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SARS-Cov-2 Whole Genome Sequencing in Ontario, August 31

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SARS-Cov-2 Whole Genome Sequencing in Ontario, August 31 WEEKLY EPIDEMIOLOGICAL SUMMARY SARS-CoV-2 Whole Genome Sequencing in Ontario, September 21, 2021 This report summarizes the results of SARS-CoV-2 whole genome sequencing completed by Public Health Ontario as of September 16, 2021 and partner laboratories in the Ontario COVID-19 Genomics Network as of September 15, 2021. Background The continued monitoring of global SARS-CoV-2 genomic data has identified changes in the 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). Current VOCs include B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta). WGS has also identified a number of variants of interest (VOI), which may share one or more mutations in common with a VOC, but do not have sufficient evidence at this time to be categorized as a VOC (i.e. evidence of increased transmissibility, disease severity, or immune escape). These variants are also characterized and monitored through genomic surveillance. A VOI may be re-classified as a VOC where there is sufficient scientific evidence to support this designation. The VOC/VOI categories used in this report were derived from the Public Health Agency of Canada (PHAC)1, the World Health Organization (WHO)2, and the European Centre for Disease Prevention and Control (ECDC).3 The Ontario COVID-19 Genomics Network (OCGN) performs WGS on samples received for SARS-CoV-2 diagnostic testing or VOC PCR testing. Sequences are processed using bioinformatics analyses and assigned a Pango lineage4 using the pangolin tool5, allowing for the identification of VOC, VOI and other lineages. SARS-CoV-2 Whole Genome Sequencing in Ontario Page 1 of 23 Highlights From August 8 to September 4, 2021, there were 8,789 cases sequenced by the Ontario COVID- 19 Genomics Network for representative surveillance. The majority were Pango lineage B.1.617.2 (Delta; 98.6%), followed by B.1.621 (Mu; 0.9%), and B.1.1.7 (Alpha; 0.4%). The proportion of cases that were B.1.617.2 (Delta) remained stable between August 22 to August 28 (99.4%) and August 29 to September 4 (98.9%). B.1.617.2 (Delta) remains the dominant lineage. The proportion of cases that were B.1.621 (Mu) remained stable between August 22 to August 28 (0.4%) and August 29 to September 4 (0.5%). From January 1, 2021 to September 4, 2021, a total of 229 cases have been identified as B.1.621 (Mu). There have been no cases of C.1.2 identified by the Ontario COVID-19 Genomics Network to date. The OCGN has implemented a representative surveillance strategy which allows for provincial estimates of the prevalence of VOC, VOI, and other lineages. As of August 27, the OCGN has moved to sequencing 50% of eligible samples due to increasing case counts. For cumulative whole genome sequencing results, the selection of samples has historically been influenced by laboratory testing algorithms. This has created a sampling bias prior to the implementation of representative surveillance that prevents the interpretation of relative proportions of circulating lineages during that time. SARS-CoV-2 Whole Genome Sequencing in Ontario Page 2 of 23 Representative Surveillance Table 1. Number of COVID-19 cases, number and percentage of cases sequenced for representative surveillance by week, Ontario, August 8 to September 4, 2021 Week Number of cases Number sequenced Percentage sequenced Week 32 (August 8 to August 14) 3,226 2,271 70.4% Week 33 (August 15 to August 21) 4,252 3,066 72.1% Week 34 (August 22 to August 28) 4,856 2,326 47.9% Week 35 (August 29 to September 4) 5,193 1,126 21.7% Total 17,527 8,789 50.1% Note: ‘Number of cases’ is the number of confirmed positive cases of COVID-19 in Ontario. Date was assigned to best align with sample collection date, which may differ from other PHO products. ‘Number sequenced’ is the number of cases sequenced for representative surveillance. Results may not be representative of Ontario overall, and do not include all samples tested for other reasons including travel, outbreak investigation, coroner’s cases, reinfection or possible vaccine escape. For representative surveillance: The Ontario COVID-19 Genomics Network (OCGN) began sequencing 100% of eligible samples on June 14 and 50% on August 27. Week was assigned based on earliest date available for a sample. If more than one sample was sequenced for a case, the most recent sample was included. Results for recent weeks are incomplete as not all sequencing and bioinformatics analyses were complete at the time of data extraction and will be included in subsequent reports. Data source: CCM, PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program SARS-CoV-2 Whole Genome Sequencing in Ontario Page 3 of 23 Figure 1. Percentage of COVID-19 cases by top 6 most prevalent VOC/VOI lineages and week, representative surveillance, Ontario, May 2 to September 4, 2021 Note: VOC/VOI designations include descendant lineages as defined by PHAC, ECDC, and WHO. Results may not be representative of Ontario overall, particularly in earlier weeks. The proportion of samples PHO sequenced for representative surveillance has changed over time, from 10% of eligible samples on May 2 (week 18) to 50% on May 30 (week 22), 100% on June 14 (week 24), and 50% on August 27 (week 34). Other VOC PCR testing laboratories were asked to submit 10% of eligible samples to the Ontario COVID-19 Genomics Network (OCGN) on May 26, 50% on June 2, 100% on June 14, and 50% on August 27. Week was assigned based on earliest date available for a sample. If more than one sample was sequenced for a case, the most recent sample was included. Results for recent weeks are incomplete as not all sequencing and bioinformatics analyses were complete at the time of data extraction and will be included in subsequent reports. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program SARS-CoV-2 Whole Genome Sequencing in Ontario Page 4 of 23 Table 2. Number and percentage of cases by VOC/VOI Pango lineage and week, representative surveillance, Ontario, August 8 to September 4, 2021 Week 32 Week 33 Week 34 Week 35 Total Pango lineage (WHO label) (August 8 – August (August 15 – August (August 22 – August (August 29 – (August 8 – 14) 21) 28) September 4) September 4) Variant of concern (VOC) Blank cell Blank cell Blank cell Blank cell Blank cell B.1.1.7 (Alpha) 19 (0.8%) 13 (0.4%) 4 (0.2%) 3 (0.3%) 39 (0.4%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 2 (0.1%) 1 (0.0%) 0 (0.0%) 3 (0.3%) 6 (0.1%) B.1.617.2 (Delta) 2,203 (97.0%) 3,035 (99.0%) 2,312 (99.4%) 1,114 (98.9%) 8,664 (98.6%) Variant of interest (VOI) Blank cell Blank cell Blank cell Blank cell Blank cell A.23.1 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.1.318 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.427/B.1.429 (Epsilon) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.526 (Iota) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.3 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 45 (2.0%) 17 (0.6%) 9 (0.4%) 6 (0.5%) 77 (0.9%) C.37 (Lambda) 1 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.3 (Theta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 1 (0.0%) 0 (0.0%) 1 (0.0%) 0 (0.0%) 2 (0.0%) Total sequenced 2,271 (100%) 3,066 (100%) 2,326 (100%) 1,126 (100%) 8,789 (100%) Note: VOC/VOI designations include descendant lineages as defined by PHAC, ECDC, and WHO. The proportion of eligible samples sequenced by the Ontario COVID-19 Genomics Network (OCGN) decreased from 100% to 50% on August 27. Week was assigned based on the earliest date available for the sample.
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