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Cracking the COVID-19 Code

Over the past few decades, advancements in science have greatly improved the methods that are used to study infectious diseases. One of the most powerful of these advancements is genomics – studying infectious diseases on a deeper genetic level to uncover pathogens or “blueprints” of a virus.

Understanding the genetic makeup of the virus that causes COVID-19 is a vital tool that is helping scientists explore its origins, evolution, distribution and severity. It also allows scientists to track emerging variants, confirm the accuracy of laboratory tests and help answer questions on immunity. Genomics empowers scientists to find long-lasting safe vaccines and ensure the effectiveness of treatments for a disease. This knowledge is critical to informing public health policies and gives officials the ability to take concrete actions to protect the health of Canadians.

In Canada, there is a large national effort to coordinate this important genomics work through a network of scientists who are focused on cracking the COVID-19 code using genome sequencers, supercomputers and advanced data analytics. The Public Health Agency of Canada’s National Microbiology Laboratory (NML) is partnering with Genome Canada, Canadian public health laboratories, healthcare partners and academic researchers to lead this work. With their shared knowledge, this collaboration of experts provides Canadian public health authorities and policy makers with insights that help guide the public health response to the pandemic.

NML’s history with genomics

NML scientists have a wealth of experience using genomics to investigate infectious diseases. In 2003, the NML team was involved in generating the first genome sequence of the virus that caused SARS, also a type of coronavirus. The genomics work by the team helped contribute to finding reliable tests and advancing our overall coronavirus knowledge.

Dr. Gary Van Domselaar currently leads the Bioinformatics team at NML and has contributed tremendously to public health research. “From SARS, we learned that genome sequencing is very important for keeping Canadians safe,” explains Dr. Van Domselaar. “Immediately after the NML team heard about this unknown infectious disease that was spreading in China in late December 2019, they began developing a sequencing approach to tackle the new virus. Global efforts to sequence the virus helped the research community track the pandemic and provide clues on possible ways to treat infections.”

Pulling it all together

In April 2020, Canadian genomics experts, including Dr. Van Domselaar, assembled a team of highly skilled scientists to establish the Canadian COVID-19 Genomics Network (CanCOGeN). Together, these scientists have coordinated their research efforts by sharing the virus' genomic data and pooling resources to accelerate their research to inform policy and decision makers. Outcomes from the CanCOGeN initiative help track the virus’ impact, evolution and transmission patterns across the country and around the world.

“Sharing genomic data enhances our research,” explains Dr. Natalie Knox, Senior NML Research Scientist. “It allows us to build on each other’s discoveries and helps us inform one another on public health recommendations.”

This network was critical in identifying Canada’s first cases of the COVID-19 variant first identified in the United Kingdom in December 2020. “Through our participation in CanCOGeN, our group searches SARS-CoV-2 genomic data on the national scale for priority mutations, variants and lineages of international and national importance like the variants first observed in the UK and South Africa,” explains Dr. Gary Van Domselaar. “In addition to identifying important emerging changes in the virus, the findings of these surveillance activities are key to providing guidance on strategies that quickly identify these variants within Canada and inform public health measures, such as travel restrictions, that help mitigate their introduction and spread.”

The answers behind the munch and crunch

Genomic data from positive COVID-19 cases can also provide additional evidence to identify related cases or matches in cluster investigations. Similar to how you would create a family tree, scientists assign genetic lineages to classify the virus to track their genetic changes.

“The virus that causes COVID-19 has genetic similarities to SARS but also has unique genetic and biological features that need exploring,” said Dr. Jennifer Tanner, NML Research Scientist. “Although this virus that causes COVID-19 evolves slowly relative to other viruses, it is quite complex, and should never be underestimated. Our goal is to munch and crunch high-resolution genomic data to improve our understanding of the virus and how it behaves.”

Tracking the genetic evolution of COVID-19 helps scientists confirm the accuracy of laboratory tests used to diagnose the disease. The Polymerase Chain Reaction (PCR) lab test typically focuses on two regions of the viral genome to detect positives cases. If any genetic changes were to occur in those regions, it could affect our ability to accurately diagnose COVID-19. Monitoring genetic changes in these regions allows scientists to flag any possible adjustments required to keep our diagnostic lab tests accurate.

The team at the NML is actively evaluating mutations to better understand their potential implications in terms of transmission, clinical presentation, antibody immunity and vaccine development.

Building for the future

Canadian scientists have built a strong network of experts to share and leverage genomic data. Using genomics and advanced data analytics, they are unravelling the tough questions behind COVID-19. This work not only strengthens Canada’s fight against the pandemic but also prepares Canadian scientists for future outbreaks.


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