  The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2
genomes from patient samples to track viral evolution and inform public health
response. Millions of SARS-CoV-2 genome sequences have been deposited in global
public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN -
VirusSeq), a consortium tasked with coordinating expanded sequencing of
SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian
VirusSeq Data Portal, with associated data pipelines and procedures, to support
these efforts. The goal of VirusSeq was to allow open access to Canadian
SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that
were unavailable in other repositories and that meet FAIR standards (Findable,
Accessible, Interoperable and Reusable). The Portal data submission pipeline
contains data quality checking procedures and appropriate acknowledgement of
data generators that encourages collaboration. Here we also highlight Duotang,
a web platform that presents genomic epidemiology and modeling analyses on
circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents
dynamic changes in variant composition of SARS-CoV-2 in Canada and by province,
estimates variant growth, and displays complementary interactive
visualizations, with a text overview of the current situation. The VirusSeq
Data Portal and Duotang resources, alongside additional analyses and resources
computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely
available. Together, they provide an updated picture of SARS-CoV-2 evolution to
spur scientific discussions, inform public discourse, and support communication
with and within public health authorities. They also serve as a framework for
other jurisdictions interested in open, collaborative sequence data sharing and
analyses.
