Modelling Resources2022-09-01T14:56:19-04:00

CoVaRR-Net’s Genomic Epidemiology
Analyses & Mathematical Modelling Notebook

About our notebook

CoVaRR-Net has been gathering and analyzing genomic and epidemiological data on SARS-CoV-2 for the investigation of the evolution and spread of the virus across Canada. Assembled from a variety of public sources, including the Canadian VirusSeq Data portal, the aggregate data in our Duotang notebook serves as a unique source for tracking the spread of different variants of the virus in the country.

We invite you to use our resulting analyses to spur further research, use in reports, support discussions with scientific communicators for public dissemination, and enable code reuse by public health authorities/laboratories for their internal use.

For the first year of the pandemic, viral sequences in Canada represented a wide variety of lineages, which spread at similar rates. In November 2020, the first variant of concern (VOC) displaying a substantially higher transmission rate was discovered in the United Kingdom (Alpha). By summer 2021, VOCs Alpha and Gamma were the most sequenced lineages in Canada. As Delta advanced in late summer 2021, its sublineages AY.25 and AY.27 constituted sizable proportions of this wave. Omicron arrived in November 2021, leading to the largest surge in cases yet seen during the pandemic in two waves, the first driven primarily by BA.1 and BA.1.1, and the second by the faster spreading BA.2 sublineage.

Modelling Projections

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