Results from the funded study: Genomic Surveillance and Modelling for the COVID-19 Variant Endgame

Pillar 6
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)

Over the summer and fall of 2021, CoVaRR-Net scientists, as part of the Canadian COVID Genomics Network (CanCOGeN), partnered with the National Microbiology Laboratory (NML) and the Canadian Public Health Laboratory Network (CPHLN) to investigate the Delta variant and its diverse sub-lineages, which collectively became dominant around the world. This active monitoring of the viral sequences found that there were two Delta sub-lineages that were circulating in Canada, in particular in the Western provinces.

The first sub-lineage – AY.25 – was predominantly found in the USA. However, it also spread rapidly across Canada. The mutational composition of the Canadian AY.25 sequences suggested that its increased prevalence in Canada was likely due to domestic transmission, and not to repeated re-introductions from international sources.

The second sub-lineage of interest was AY.27, which was almost exclusively Canadian. Researchers of the study identified that a new mutation of interest, S:Q613H, had arisen in Alberta early on. This mutation was found to have spread widely across Canada, such that 75% of sequences at the time contained it. S:Q613H was flagged as worthy of further investigation because it was located in a part of the spike protein that could increase transmissibility.

The results of this work were posted as a report on an international virology website where scientists tracking the evolution of the coronaviruses communicate and engage each other on their latest findings. This report developed by CoVaRR-Net researchers to measure the growth advantage of variants was shared with the international community, offering new analytic methods.

Carmen Lia Murall, Raphael Poujol, Aaron Petkau, Benjamin Sobkowiak, Adrian Zetner, Susanne A. Kraemer, Arnaud N’Guessan, Sana Naderi, Erin E. Gill, Jorg Fritz, Fiona S.L. Brinkman, Julie Hussin, Natalie Prystajecky, Tarah Lynch, Matthew A. Croxen, Ryan McDonald, Keith MacKenzie, Caroline Colijn, Gary Van Domselaar, Sarah P. Otto, B. Jesse Shapiro, and The Canadian COVID-19 Genomics Network (CanCOGeN) Virus Sequencing Consortium 28. Monitoring the evolution and spread of Delta sublineages AY.25 and AY.27 in Canada., posted November 2021.