Rapid release of an easily accessible SARS-CoV-2 genome analysis pipeline

  • Project Leaders: Chanson Brumme
  • Institutions: University of British Columbia (UBC)
  • Budget: $76500
  • Competition: Rapid Response Funding for COVID-19 Research Projects
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2020
  • Status: Active

This project will create a simple open-source software package that will help analyze viral genomic data from the COVID-19 pandemic. This tool will be created by adapting an existing data analysis tool, funded by Genome BC, that has proved successful in identifying drug resistance in other viral diseases including HIV and Hepatitis C. By making it extremely easy to use, the team hopes that this new tool will be rapidly adopted by scientists around the world, even in areas with limited computational infrastructure. It will fill a gap in the analysis pipeline for SARS-CoV-2 virus genomes. Within a week of launch it is estimated that this tool will enable end users to contribute genomic data about the novel coronavirus to public repositories. By sharing this data publicly, researchers around the globe will be able to utilize this data to track the origins, geographic spread and evolution of the virus in real time. This genomic data will also be useful for the development for medications and vaccines for use against the virus.

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During the Canada Post strike announced September 25, 2025, the following measures will be undertaken to minimize service disruption to BC-CfE clients and providers.

  • The BC-CfE Laboratory has transitioned to private courier for delivery of outgoing reports and documents. Results required urgently can be faxed upon request. (Lab Contact Information: Phone 604-806-8775; FAX 604-806-9463)
  • The BC-CfE Drug Treatment Program (DTP) will fax outgoing forms and documents to the provider’s office. (DTP Contact Information: Phone 604-806-8515; FAX 604-806-9044)
  • St. Paul’s Hospital Ambulatory Pharmacy has transitioned to private courier for delivery of medications. We recommend requesting medication at least 2 weeks in advance in case of delivery delays, particularly to rural/remote parts of BC. (Contact Information: Phone 1-800-547-3622; FAX 604-806-8675)

During the Canada Post strike, we recommend that documents be faxed or couriered to our sites, versus utilization of regular mail service

The BC-CfE Laboratory is streamlining reporting processes for certain tests in order to simplify distribution and record-keeping, and to ensure completeness of results. Beginning September 2, 2025, results for the ‘Resistance Analysis of HIV-1 Protease and Reverse Transcriptase’ (Protease-RT) and ‘HIV-1 Integrase Resistance Genotype’ tests will be combined into a single ‘HIV-1 Resistance Genotype Report’.
For more details and example reports, please click on the button below

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