Genome capture project aims to detect COVID-19, the flu, or anything else that ails you

Led by University of Regina

A cough, shortness of breath, fever, and chills–-is it COVID-19, the flu, or a combination of the two?

“Co-infection is a problem because any time your body has to fight multiple infectious diseases, it can compromise the ability of your immune system to protect you,” says Dr. Andrew Cameron, a microbial geneticist at the University of Regina.

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Cameron, together with Manitoba’s Cadham Provincial Laboratory and Saskatchewan’s Roy Romanow Provincial Laboratory, received funding to lead Genome Prairie’s COVID-19 Rapid Regional Response (COV3R) project. The COV3R team also includes members of the Institute for Microbial Systems and Society at the University of Regina where Cameron is co-director, as well as the British Columbia Centre for Disease Control.

Genome Prairie provided $240,000 in funding for the project, and the Saskatchewan Health Research Foundation (SHRF) contributed $50,000, while the Centre for Disease Control in B.C., the Roy Romanow Provincial Laboratory in Saskatchewan, and the Cadham Provincial Laboratory in Manitoba provided in-kind support.

Using genome capture, the COV3R initiative aims to tackle the problem of detecting co-infections in humans, and in the process provide powerful new tools for public health.

“Co-infection by respiratory pathogens is bad for patients, yet we know very little about co-infection in the context of the COVID-19 pandemic. Integrating the genomic detection of respiratory viruses and bacteria to better understand the severity of COVID-19 infection will directly and immediately improve public health interventions and clinical treatment plans,” says Cameron.

This technique will also give researchers the ability to test for all viral groups, even those scientists don’t yet know about.

“Misdiagnosis is a problem with infectious diseases because of the limited number of signs and symptoms that people experience – such as a fever, a sore throat, and a headache. So even in the modern day with all our advanced techniques, we still sometimes attribute disease to the wrong culprit.”

Cameron says that genome capture can help in diagnosing infectious diseases by adding a powerful tool for provincial public health testing labs.

“Our work with genome capture will directly complement genetic sequencing of 150,000 coronaviruses as part of Genome Canada’s Canadian COVID-19 Genomics Network (CanCOGeN) initiative,” explains Cameron. “We will sequence coronavirus genomes along with co-infecting viruses, then can examine the Manitoba and Saskatchewan coronavirus infections in broader provincial, national, and international contexts through integration with CanCOGeN.”

Another key feature of genome capture testing is that it offers the ability to track viruses by their unique genetic makeup. This allows public health officials to compare, for example, coronavirus causing COVID-19 cases in different parts of a province or region with virus strains from elsewhere to find out where the disease is coming from and how it’s moving through communities.

The COV3R team is also developing a unique tool that efficiently captures genetic material and compares it against all coronaviruses known to infect animals, which will be a valuable asset in the current pandemic and for early detection of coronavirus pathogens in the future. “Whole genome sequencing is revolutionizing epidemiology. This technology has the potential to discover so much. With it, we might find something circulating here that we didn’t know we had. No other technology comes close,” says Cameron.

The technology will also address the added problem of what the pandemic is doing to testing capacity.

“Laboratories, and the experts who run them, are flooded with COVID-19 testing, forcing them to reduce testing for other respiratory pathogens. This means information about other diseases in Canada is being missed at the moment because COVID-19 is the priority,” says Cameron. “Our project will help to address this gap.”

Dr. Gerald Brown, Genome Prairie’s interim President and CEO, says Genome Prairie is thrilled to be supporting the research team’s work.

“The COV3R project represents our organization’s ability to bring together the best researchers in our Prairie provinces to respond rapidly and effectively to an emerging issue,” says Brown.

Dr. Kathleen McNutt, Vice–President (Research) at the University of Regina, says without this work the people of Saskatchewan, Manitoba, and B.C. will likely be hit even harder by the coronavirus, especially in the fall when cold and flu season re-emerges.

“Thanks to the support from Genome Prairie and SHRF, the work that Dr. Cameron and the COV3R team are doing is poised to make a dramatic difference in detecting COVID-19, and a multitude of other viruses and bacteria that are yet unknown,” says McNutt. “It is not an overstatement to say this research is a matter of life and death.”

SHRF CEO Patrick Odnokon says SHRF has been a strong supporter of Cameron and his team since 2013, including earlier work evaluating whole genome sequencing to enhance our understanding of disease transmission.

“Dr. Cameron is a perfect example of the expertise that exists in Saskatchewan to seek solutions to health challenges faced by our province and across the globe. The impact of this work will not only benefit public health during the current pandemic, but it will demonstrate what is possible when we nurture and support home-grown talent and collaboration to prepare for potential health crises in the future.”

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