Mary Wilson
Well-known member
WEEKLY EPIDEMIOLOGICAL SUMMARY
This report summarizes the results of SARS-CoV-2 whole genome sequencing completed by the Ontario
COVID-19 Genomics Network as of January 2, 2025.
Background
The continued monitoring of global SARS-CoV-2 genomic data has identified changes in the virus’
genome as it spreads through populations. These random changes or mutations arise as a virus evolves
over time. The accumulation of these mutations can result in a new lineage of the virus, which is a
common occurrence. These new lineages will differ slightly in genome sequence and are termed
variants. Although many variants will have no difference in the ability to spread or cause disease, some
variants have mutations which may enhance virulence, transmissibility, and/or allow the virus to escape
natural or vaccine-induced immunity.
The identification of variants and mutations occurs through whole genome sequencing (WGS) of select
samples. Through global surveillance of SARS-CoV-2 genomes, a number of variants have been identified
with evidence of clinical and/or public health significance, termed variants of concern (VOC). Variants
designated as VOCs include B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron), some of which have been de-escalated due to their diminishing prevalence globally. 1-3
As SARS-CoV-2 continues to evolve, lineages will naturally divide into descendant sublineages - a
genetically closely related group derived from a common ancestor. The descendant branches are given
new lineage aliases, such as for B.1.1.529 (Omicron) lineages (e.g., BA.2 [alias for B.1.1.529.2] and JN.1 [alias for B.1.1.529.2.86.1.1]). When a host is infected with two or more descendant lineages,
lineages can recombine to form a new recombinant lineage (e.g., KP.3.3 and KS.1.1 to form XEC). New
designations represent refined genetic groups that can be tracked separately. As more research is
conducted, there may be evidence of an important difference in terms of transmissibility, severity, or
immune escape, at which time WHO may assign a new Greek letter classification to a lineage.
The Ontario COVID-19 Genomics Network (OCGN) performs WGS on all eligible positive SARS-CoV-2
samples (see Technical Notes for details). Sequences are processed using bioinformatics analyses and
assigned a Pango lineage4 using the pangolin tool5, allowing for the identification of lineages.
Highlights
• In the most recent week (December 15 to December 21), a total of 797 cases were sequenced.
KP.3.1.1 was the most prevalent lineage (23.8%), followed by XEC (22.8%), and MC.1 (8.2%).
• The proportion of KP.3.1.1 increased from 18.5% (December 8 to December 14) to 23.8%
(December 15 to December 21).
• Based on the Nowcast model, KP.3.1.1 is projected to decrease to 9.0% (95% CI: 7.1% - 11.3%)
by January 8, 2025.
• The proportion of XEC decreased from 31.9% (December 8 to December 14) to 22.8% (December 15
to December 21).
• Based on the Nowcast model, XEC is projected to decrease to 21.6% (95% CI: 17.5% - 26.3%) by
January 8, 2025. The weekly relative growth rate of XEC is 1.15 (95% CI: 1.10 - 1.21) times that of
KP.3.1.1. ...
https://www.publichealthontario.ca/...lang=en&hash=FDD23C4D14B820CB36405D4FD73E6B95
This report summarizes the results of SARS-CoV-2 whole genome sequencing completed by the Ontario
COVID-19 Genomics Network as of January 2, 2025.
Background
The continued monitoring of global SARS-CoV-2 genomic data has identified changes in the virus’
genome as it spreads through populations. These random changes or mutations arise as a virus evolves
over time. The accumulation of these mutations can result in a new lineage of the virus, which is a
common occurrence. These new lineages will differ slightly in genome sequence and are termed
variants. Although many variants will have no difference in the ability to spread or cause disease, some
variants have mutations which may enhance virulence, transmissibility, and/or allow the virus to escape
natural or vaccine-induced immunity.
The identification of variants and mutations occurs through whole genome sequencing (WGS) of select
samples. Through global surveillance of SARS-CoV-2 genomes, a number of variants have been identified
with evidence of clinical and/or public health significance, termed variants of concern (VOC). Variants
designated as VOCs include B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron), some of which have been de-escalated due to their diminishing prevalence globally. 1-3
As SARS-CoV-2 continues to evolve, lineages will naturally divide into descendant sublineages - a
genetically closely related group derived from a common ancestor. The descendant branches are given
new lineage aliases, such as for B.1.1.529 (Omicron) lineages (e.g., BA.2 [alias for B.1.1.529.2] and JN.1 [alias for B.1.1.529.2.86.1.1]). When a host is infected with two or more descendant lineages,
lineages can recombine to form a new recombinant lineage (e.g., KP.3.3 and KS.1.1 to form XEC). New
designations represent refined genetic groups that can be tracked separately. As more research is
conducted, there may be evidence of an important difference in terms of transmissibility, severity, or
immune escape, at which time WHO may assign a new Greek letter classification to a lineage.
The Ontario COVID-19 Genomics Network (OCGN) performs WGS on all eligible positive SARS-CoV-2
samples (see Technical Notes for details). Sequences are processed using bioinformatics analyses and
assigned a Pango lineage4 using the pangolin tool5, allowing for the identification of lineages.
Highlights
• In the most recent week (December 15 to December 21), a total of 797 cases were sequenced.
KP.3.1.1 was the most prevalent lineage (23.8%), followed by XEC (22.8%), and MC.1 (8.2%).
• The proportion of KP.3.1.1 increased from 18.5% (December 8 to December 14) to 23.8%
(December 15 to December 21).
• Based on the Nowcast model, KP.3.1.1 is projected to decrease to 9.0% (95% CI: 7.1% - 11.3%)
by January 8, 2025.
• The proportion of XEC decreased from 31.9% (December 8 to December 14) to 22.8% (December 15
to December 21).
• Based on the Nowcast model, XEC is projected to decrease to 21.6% (95% CI: 17.5% - 26.3%) by
January 8, 2025. The weekly relative growth rate of XEC is 1.15 (95% CI: 1.10 - 1.21) times that of
KP.3.1.1. ...
https://www.publichealthontario.ca/...lang=en&hash=FDD23C4D14B820CB36405D4FD73E6B95