New COVID-19 portal aims to nationalize genomic data sharing

Canada is poised to launch a national portal that will provide an almost real-time snapshot of the evolving COVID-19 pandemic across Canada, including the detection and spread of variants of concern.

The new Canadian VirusSeq Data Portal, to be launched by the end of April, will bring together SARS-CoV-2 genome sequences and associated metadata from sources including the National Microbiology Laboratory and provincial public health labs from coast to coast. As an open resource, it will be accessible to scientists, public health officials and other stakeholders supporting Canada’s pandemic response.

By creating the portal, scientists will also be establishing the national data infrastructure Canada needs to track future pandemics using viral genome sequences.

From the start of the pandemic, open data sharing has accelerated research and supported evidence-based public health and public policy decisions in Canada and internationally. But barriers to sharing SARS-CoV-2 genome sequences, which are used to detect, diagnose and predict the spread of new viral variants, still exist. The new portal aims to overcome these barriers.

“As you know now, SARS-CoV-2 sees no borders, no provinces. And that's actually how we need to manage the data,” said Dr. Catalina Lopez-Correa, executive director of the Genome Canada-led Canadian COVID Genomics Network (CanCOGeN), in an interview with Research Money.

CanCOGeN was launched in April 2020 to expand Canada’s sequencing, surveillance and research capacity for SARS-CoV-2.

“There is a lot of data sharing happening between public health labs. The national portal is opening that data to the academic community, to the scientists in Canada, [who] could start analyzing that data in so many other ways," said Dr. Lopez-Correa.

"They have the tools, they have the knowledge, but they don't have the data."

Genome data produced at public health labs across the country is being used to inform decision makers on the front lines of the pandemic response. It is also being submitted to international repositories, such as GISAID, the world’s largest database of coronavirus sequences. But using Canadian data contributed to GISAID has proven difficult because of limits it places on data redistribution. (This policy prompted scientific leaders to pen an open letter in late January urging the research community to submit data to fully open databases. The letter was signed by Lopez-Correa.)

Building a made-in-Canada portal, as the United Kingdom and several other countries have done, will streamline access and make data sharing more effective. 

Dr. Guillaume Bourque, a professor in the department of human genetics at McGill University, is leading the development and implementation of the platform. The proposal was made in response to a rapid funding opportunity launched by CanCOGeN in support of the Government of Canada’s $53-million Variants of Concern Strategy.

Genome Canada will act as a custodian for the data submitted to the portal, which will include genetic sequence and related clinical and epidemiological data, such as geographic location and sample collection date.

In an interview with Research Money, Bourque said the new initiative will help harmonize the collection of data from labs across Canada and its presentation. “We can make sure that the data are standardized across the country, facilitating analysis between provinces and so on,” he said.

But there are still barriers to overcome to meet the team's ambitious timeline. “The part that takes time is agreeing on what data can actually be contributed to the portal. We're also working with the public health labs to figure out how to insert this into their workflow, so it doesn’t add to the pressure they are already facing,” Bourque said.

Data sharing could improve healthcare response to other diseases

Beyond COVID-19, the national portal could have a positive impact on Canada's response to future pandemics and other healthcare initiatives.

"I think it's important for people to know that we're not talking here about a cool scientific project. We're talking about a tool that could potentially save lives," Lopez-Correa said.

Building the data infrastructure for genomic epidemiology — the science of mapping mutations inside the genome and using that information for public health purposes — could support personalized medicine initiatives where genomics is central, according to Lopez-Correa. 

“Genome Canada has initiatives around rare diseases, where we're really advancing the idea of data sharing between provinces. Having the national portal for SARS-CoV-2 will help us make case for data sharing in other areas [of medicine] beyond infectious diseases," she added.

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