Blog Archives - Ontario Genomics

Engineering Biology: Repurposing life’s vast toolkit for better products

October 21, 2024 by Luana Langlois Fiorotto Leave a Comment

In the pursuit of a greener and more sustainable future, biomanufacturing has emerged as a revolutionary approach with the potential to transform industries while minimizing their environmental impact.

Biomanufacturing, also known as bio-based manufacturing or bio-fabrication, is the process of using living things, mostly in the form of micro-organisms (bacteria, yeasts, algae etc.), cells, or enzymes, to produce a wide range of products, including chemicals, fuels, materials, food and ingredients, and even medicines. The applications of biomanufacturing are vast – it has been estimated that up to 60% of the physical inputs of the world’s economy could be produced by biological means! (Ref 1) Using the power of living organisms, biomanufacturing offers an eco-friendly and sustainable alternative to traditional manufacturing methods that rely heavily on non-renewable resources and produce harmful byproducts.

Ref 1 – The Bio Revolution: Innovations transforming economies, societies,
and our lives, McKinsey & Company (2020)

So how does this work? The first thing to understand is that most of the materials, medicines, and foods we use every day are made up primarily of carbon, like all living things. Most of the carbon we use for manufacturing comes from either naturally occurring sugars or petroleum/oil. Living things have evolved to use carbon in almost infinite ways, giving us an equally vast ability to produce carbon-based products using natural means. So, most of the things we already make can be made by living things!

But what if we can’t find an organism that naturally creates the product we’re looking for? What if we find one, but it doesn’t produce enough of our molecule of interest to make economic sense? Here is where synthetic biology (synbio, or engineering biology) comes in. Synbio is a multidisciplinary field that brings together biology, chemistry, engineering, and computer science to turn micro-organisms into tiny factories that churn out products better than their natural counterparts. Synbio enables scientists to engineer micro-organisms and other biological systems to perform specific tasks with remarkable precision.

Canada is rich in natural resources, which has led to the development of numerous industries. However, the outcome is that waste produced is often disposed of in less-than-ideal ways. Fortunately, MetaCycler BioInnovations, is looking to change this narrative. The company, which is a spin-off from wasteCANcreate project member Dr. Trevor Charles’ lab at the University of Waterloo, is looking to divert food waste from landfills and produce valuable bio-plastic polymers that are being developed to have the same favourable characteristics as traditional oil-based plastics without creating harmful byproducts along the way. Similarly, YZymes Inc., a start-up company from Dr. Emma Master’s lab (also a wasteCANcreate project member) at the University of Toronto, produces chemical precursors for the production of bio-nylon and various commercially important resins, coatings, and adhesives, from tree biomass and leftover distillers’ grains, which are byproducts of the forestry and corn-based ethanol industries.

Key Advantages to Synbio in Biomanufacturing

Customization: Synbio allows researchers to tailor micro-organisms to produce desired compounds efficiently. This level of customization means that biomanufacturing can be adapted to a wide array of applications, from sustainable materials to biofuels, catering to the needs of a wide variety of industries. It will even allow us to create materials that don’t currently exist.
Resource Efficiency: Biomanufacturing relies on renewable resources, such as plant biomass or waste streams, as feedstock for micro-organisms. This approach reduces dependence on fossil fuels and minimizes greenhouse gas emissions which is less harmful to the environment.
Waste Reduction: Traditional manufacturing often generates significant waste and harmful byproducts. But biomanufacturing has the potential to create products and processes with minimal waste, making it more sustainable and efficient.
Low Carbon Footprint: As biomanufacturing largely relies on biological processes, it results in a smaller carbon footprint compared to conventional manufacturing methods.

Biomanufacturing holds the promise of revolutionizing the way we produce goods and achieve sustainability goals. With synbio platforms as its backbone, this emerging field presents a viable pathway to address the severe climate challenges our planet faces today. By embracing biomanufacturing technologies, we can move closer to a more sustainable world, where economic prosperity goes hand in hand with environmental responsibility. However, there are still challenges that need to be overcome before biomanufacturing can truly revolutionize our world – we’ll talk about that another time on the blog!

In case you missed it, we discussed “Turning Waste into Value: A Pathway to Upcycling” in our last post – check it out!

Blog: When life sciences meet innovation, the world can heal itself

August 7, 2024 by Maggie Blood Leave a Comment

SiREM’s groundbreaking work in Ontario for the world

The marvels of biotechnology are what drive the ground-breaking bioremediation work being done at Guelph-based company SiREM.

You’re probably familiar with bacterial cultures in dairy products like yogurt that give them their trademark taste, smell and texture. SiREM, and their partners at the University of Toronto and the Federated Co-operatives Limited (FCL), have been developing and scaling up bacterial cultures of their own to help various industries clean up chemicals left over from their operations in a safer way that is better for the planet.

The idea is to do away with the destructive “dig-and-dump” method of dealing with contaminated soil and use SiREM’s bioaugmented bacterial cultures instead. Injecting their sustainably produced microbes into groundwater to quickly and naturally break down toxic substances is a far more environmentally friendly and efficient way to clean-up common contaminants in the oil and gas sectors.

Ontario Genomics started supporting this exciting work back in 2016 with a $1 million in funding through the Genomic Applications Partnership Program (GAPP), which according to SiREM’s principal scientist, Sandra Dworatzek, has boosted their success.

Their bioaugmentation cultures have received approval for use by Environment Canada and Health Canada and are currently being used at 15 sites across North America on a wide range of chemicals including chlorinated solvents, benzene, toluene, ethylbenzene, and xylenes.

Download the SiREM pdf

Turning Waste into Value: A Pathway to Upcycling

May 3, 2024 by Luana Langlois Fiorotto Leave a Comment

When it comes to natural resources and the climate crisis, cutting back on waste and boosting sustainability are more important than ever before. Food waste alone is responsible for half of agriculture-related greenhouse gas emissions and is a major cause of environmental damage. Fortunately, innovative solutions are coming to the rescue, and one of them is waste upcycling through bioconversion, which uses naturally occurring and/or engineered microbes to convert food waste into valuable products like bioplastics.

What is Upcycling?

It’s the process of transforming waste into new products of higher value, like when someone finds an old piece of furniture on the roadside, gives it a new coat of paint, and makes it better than new. A new program called wasteCANcreate is doing exactly this, with a high-tech spin!

Ontario Genomics, Agriculture & Agri-Food Canada and industry partners have come together to convert food waste (what you put into your green bin) into various products that would normally be made from oil. Microbial upcycling of food waste into bioplastics puts microorganisms like bacteria and yeasts to work to convert the food waste into bioplastics, textiles like nylon, and other useful materials.

The three main goals for this project:

Reduce greenhouse gas emissions from sources like decomposing food waste
Eliminate our need for fossil fuels to create necessary materials
Create lasting economic opportunities for Canadian industries

Novel ideas like this are being brought to life to revolutionize manufacturing processes and are a key part of the circular economy, which aims to cut waste and pollution, repair damaged ecosystems, and have a positive impact on the world economy.

Initiative members at a workshop in the Spring of 2023. This initiative brings together world-class academic leaders, innovative industry partners, and others to accelerate the development and testing of bioplastics for various applications.

Microbes to the Rescue!

Microbes can be used as tiny factories and are at work all around us – think about your gut flora and the microbes that help make beer, yogurt, and bread. Putting them to use helps reduce our need for traditional plastics, which are most often non-biodegradable and a significant threat to the environment. Bioplastics, on the other hand, are made from biological raw materials and decompose more easily.

Plastics are everywhere you look. Plastic bags, cutlery, containers, and toys are obvious examples, but plastics are also found in most clothing, vehicles, furniture, and even in cosmetics and sunscreens! Plastics are cheap to make and last a long time, making them hard to get rid of. In Canada alone, we produce 4.8 million tons of plastic each year and 29,000 tons end up in the environment, including our waterways.

The upcycling process involves using microorganisms to break down the waste material and convert it into organic acids. These organic acids are then used to produce biodegradable plastics and additives for other products. Biodegradable plastics can replace oil-based plastics, meaning they will be much more easily disposed of and won’t stay in the environment for centuries to come.

Curbing Greenhouse Gas Emissions

When food waste is sent to landfills, it decomposes and released methane gas into the atmosphere. Methane is a greenhouse gas and a major contributor to global warming that is over 25 times more potent than carbon dioxide! So, when we upcycle food waste into bioplastics, we reduce the waste sent to landfills and minimize the production of methane gas.

Economic Benefits

Since there’s no shortage of global waste, using it as a key ingredient for bioplastics is a brilliant idea! The food waste we have now costs us money to handle and store it while it decomposes. This means that any value extracted from this resource will help improve the economy as a whole. The process also creates a circular economy where waste becomes a valuable resource.

Upcycling food waste into bioplastics is an innovative, yet common sense solution for the very real problem of waste management facing Canada and the world. The best part is, the wasteCANcreate program is already at work perfecting this process so it can be used across the country and around the world.

Stay in the loop on exciting developments in our circular future!

This is the first in a series of blog posts detailing wasteCANcreate, Canada’s biomanufacturing opportunities, and the shift towards a circular economy. Stay tuned for more!

Blog: Look How Far We’ve Come

April 25, 2024 by Maggie Blood Leave a Comment

It was 71 years ago when scientists published groundbreaking research on the structure of DNA. That teamwork grew to become the internationally funded Human Genome Project which culminated in the most complete mapping of the human genome in May 2021. Genomics is all about DNA, and it’s DNA that tells us about life in all forms. It’s the basis of biology which is now fuelling biotechnology innovation. These technologies now have the power to move us away from environmentally damaging manufacturing methods.

After all, climate, food and health are all connected. Climate change is disastrous for food production and supply chains, as well as the health and well-being of everyone on this planet. The good news is, incredible solutions and technologies to address all of these very serious problems currently exist, likely in your own backyard!

Ontario Genomics has been leading the charge in the province since 2000 by supporting cutting-edge science to find homegrown solutions to challenges the world faces like climate change, food insecurity and in healthcare. We’ve done this by raising more than $3.7 billion for genomics applied research in the province which has created more than 20,000 jobs. We have over 330 projects and more than 500 partnerships!

Whether you realize it or not, DNA is all around us. What began decades ago as research to better understand what humans are made of, has since bloomed to include new ways of producing food and improving agricultural techniques as well as clean technology which is providing a new path to make and power the things we need.

One example is the wasteCANcreate program, which is bringing together Canadian researchers and industry partners in Aylmer, Burlington, Orillia, Vancouver and Regina spanning the energy, agriculture and food, plastic films and performance textiles sectors to bring real-world solutions to Ontario, Canada, and the rest of the world.

By using precision fermentation, microbes are used to turn food waste like potato peels into usable products like biodegradable plastics and fibres to create yoga pants! This new method of upcycling also reduces greenhouse gas emissions, replaces the need for petroleum-based plastics and is an economic boost to the province through job creation.

According to Ontario Genomics’ 2021 Cellular Agriculture Report, food biomanufacturing alone could explode to become a $7.5 billion industry creating 86,000 jobs by 2030, with greater growth projected in the long term. That’s why we’re involved with several food and agriculture projects and companies around the province, including the biggest Canadian cellular agriculture project ever that is led by McMaster University where researchers are developing efficient and economical ways to produce cultivated meat on a large scale.

While more commonly heard of cellular/cultivated products like red meat, poultry, seafood, foie gras and pet food are being made, dairy, eggs, honey and even chocolate are created through the same process! Food ingredients like these proteins, enzymes, flavour molecules, vitamins, pigments and fats can also be incorporated with existing products to create hybrid foods. This cellular agriculture technology is also creating textiles such as leather, wool, silk and cotton.

Amazing innovations like this may have seemed like a sci-fi fantasy years ago, but DNA is currently inspiring these kinds of creations here in Ontario. Work like this being done in this province can help propel Canada into global powerhouse status in the biotech-based economy. One way we’re helping to make this happen is through our annual SynBio conference that brings together national and international leaders in the field of engineering biology to build inter-sector partnerships.

Ontario Genomics has a very exciting partnership with FedDev Ontario for our BioCreate accelerator program that provides financial support, business and technical guidance to start-ups in southern Ontario to move the province’s biotechnology scene forward and get game-changing solutions scaled up and put into real world use as quickly as possible.

We’re currently supporting 16 companies in the health, cleantech and food and agriculture sectors, with more on the way! There are a lot of very smart and capable people doing amazing things in the province and it’s also incredibly encouraging to see that half of these companies are either run by women CEOs or have women on their leadership team. That stat alone shows science has also evolved greatly over the years, especially when you consider Rosalind Franklin’s discovery of DNA’s structure in 1953 has been greatly overlooked in the history books.

With all this in mind, we wish you a happy DNA Day – it’s incredible how far we’ve come, and you should feel a part of where we’re going!

Blog: Cracking the Rare Disease Code

April 16, 2024 by Maggie Blood Leave a Comment

EpiSign’s groundbreaking work in Ontario for the world

For years, Ontarians have been hearing about our crumbling health care system but there are many silver linings to the cloudy situation our hospitals are dealing with.

One of them is the groundbreaking work Dr. Bekim Sadikovic at Lawson Health Research Institute and London Health Sciences Centre has been doing with biotech company, Illumina. In their quest to better detect rare diseases, Dr. Sadikovic has created the clinically validated EpiSign test, which uses machine-learning algorithms and compiles them into the EpiSign™ Knowledge Database.

Thanks to funding from Ontario Genomics, Genome Canada and their Genomic Applications Partnership Program (GAPP), the EpiSign™ project is helping doctors cut down on long and agonizing diagnosis wait times by efficiently bringing answers and treatment options to more of the 1 in 15 Canadian children born with a rare disease.

Not only does this mean peace of mind and quicker access to the right support for those children, it’s critical relief to our health care system by speeding up the diagnosis process and easing the pressure on hospitals since 1 in 4 pediatric hospital beds are occupied by a child with a rare disease.

This incredible work has been an evolution. After all, projects like these don’t happen overnight! It takes many years of collaboration and many rounds of funding. When Dr. Sadikovic’s team applied for their first round of GAPP funding in 2019, they were able to detect 19 different disorders across 30 genes. Five years later, the most recent version of EpiSign™ has 116 different indicators covering 126 disorders. This number will only continue to grow in the years to come and while this much needed innovation was created here in Ontario, it’ll be a benefit to the rest of the world.

Download the EpiSign pdf

Investment in Genomics-led Precision Health Initiative Delivers Rare Disease Diagnosis in Ontario

April 26, 2022 by ontarioadmin

This study mining cancer genetics for targeted treatment options is an integral part of the All for One Canada-wide initiative geared towards providing equitable access to genome-wide sequencing for diagnosis and treatment of genetic disease.

Ontario Genomics is pleased to play an integral role in the All for One precision health initiative to advance a new standard of health care for Canadians, expanding access to genome-wide sequencing for diagnosis and treatment of life-threatening genetic diseases.

The $39 million All for One initiative includes $13 million in federal investment through Genome Canada and $26 million in co-funding from industry, health care organizations, provincial and other partners brought in through six regional Genome Centres, including Ontario Genomics.

As part of this initiative, CHEO and the Hospital for Sick Children (SickKids), in collaboration with the Ontario Ministry of Health are piloting an optimized clinical genome-wide sequencing service for patients with rare diseases in Ontario. This project is receiving $950,000 from Genome Canada, through Ontario Genomics.

Currently, more than one-third of the estimated 930,000 Ontarians with a rare disease lack a genetic diagnosis, despite lengthy and costly investigations. Advances in precision health—which harnesses the power of genome sequencing to diagnose and inform treatment of genetic conditions—are revolutionizing health care, but access to clinical genomic testing across Canada remains inconsistent, which was the case for most of Anna\’s life.

Genome-wide sequencing pilot project helps Ontario families get answers

Anna had a childhood filled with regular injuries as a result of persistent muscle weakness, with hundreds of doctor’s visits. Her clinical team at CHEO completed dozens of tests, including muscle biopsies, metabolic testing and at least five different genetic tests, but no conclusive diagnosis was reached.

Conventional genetic testing involves testing subsets of genes, often leading to multiple tests and investigations, which can present a complicated and time-consuming process for clinicians, patients and families. In contrast, Genome-Wide Sequencing can search all known genes for variants that could be disease-causing, providing a much more comprehensive look at a patient’s genetic data.

Isla had severe jaundice, skin rashes, extremely low energy, difficulty feeding and problems with growth associated with high levels of inflammation markers in her blood at just one week of age. She spent over a year in and out of SickKids with high fevers, infections, breathing issues and extreme acid reflux. Her clinical team addressed the symptoms while they searched to find the underlying cause, but tests to check her blood, bone marrow, immune system, DNA and more yielded nothing.

A diagnosis can often be the first step to accessing targeted care and for families, it can provide emotional relief and improved access to support and resources.

Isla was started on a biologic drug to reduce her inflammation levels with the hopes it would help address her other health issues. Still, her clinical team and her family wanted an explanation for all of Isla’s health concerns to help optimize treatment and prevent complications. Isla had exome sequencing as one of the last diagnostic options, which found a new DNA change in a gene called CDC42, which is known to cause severe inflammation. Armed with this knowledge, Isla’s family and clinical team were confident that their treatment plan was the right one.

Anna had genome sequencing as part of GSO’s quality improvement study to evaluate the benefit of interrogating the entire genome. GSO reported that she has a rare genetic condition because of two variants affecting a gene called SELENON. She inherited one variant from her mother and one from her father. Genome sequencing was critical to the identification of these variants in Anna as they were not detectable via the previous testing technologies and would not have been identified using exome sequencing. Although she is small for her age and her bone development is delayed, she takes swimming lessons, does her best to keep up with friends at recess, gets good grades and is an avid reader. Like any 12-year-old, she loves spending time on her tablet playing games. “More than I probably should,” Anna says.

“It took 12 years to finally put a name to what Anna was experiencing every day since she was an infant. When we got the genome sequencing results and diagnosis, it was the first time in 12 years that we were able to read something with a name on it and say, ‘That’s it! That’s what we’ve been dealing with,’” said Mallory Boileau, Anna’s mother. “It would be great for families to get this type of answer at the beginning of their journey. Twelve years is a long road not to have answers.”

Now, Anna’s family and care team can keep an eye out for potential complications that are associated with her diagnosis. Mallory says, “The not knowing is sometimes more terrifying than anything. We’re no longer guessing all the time and can address things before they become an issue. It’s such a relief.”

Isla’s family is thankful, too. “After Isla started her treatment, you could tell how much better she was feeling. Isla started to have more energy and began smiling and even laughing,” says Miki Simmons, Isla’s mother. “At four years old, Isla’s keeping up with all her older siblings and I’m not sure where we would be if we didn’t have the treatment plan and diagnostic answers that we did when she was a baby.”

“Early diagnosis of rare diseases at the molecular level is vital to shorten the diagnostic journey of rare disease patients, like Anna and Isla, and make sure they can access appropriate care as soon as possible. This partnership uses genomics tools to inform provincial and cross-provincial policies that improve rare disease diagnosis and quality of life.” – Dr. Bettina Hamelin, President and CEO, Ontario Genomics

This project advances a new standard of health care for Ontarians and Canadians, expanding access to genome-wide sequencing for diagnosis and treatment of life-threatening genetic diseases.

“Our government is proud to support this pilot with CHEO and SickKids, which is already helping Ontario families just one year into implementation. This promising project will improve patient outcomes by providing timely access to genetic diagnoses, which is another way Ontario is building a better-connected health-care system, centred on the needs of patients.” – Christine Elliott, Ontario’s Deputy Premier and Minister of Health

With pan-Canadian reach and strong partnership from provincial and regional health services authorities, All for One will be a core building block of a coordinated human health genomics ecosystem in Canada, bridging clinical care and cutting-edge research.

Partner Quotes

“Quick access to comprehensive genetic testing, like exome or genome sequencing, must be a cornerstone of health care for children and youth who have suspected, but undiagnosed, genetic conditions. With GSO, not only are we able to provide this testing, but we’re also preparing for the future when genome sequencing may become the new standard-of-care clinical test for these patients. This pilot is another step in the path to achieve SickKids’ vision of Precision Child Health, where every patient and family receives individualized care.” – Dr. Martin Somerville, Division Head of Genome Diagnostics, SickKids

“For parents like Anna’s, there is an unbelievable and largely unseen stress that goes with not knowing what is causing their child’s condition. Along with this stress is a desperate desire to find answers and do the best thing for them. And having that uncertainty linger for years and years is such a burden. As clinicians, we want to provide more certainty to these families as soon as possible. We hope the findings from our project will bring that possibility closer to a reality.” – Dr. Kym Boycott, Chair, Department of Genetics, CHEO

About Ontario Genomics

Established in 2000, Ontario Genomics (OG) is a not-for-profit organization leading the application of genomics-based solutions to drive economic growth, improved quality of life and global leadership for Ontario. Ontario Genomics plays a vital role in advancing projects and programs like wastewater surveillance by supporting the development of their proposals, helping them access diverse funding sources, and finding the right industry partners to take this research out of the lab to apply it to the world’s most pressing challenges. Since its inception in 2000, Ontario Genomics has raised more than $1.27 billion for genomics applied research in Ontario and directly supported more than 9,100 trainees and jobs. We have 110+ active projects, 500+ impactful partnerships and have secured $1.34 billion in follow-on investments.

Ontario Researchers Receive Over $39 Million to Support Innovative Research and Technology Development in Natural Resources and Environment Sectors

July 27, 2021 by ontarioadmin

Toronto, July 27, 2021 – Ontario Genomics announces a total investment of over $39 million into the Large Scale Applied Research Program (LSARP) projects from across Ontario that will help address the impact of climate change and pollution.

Genome Canada announced funding for eight Canadian projects under the Genomic Solutions for Natural Resources and the Environment competition with an overall budget of $58.6 million. Five of the eight projects involve Ontario researchers, with over $39 million of the nationwide budget being received by provincial researchers.

The Global Risks Report 2020 from the World Economic Forum ranked biodiversity loss as one of the top five threats confronting humanity. The University of Guelph’s BIOSCAN-Canada project is harnessing new genomics technologies to make DNA barcoding faster and less expensive. This will help slow biodiversity loss, improve Indigenous relations through consultation, increase the sustainability of our agricultural and forestry sectors, and strengthen Canada’s leadership in global conservation efforts.

“By illuminating biodiversity with genomic approaches, BIOSCAN–Canada will foster environmental sustainability in settings spanning our nation – from agriculture in New Brunswick to forestry in British Columbia and wildlife management in Nunavut.” Dr. Paul Hebert, Director, Centre for Biodiversity Genomics, University of Guelph.

In Canada, 29,000 tonnes of plastic leak into the environment and oceans every year, creating severe environmental problems. Another 2.8 million tonnes of plastic are sent to Canadian landfills, which creates a latent problem for future generations. A Queen’s University project is working to drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics. This project will identify and engineer bacteria and enzymes that can break down plastics into recyclable components or into valuable fine chemicals more effectively than chemical conversion-based technologies.

“Through open science our team of 21 investigators from across 6 universities will develop a systems approach to innovate toward a zero-waste plastic future: from genomes to new enzymatic processes, fully integrated with environmental, social, economic, and policy research to facilitate uptake.” Dr. Laurence Yang, Assistant Professor, Queen\’s National Scholar in Systems Biology.

In collaboration with Genome Alberta, the TRIA-FoR project will adopt a state-of-the-art multidisciplinary and integrative approach to develop genomics-informed knowledge, tools and application frameworks that mitigate risk for the present mountain pine beetle epidemic and improve resiliency in future epidemics. The current mountain pine beetle epidemic has killed approximately 20 million hectares of mainly lodgepole pine forests in British Columbia and Alberta and this project aims to use genomics-based solutions to help remedy the situation.

Learn more about these LSARP projects:

Sewage Surveillance: Detecting SARS-CoV-2 Variants in Wastewater across Ontario

June 2, 2021 by ontarioadmin

Ontario Genomics, University of Guelph, University of Ottawa and CHEO announce a game-changing initiative to analyze COVID-19 in wastewater to improve public health response and better understand outbreaks in communities across Ontario.

June 2, 2021 – Ontario Genomics, Genome Canada, and Illumina are investing in a first-of-its-kind SARS-CoV-2 wastewater surveillance initiative across Ontario. This cutting-edge project will enhance critical province-wide coordination and viral surveillance and support provincial and national efforts to understand how the virus that causes COVID-19, SARS-CoV-2, is changing over time.

This project is made possible through an investment of over $338,000 from Genome Canada, Ontario Genomics and Illumina. The funding supports Ontario-wide research efforts, led by Dr. Lawrence Goodridge, University of Guelph, and co-led by Dr. Rob Delatolla, University of Ottawa. It also harnesses the power of an extensive network that consists of members and collaborators from across Ontario and Canada, including the Children’s Hospital of Eastern Ontario (CHEO), University of Waterloo, University of Windsor, Ryerson University, Health Sciences North Research Institute (HSNRI), Public Health Agency of Canada (PHAC) among others.

“I am proud of Ontario’s leadership in SARS-CoV-2 surveillance in wastewater. Through a coordinated approach, leveraging the province’s deep genomics resources and capacity, this project will provide early signals of worrisome viral changes and equip public health with evidence for timely decision making,” said Dr. Bettina Hamelin, President and CEO, Ontario Genomics. “Our end-to-end view of Ontario’s genomics ecosystem has enabled Ontario Genomics to break down silos and harness genomics expertise in the fight against COVID-19.”

Since the start of the pandemic, many countries have been using wastewater monitoring to identify potential outbreaks before they are detected in people through clinical testing. SARS-CoV-2 can be recognized in human waste up to a week before individuals develop symptoms and in people who remain asymptomatic but may spread the virus. By collecting fecal matter at key wastewater collection sites (for example, long-term care facilities, schools, universities, etc.), we can get an early warning sign at the population level and pre-empt further spread by local public health interventions.

“Using wastewater surveillance to assist in predicting COVID-19 caseloads in Ontario is an excellent example of how genomics research was adapted in the face of the pandemic. This demonstrates how sustained, long-term investments in genomic research prepare us for the unexpected,” said Dr. Rob Annan, President and CEO, Genome Canada. “Genome Canada looks forward to helping leverage this important initiative into national solutions for future pandemic readiness.”

Several jurisdictions in Canada, including Ontario through it’s wastewater surveillance initiative, have been using a surveillance technology (qRT-PCR) to monitor SARS-CoV-2 levels over time. By leveraging modern genomic techniques (metagenomics), this project will enable researchers to identify known Variants of Concern (VOCs) while also staying ahead of the curve on potential new emerging viral changes that could become concerning. Participation of the research team in the wastewater surveillance initiative and strong partnerships between the research team and public health agencies ensure that the results will be shared for rapid actioning as necessary.

“I want to thank Genome Canada, Ontario Genomics and Illumina for their leadership in detecting Variants of Concern through this project, which will support Ontario’s wastewater surveillance initiative by enhancing how we track the spread of the virus,” said Hon. Jeff Yurek, Ontario Minister of the Environment, Conservation and Parks. “It is through investments and partnerships like this one, in addition to the government’s COVID-19 wastewater surveillance initiative, that we are able to expand wastewater sampling and analysis provincewide and enable more timely decisions about how and where to mobilize resources in response.”

“Only a small percentage of clinical samples in Ontario are being sequenced to identify VOCs,” said Dr. Lawrence Goodridge, who holds the Leung Family Professorship in Food Safety and is the director of the University of Guelph\’s Canadian Research Institute for Food Safety. “This timely funding from Ontario Genomics and Genome Canada, and Illumina will allow for surveillance of VOCs in wastewater, increasing our knowledge regarding which VOCs are circulating in the general population.”

“We will now have a province-wide proven epidemiological tool to identify signs of viral prevalence ahead of an outbreak,” said Dr. Robert Delatolla, Associate Professor, uOttawa Faculty of Engineering and project co-lead. “It will prove to be an asset to local public health units in our shared fight against SARS-CoV-2.”

“With this investment, public health officials and researchers will be able to better interpret the wealth of public health data that we flush down the toilet every day,” said Dr. Tyson Graber, Research Associate, CHEO Research Institute. “It\’s amazing how quickly this scientific field has matured since the beginning of the pandemic; starting from basic research projects in university labs to a surveillance programme used by public health units across Ontario, providing a clearer picture of how COVID-19 is affecting their community. It is a stellar example of how open science and collaboration across disciplines can benefit all Ontarians.”

Key Facts

- Wastewater surveillance can provide critical information about COVID-19 community spread sooner than individual test results or reports of illness.
- Genomics, the study of DNA for innovation-driven solutions, plays a critical role in developing COVID-19 surveillance, diagnostics, vaccines, and public health responses.
- Variants of Concern or VOCs have mutations that make them more transmissible and/or more likely to cause severe disease with a higher mortality rate.
- Metagenomics enables the detection of all variants of SARS-CoV-2 in a mixed sample, such as that found in wastewater, allowing for population-level surveillance of the variants circulating in a population or community.
- This $338,000 investment supports the coordination of COVID-19 wastewater surveillance metagenomic resources across nine partner research centres and institutions across Ontario, in addition to the national Public Health Agency of Canada (National Microbiology Laboratory).
- Funding partners include Genome Canada, Ontario Genomics, and Illumina.

Additional Quotes

“Illumina is proud to take part in supporting this effort to empower researchers and public health experts with the sequence data of SARS-CoV-2 genomes. The added detail provided by Illumina-enabled whole genome pathogen sequencing approaches will better inform Ontario’s infectious disease surveillance strategies and prime the network for a longer-term strategy for broader pathogen surveillance.” – Michael Gallad, Senior Director, Canada and Latin America, Illumina.

“The University of Guelph is delighted and grateful to Ontario Genomics, Genome Canada, and Illumina for the generous support for this incredibly timely, cutting-edge viral surveillance partnership. This wise investment will reinforce our strong partnership with University of Ottawa and enable Professors Goodridge and Delatolla to conduct vital genomics-based surveillance for viral pathogens, and thereby safeguard public health and improve life.” – Dr. Malcolm Campbell, vice-president (research), University of Guelph.

“The University of Ottawa is extremely grateful for this funding from Ontario Genome, Genome Canada, and Illumina, which will allow the expansion of wastewater surveillance across the province. This novel project has shown how strong multi-site research collaborations can have a relevant impact in our communities.” – Dr. Sylvain Charbonneau, Vice-President, Research, University of Ottawa.

“This province-wide program to monitor for COVID-19 variants of concern is a testament to the pioneering multidisciplinary scientific work of the team at the CHEO Research Institute and University of Ottawa in partnership with Ottawa Public Health. Together they have made wastewater numbers a commonly reported metric and have helped people predict the prevalence of disease in the community.” – Dr. Jason Berman, CEO and Scientific Director, CHEO Research Institute.

About Ontario Genomics

About the University of Guelph

One of Canada\’s top comprehensive and research-intensive universities, the University of Guelph spans urban hubs and rural communities. Established in 1964, the University enjoys a reputation for innovation and excellence dating back more than 150 years to its founding colleges: Ontario Veterinary College, Ontario Agricultural College and Macdonald Institute. Today U of G’s seven colleges conduct leading-edge teaching and research in the physical and life sciences, business, arts, social sciences, and agricultural and veterinary sciences. We have nearly 30,000 undergraduate and graduate students at campuses in Guelph, Toronto and Ridgetown and 185,000 alumni in more than 160 countries worldwide. The University of Guelph, and everyone who studies here, explores here, teaches here and works here, is committed to a simple, shared purpose: to Improve Life.

About the University of Ottawa

A crossroads of cultures and ideas
The University of Ottawa is home to over 50,000 students, faculty and staff, who live, work and study in both French and English. Our campus is a crossroads of cultures and ideas, where bold minds come together to inspire game-changing ideas. We are one of Canada’s top 10 research universities—our professors and researchers explore new approaches to today’s challenges. One of a handful of Canadian universities ranked among the top 200 in the world, we attract exceptional thinkers and welcome diverse perspectives from across the globe.

About CHEO

Dedicated to the best life for every child and youth, CHEO is a global leader in pediatric health care and research. Based in Ottawa, CHEO includes a hospital, children’s treatment centre, school and research institute, with satellite services located throughout Eastern Ontario. CHEO provides excellence in complex pediatric care, research and education. We are committed to partnering with families and the community to provide exceptional care — where, when and how it’s needed. CHEO is a partner of the Kids Come First Health Team, a network of partners working to create a high quality, standardized and coordinated system for pediatric health care that is centred around children, youth and their families. Every year, CHEO helps more than 500,000 children and youth from Eastern Ontario, western Quebec, Nunavut and Northern Ontario.

Download the Press Release pdf – Sewage Surveillance: Detecting SARS-CoV-2 Variants in Wastewater across Ontario

Ontario Agriculture & Agri-Food Sector to Benefit from Provincial Investment

May 3, 2021 by ontarioadmin

May 3, 2021 – The Government of Ontario and other partners are investing nearly $27 million into five Ontario Genomics-led and co-led projects in the Large Scale Applied Research Program (LSARP) with applications in the agriculture and agri-food sector. This Genome Canada program supports large-scale genomics applied research projects using genomics approaches to address challenges in Canada’s key economic sectors and create socio-economic benefits for Canada. The provincial government invested over $4 million with additional funding from Genome Canada ($9.7 million) and industry and research partners for a total of $27 million in support for these job-creating projects.

Ontario Genomics plays a vital role in advancing these projects by supporting the development of their proposals, helping them access diverse funding sources, and finding the right industry partners to take this research out of the lab to apply it to the world’s most pressing challenges. Since its inception in 2000, Ontario Genomics has raised more than $1.27 billion for genomics applied research in Ontario and directly supported more than 9,100 trainees and jobs. We have 110+ active projects, 500+ impactful partnerships and have secured $1.34 billion in follow-on investments.

Ontario’s agriculture and agri-food sector supports one in eight Ontario jobs and accounts for over 30% of Canada’s total GDP.

“While Ontario’s agriculture and agri-food sector is strong and growing, its demands and challenges are also rising. Global food insecurity, competition, and technological disruptions are on the rise because of epidemics, climate change, and economic constraints. Fortunately, genomics-based innovations and technologies provide significant opportunities to advance and modernize Ontario’s agriculture and agri-food sector for a critical competitive advantage.” – Dr. Bettina Hamelin, President and CEO, Ontario Genomics.

“As we recover from the COVID-19 pandemic, our government is committed to investing in projects that support research and innovation in the agri-food and agriculture sectors. By investing in projects supported by Ontario Genomics, our government is supporting research and technological advances in the sector to ensure the sustainability of the agriculture and agri-food sectors.” – Ross Romano, Ontario’s Minister of Colleges and Universities.

One of the projects funded in this round, the “GEN-FISH” project, led out of the University of Windsor, is using genomic approaches to develop toolkits based on so-called environmental DNA (eDNA) from water samples that will provide quantitative assessments of the health of fish and the stressors they face. Collectively, these toolkits will enable a complete and accurate assessment of the status of Canada’s freshwater fish resources. This will save millions of dollars in fish survey costs and will result in additional indirect savings through more effective and directed management action. Furthermore, and most importantly, this project will ensure the sustainability of Canada’s freshwater fish resources for generations to come. This project has already piqued the interest of numerous industries in the environmental sector.

“Despite freshwater fishes being critical for Ontario’s economy, food security and aquatic ecosystem health, over 25% of its freshwater fish species are considered “at risk.” The Genomic Network for Fish Identification, Stress and Health (GEN-FISH) brings together 25 experts from across Canada to address the startling loss of fish biodiversity using genomic tools integrated with cutting-edge social science methods. Our work will help stakeholders effectively conserve and manage fish stocks through assessment of fish community composition and health, facilitated by extensive collaboration and consultation with fishery professionals.” – Dr. Daniel Heath, Project Lead & Professor, University of Windsor.

“The project strives to enhance local capacity by supporting traditional ecological knowledge preservation and inclusion to ensure outcomes address local research priorities, specifically food security and subsistence fisheries, and potential opportunities for sustainable economic development options. FISHES will work closely together with traditional knowledge holders and scientists, local and regional governments, Ministère des Forêts, de la Faune et des Parcs and Fisheries and Oceans Canada on seven species of fish across the North (including Northern Ontario) to establish new methods for stock identification and delineation of mixed stocks to enhance sustainable co-management for communities.” – Dr. Stephan Schott, Project Co-Lead & Associate Professor, Carleton University.

Another project that has been funded, aims to use genomic tools to develop BeeCSI – a new health assessment and diagnosis platform powered by stressor-specific markers. “Our Ontario and Genome Canada funded project will help us develop tools that beekeepers can use to understand the stressors affecting their colonies. This will be of great benefit to beekeepers who are losing a large number of their colonies every winter to unknown causes. The funding is also very timely as COVID-19 has hit beekeepers particularly hard.” – Dr. Amro Zayed, Project Lead & Professor, York University.

Our 4DWheat project is important because wheat alone provides 20% of the proteins and 20% of the calories of the world’s population. Canada is one of the largest wheat exporters of the world. With 1 million acres planted to wheat in Ontario and a farm-gate value of $440 million, Ontario is incontestably an important contributor. “This is why Canada, and Ontario, feed the world. However, in order to continue to be the leader that we are, we must address the yield gap. Indeed, there is a disparity between population growth and food production prediction for the next 30 years. To address such gap, 4DWheat is exploring the potential to improve wheat by accessing genetic diversity from wild relatives. 4DWheat is a ‘thinking outside the box’ project that aims to harness Diversity, advance Domestication, enable Discovery and expedite Delivery.” – Dr. Sylvie Cloutier, Agriculture & Agri-Food Canada (AAFC) Co-lead of the 4DWheat project.

The dairy cattle resilience project led by Dr. Christine Baes is making strides in the agri-food industry. “The Resilient Dairy Genome Project addresses a number of important issues related to human and animal health, environmental impacts, sustainability and social acceptability, while responding to the growing need for safe, affordable, nutritious and high-quality protein. The genetic selection index for resilience under development will allow more accurate selection for fertile, disease resilient and environmental efficient animals. This approach will result in wider benefits to Canadian society, like reduced reliance on antibiotics, better animal welfare, reduced methane emissions and reduced land required for feed production. The strong partnership between academia and industry, including over 40 national and international partners, will ensure the collection of new data, and broad application of project outputs for the benefit of Canadian and global food security and sustainability.” – Dr. Christine Baes, Project Lead & Associate Profession, University of Guelph.

Learn more about these five funded LSARP projects:

Major Investment in Genomics Research and Industry to Improve Ontario Healthcare and Environment

May 3, 2021 by ontarioadmin

May 3, 2021 – The Government of Ontario is investing nearly $3 million in three Ontario Genomics-led projects as part of the Genomic Applications Partnership Program (GAPP). This program funds industry-partnered projects that use genomics tools and technologies to address real-world challenges and opportunities with the intent to create numerous downstream impacts for Ontario, such as job creation and revenue generation. Additional funding from Genome Canada ($4.2 million), industry and research partners brings the total investment into these projects to $13 million.

Ontario is a world leader in genomics research, producing breakthroughs in science and transforming our understanding of the world around us. Genomics technologies and applied research are already being used to tackle important challenges and develop innovative solutions across diverse sectors of the economy, including human health and the environment.

This investment will support researchers at the University of Toronto and The Hospital for Sick Children. In collaboration with industry partners, including Bright Angel Therapeutics and Nanostring, these genomics-based projects will have real, positive impacts on our healthcare system, as well as the environment and well-being of Canadians.

“Partnerships between the researchers and industry are the cornerstone of Ontario’s thriving innovation community. By supporting the development and uptake of new technologies that provide game-changing solutions to the world’s most pressing challenges, Ontario Genomics is helping to nurture healthy people, a healthy economy, and a healthy planet for generations to come.” – Dr. Bettina Hamelin, President and CEO, Ontario Genomics

“Our government is dedicated to improving the health and wellbeing of Ontarians. By investing in Ontario Genomics, we’re supporting significant advancements in research and innovation in the healthcare sector to ensure Ontarians have access to state-of-the-art healthcare services and technologies. These projects aren’t only aimed at improving the healthcare and wellbeing of Ontarians, but also putting Ontario on the map as a global leader in research and innovation in the healthcare sector. ”- Ross Romano, Ontario’s Minister of Colleges and Universities.

“With GAPP funding, in partnership with NanoString and SickKids, we are excited to be developing a novel diagnostic test that will allow us to uncover the molecular pathways that are driving each patient’s cancer. This test is the first of its kind and will help us to optimize targeted therapy for cancer patients from across Ontario,” said Dr. Cynthia Hawkins, Project Lead & Neuropathologist, The Hospital for Sick Children.

“SickKids is pioneering the development of diagnostics that utilize both protein and mRNA biomarkers to identify patients who will respond to targeted therapies. Their selection of nCounter® as the platform of choice for this effort shows its unique potential to gather meaningful, high-quality multi-modal data to advance precision medicine for kids with cancer,” said Sean Ferree, Vice President of Customer Experience, NanoString. “It\’s an honour to receive GAPP support and to work together to better understand the characteristics that make treatments effective.”

“Bright Angel Therapeutics is very grateful for the support from Ontario Genomics in securing the GAPP investment.   The partnership with the University of Toronto gives the company access to state-of-the-art genomic tools, expertise and resources to assist us in advancing our lead antifungal drug development program from the bench to the bedside.  Government investments, such as this one, provide vital resources to early-stage companies that enable them to build out their technology platforms, position themselves for subsequent private investment rounds and build out the innovation ecosystem.” – Dr. Dominic Jaikaran, President & CEO Bright Angel Therapeutics

“This investment will catalyze the translation of genomics-driven fundamental science focused on discovery of vulnerabilities in fungal pathogens into new strategies to overcome drug resistance and treat life-threatening fungal infectious disease.” – Dr. Leah Cowen, Associate Vice President, Research, University of Toronto.

Learn more about the three funded GAPP projects:

Targeting fungal stress responses to provide first-in-class treatment for drug-resistant fungal pathogens (Receptor – Bright Angel Therapeutics): This project will develop a novel anti-fungal drug that will tackle drug resistance at its root. This new treatment option would help fill an urgent, unmet clinical need, reduce morbidity and mortality caused by fungal infections, and provide significant savings to the Canadian healthcare system, which currently spends $345 million on treating invasive fungal infections.
Field Validation of Technologies for Anaerobic Benzene and Alkylbenzene Bioremediation (Receptor – SiREM): This project aims to demonstrate the efficacy of a broad set of novel and specialized anaerobic bioaugmentation cultures in pilot trials at three different benzene contaminated sites. The team will use metagenome-enabled analysis, groundwater modelling, and tracking of the microbial populations and functional genes to improve overall remediation outcomes and restore ecosystem health.
NanoString nCounter® Vantage 3D platform-based complementary diagnostic tests for precision medicine in pediatric cancers (Receptors – The Hospital for Sick Children and Nanostring): To best guide therapeutic choices, this project aims to amalgamate proteomic data with genomic and transcriptomic information to create laboratory-developed (LDT)-complementary diagnostics for the most common pediatric cancers. Additionally, this project has international (NanoString) and Ontario-based (SickKids) co-receptors deriving benefits from this diagnostic technology.