27 September, 2023

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Contributing authors:

Data analysis, code, and maintenance of this notebook: Carmen Lia Murall, Raphaël Poujol, Susanne Kraemer, Arnaud N’Guessan, Sarah Otto, Art Poon, Jesse Shapiro, Fiona Brinkman, Justin Jia, Zohaib Anwar and Erin Gill. Input and direction by other members of Pillar 6 and CAMEO, which include: Caroline Colijn, Jorg Fritz, Morgan Langille, Paul Gordon, Julie Hussin, Jeff Joy, and William Hsiao.

Sequence collection, generation, release, and feedback on analyses: Canadian laboratories as part of the CPHLN and CanCOGeN are making these data publicly available and contribute feedback on analyses presented here. A complete list of lab authors is in this repository, and more details are below in the Acknowledgement section.

NOTE: Due to the amount of visualizations provided in this notebook, this page may take up to 30 seconds to load completely. We apologize for the inconvenience.

SARS-CoV-2 In Canada

Introduction

This notebook was built to explore Canadian SARS-CoV-2 genomic and epidemiological data with the aim of investigating viral evolution and spread. It is developed by the CAMEO team (Computational Analysis, Modelling and Evolutionary Outcomes Group) associated with the Coronavirus Variants Rapid Response Network (CoVaRR-Net) for sharing with collaborators, including public health labs. These analyses are freely available and open source, enabling code reuse by public health authorities and other researchers for their own use.

Canadian genomic and epidemiological data will be regularly pulled from various public sources (see list below) to keep these analyses up-to-date. Only representations of aggregate data will be posted here.

Important limitations

These analyses represent only a snapshot of SARS-CoV-2 evolution in Canada. Only some infections are detected by PCR testing, only some of those are sent for whole-genome sequencing, and not all sequences are posted to public facing reposittories. Sequencing volumes and priorities have changed during the pandemic, and the sequencing strategy is typically a combination of prioritizing outbreaks, travellers, public health investigations, and random sampling for genomic surveillance.

For example, specific variants or populations might be preferentially sequenced at certain times in certain jurisdictions. When possible, these differences in sampling strategies are mentioned but they are not always known. With the arrival of the Omicron wave, many jurisdictions across Canada reached testing and sequencing capacity mid-late December 2021 and thus switched to targeted testing of priority groups (e.g., hospitalized patients, health care workers, and people in high-risk settings). Therefore, from this time onward, case counts are likely underestimated and the sequenced virus diversity is not necessarily representative of the virus circulating in the overall population.

Thus, interpretation of these plots and comparisons between health regions should be made with caution, considering that the data may not be fully representative. These analyses are subject to frequent change given new data and updated lineage designations.

The last sample collection date is 04 September, 2023

Current situation

There continues to be a substantial diversity of SARS-CoV-2 in Canada, with EG.5.1 subvariants, including EG.5.1.1 the most prevalent in many regions, along with XBB.1.16.6, EG.6.1, FL.1.5.1, and a mix of some some other XBB subvariants all with growing immune evasive mutations. The immune evasive S:F456L mutation is in the vast majority of samples (now over 75%) and continues to steadily increase in prevalence. The mutation S:478R is occurring in multiple variants showing growth. Multiple subvariants of XBB.1.16, XBB.1.9, XBB.1.5 and CH.1.1, have independently obtained the two mutations S:F456L and S:L455F (of interest due to their potential to provide additional immune evasion - and referred to as “FLIP” mutations due to their “exchange of L and F) and are now growing significantly in multiple regions, including the EG.5.1.1 subvariant HK.3 and the CH.1.1 subvariant DV.7.1. However, such collective variants with these”FLIP” mutations are still in low numbers (up to 15% of cases, except in NL and NB where they are up to 40%) so they will not be having an impact yet.

Sequences are also still being monitored closely to identify or track any highly divergent variants (variants with sudden, large mutational changes. This includes BA.2.86, tracking additional mutations of concern that are arising in it.

Variants of current interest, due to their current/potential growth advantage, mutations of potential functional significance, or spread in other countries (Bold only denotes changes since the last Duotang release - not necessarily those of greatest interest):

  • DV.7.1 (CH.1.1 subvariant with S:F456L and S:L455F)
  • EG.5.1 (XBB.1.9.2 with S:F456L plus S:Q52H plus some notable non-spike mutations)
  • EG.5.1.1 (EG.5.1 subvariant that has been growing significantly versus other current variants).
  • EG.5.1.3 (Another EG.5.1 subvariant growing notably)
  • HK.3 (EG.5.1.1 with with S:F456L and S:L455F)
  • JJ.1 (EG.5.1.4 with S:F456L and S:L455F - still being reported often as EG.5.1.4)
  • FL.1.5.1 (XBB.1.9.1 with S:701V, ORF1a:G993S, S:456L and S:478R, with an interest in those with S:L455F) and other possible FL.1 subvariants with S:478R)
  • XBB.1.16 which has S:T478R (with a particular interest in those with S:F456L like XBB.1.16.6 and also S:L455F)
  • XBB.1.9.1, XBB.1.9.2, FL.5 (which have non-spike mutations of note, with a particular interest in those with S:Q613H OR with S:F456L plus NS6:Y49H (aka orf6:y49h)

…plus any highly divergent variants (like most recently BA.2.86) and sublineages with additional combinations of the mutations below.

  • S:Q:52H (due to association with EG.5.1)
  • S:L455F (in particular if present with S:F456L)
  • S:F456L (evidence of increased immune evasion versus recent variants and a mutation growing in prevalence in multiple lineages in multiple regions)
  • S:T478R (aka S:K478R - the S:T478K mutation occurred first). Evidence of increased infectivity when introduced into XBB.1.5. Associated with XBB.1.16 (which has additional mutations like S:E180V that may counteract this mutations advantage) but now seen in additional variants like XBB.2.3.
  • S:P521S (evidence it could increase human ACE2 receptor binding/infectivity - associated with XBB.2.3 variants)
  • S:Q613H (growing and seen in XBB.1.5, CH.1.1 and XBB.1.9.1)
  • ORF1b:D1746Y (aka NSP14_D222Y - in XBB.1.16 variants)
  • Orf1b:G662S aka NSP12_671 (in the context of a BA.2.86 subvariant) which has been found previously in other variant backgrounds to boosts viral replication at lower temperatures https://doi.org/10.1016/j.celrep.2023.113077
  • ORF9b:I5T (note its a synonymous mutation in the overlapping N gene)
  • ORF9b:N55S (synonymous mutation in N)

Plus other mutations identified through deep mutation scanning and the SARS-CoV-2 RBD antibody escape calculator. See:

With thanks to the global team of variant hunters which play a key role in identifying new variants of note.

Omicron sublineages in Canada

There are 391 unique named variants currently circulating in Canada since 2023-05-07 (last 120 days). Please see Pango lineage table for number of sequences per lineage present.

Here we take a look, sub-dividing the major sub-lineages currently circulating in Canada. (Click and drag to zoom, double click to reset. Clicking on an item in the legend will hide it, double clicking an item in legend will hide everything else but that item.)

Last 120 days

Last 120 days sublineages starting from 2023-05-07 (Frequency Table Download)

BA.1

BA.1 sublineages (Frequency Table Download)

BA.2

BA.2 sublineages (Frequency Table Download)