as RSV,” says Dr. Shapiro. CoVaRR-Net has provided funding worth $369,000 to CAMEO to help support expanded tools and capabilities.

“Knowing when variants are spreading and how fast can help predict future spikes for COVID-19, flu, RSV, and potentially other respiratory illnesses resulting from new pathogens,” says Dr.  Otto. “The challenge will be to keep the flow of data and investment to build on these incredible scientific advances over the past few years in order to expand our preparedness toolkit and help prevent the next pandemic.”

“It took us a year to build the infrastructure to develop Duotang for SARS-CoV-2, use it internally, and then make it public. Today, however, we could potentially get a Duotang going for a new or emerging viral pathogen of concern much faster, perhaps within a week, if we had enough publicly available data,” Dr. Shapiro adds.

Knowledge translation is key

CAMEO’s rapid modelling and SARS-CoV-2 analyses have generated timely information for the national and provincial governments, public health officials, hospitals, and other healthcare providers through different stages of the pandemic since the spring of 2021, when CoVaRR-Net was formed.

“Public health authorities have consulted with CAMEO experts and have used Duotang regularly to be informed and get up-to-date information on the state of variants in Canada and the fastest-growing lineages. We have put a lot of time and effort into ensuring the reliability of that information,” says Dr. Shapiro.

“Sally and I and other CAMEO members were in briefings with the Deputy Minister of Health during the Delta and Omicron waves to share our information and analyses. We discussed questions such as, how would increasing vaccine uptake reduce the number of cases and hospitalizations in Canada? When Omicron was spreading in South Africa, but had yet to reach Canada, topics included weighing the evidence for the high transmission rate and whether similar spikes in cases would be expected in Canada,” he explains, noting that CAMEO’s fast-breaking modelling and analyses depend on the essential data collected by public health labs.

Dr. Shapiro is also gratified to see his own students bringing their expertise to public health agencies. “A good number of trainees from my lab have gone to work at the Public Health Agency of Canada (PHAC) and public health laboratories doing genomic sequencing and analysis of viral pathogens. A silver lining of the pandemic has been the closer collaboration and fluidity between academic and government researchers to support informed, evidence-based public health policies and measures to protect the health of Canadians,” he says.