As SARS-CoV-2—the causative agent of COVID-19—spreads between individuals, the virus continues to mutate. Tracking these changes is possible through genome sequencing of the virus. These changes can then be used to generate a “family tree” for this virus and its “descendants,” aiding researchers in the linking of related cases. Changes in the virus can also change disease severity or its ability to spread. Viral genome sequence data has therefore become an essential tool for public health officials to better track how the virus is both changing and spreading.
CanCOGeN-VirusSeq therefore proposes to coordinate and fund expanded genome sequencing efforts and support the sharing of the data within an open, ethical framework.
To facilitate these objectives, Genome Canada assembled a consortium that includes public health laboratories, hospitals, research institutes, large-scale genome sequencing centres, industry, and data analysis centres.
This consortium is serving the country during the current COVID-19 crisis and is becoming a scalable and coordinated genomics network in Canada for future outbreak/pandemic preparedness.
The virus timeline
The human coronavirus SARS-CoV-2, the virus responsible for the COVID-19 outbreak, first emerged in late November 2019 and within four months reached pandemic status, spreading to at least 177 countries and resulting in one of the largest shutdowns of human activities in modern history.
Critical to global efforts to control COVID-19 and its impacts has been the rapid release of the first genomic sequence on Jan 10, 2020. This not only enabled initiation of vaccine and antiviral therapeutic development, but also enabled key molecular diagnostic tests to be designed and shared within a month of the disease being reported to the WHO. These diagnostic tests, however, only have the resolution to confirm whether a person has COVID-19 or not. Genomic sequences additionally identify how related cases are to each other, so they can be used to track where the virus came from and further identify how it is spreading nationally and internationally.
February to present
Genomic sequences, rapidly shared with contextual data, have been key to confirm the source of cross-border introductions of the virus, and the identification of community transmission — informing policies for outbreak control. Continued genomic sequencing efforts are critical for modeling of the local incursion and spread of the virus. As the number of community-transmitted COVID-19 cases increases, epidemiological investigation and tracing will increasingly rely on genomic data as evidence to detect clusters. Continued genome-based surveillance after the number of cases reduces is also essential to identify and control the sources of clusters that risk a second epidemic wave.
Genomic sequence changes associated with severity of disease or eventually drug resistance can also be tracked and potentially inform patient management as the virus evolves.
Click here to learn more about the governance of CanCOGeN VirusSeq.
Source: Government of Canada
This information on this map is based on data from CanCOGeN’s provincial and territorial partners. It is current as of October 19, 2020 at 7 pm ET. For the most up to date data for any province, territory or city, and to see the text description text for the graphic, please visit the interactive version of this map.