The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

Abstract

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). In addition, the Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This Portal has been coupled with other resources like Viral AI and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this Portal, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key 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.

Keywords: data sharing; evolutionary biology; mutational analysis; open access; viral genomics.

Figure 1:. Data Flow Overview.

SARS-CoV-2 viral samples and contextual data are collected by Public Health, hospitals and labs. Some samples are selected for sequencing based on national and regional priorities. After sequencing, regional Public Health authorities select samples that will be shared publicly. Sequence and contextual data from these samples are uploaded to the Data Portal using the DataHarmonizer and FASTA Uploader. From the Portal, the public can view or download contextual and sequence data from across the country. Data can also be accessed for value-added resources, such as Duotang, ViralAI, COVID-MVP and CoVizu via the API. Green check marks on the figure indicate points in the data flow where human Quality Assurance / Quality Control (QA/QC) and/or ethics oversight take place.

Figure 2:. Overview of the data flow from VirusSeq Data Portal to Duotang.

Genomics and epidemiological data from VirusSeq is first processed by DNAStack’s Viral AI workflow. The result of this is a dataset containing SARS-CoV-2 lineage information. Duotang then retrieves this lineage information using Viral AI’s Global Alliance for Genomics and Health (GA4GH) compliant APIs for further analyses.

Figure 3.. Overview of the VirusSeq Data Portal Explore page.

The VirusSeq Data Portal allows users to browse samples stored via a web interface or API. Within the interface, the user is able to see the samples that are available, their metadata, and perform filters and queries to identify samples of interest that can then be downloaded for analysis.

Figure 4:. Duotang Webpage Overview.

Duotang contains many different interactive plots for the user to explore SARS-CoV-2 genomic epidemiology in Canada. All sections of the page are easily accessible via the menu bar, which is located on the left-hand side of the page. The first section of the page gives a text description of current variants of interest in the country. Several of the plots are highlighted in the figure above, which include different visualizations of selection on variants, phylogenetic trees and root-to-tip analyses of these trees to detect unusual genetic changes. In addition to what is shown here, the user can also view plots of the growth advantage of single lineages relative to a reference lineage (on both national and regional levels), visualize the mutational composition of actively circulating lineages via an embedded frame of COVID-MVP, review the changing proportions of different variants over time (back to April 2020, on both national and regional levels), examine molecular clock estimates for different VOIs, and utilize a searchable table to view the ancestors and description of any Pango lineage. For more details, please visit: https://covarr-net.github.io/duotang/duotang.html