CAMEO - Duotang
Doutang, VirusSeq Data portal, and Viral AI would like to improve your user experience. Please take a few minutes to respond to this survey.
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.
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
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):
…plus any highly divergent variants (like most recently BA.2.86) and sublineages with additional combinations of the mutations below.
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.
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.)