WEEKLY EPIDEMIOLOGICAL SUMMARY SARS-CoV-2 Whole in Ontario, September 21, 2021

This report summarizes the results of SARS-CoV-2 whole genome sequencing completed by Ontario as of September 16, 2021 and partner laboratories in the Ontario COVID-19 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 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 , 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 analyses and assigned a Pango lineage4 using the pangolin tool5, allowing for the identification of VOC, VOI and other lineages.

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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.

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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 Program

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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

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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. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program

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Table 3. Percentage of B.1.617.2 (Delta) cases identified (number identified/total sequenced) by public health unit (PHU), region, and week, representative surveillance, Ontario, August 8 to September 4, 2021

Week 32 Week 33 Week 34 Week 35 Total Public Health Unit (August 8 – August (August 15 – August (August 22 – August (August 29 – (August 8 – 14) 21) 28) September 4) September 4) Northwestern Health Unit 100% (6/6) 75.0% (3/4) 100% (3/3) 0.0% (0/0) 92.3% (12/13) Thunder Bay District Health 100% (2/2) 100% (4/4) 100% (4/4) 100% (2/2) 100% (12/12) Unit TOTAL NORTH WEST 100% (8/8) 87.5% (7/8) 100% (7/7) 100% (2/2) 96.0% (24/25) Algoma Public Health 0.0% (0/0) 100% (5/5) 100% (6/6) 100% (1/1) 100% (12/12) North Bay Parry Sound District 100% (3/3) 100% (2/2) 100% (2/2) 100% (5/5) 100% (12/12) Health Unit Porcupine Health Unit 100% (2/2) 100% (4/4) 100% (3/3) 100% (3/3) 100% (12/12) Public Health Sudbury & 100% (7/7) 100% (2/2) 100% (1/1) 0.0% (0/0) 100% (10/10) Districts Timiskaming Health Unit 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) TOTAL NORTH EAST 100% (12/12) 100% (13/13) 100% (12/12) 100% (9/9) 100% (46/46) Ottawa Public Health 97.0% (98/101) 96.2% (127/132) 98.1% (101/103) 100% (2/2) 97.0% (328/338) Eastern Ontario Health Unit 33.3% (4/12) 100% (13/13) 97.0% (32/33) 100% (3/3) 85.2% (52/61) Hastings Prince Edward Public 100% (5/5) 100% (22/22) 100% (20/20) 100% (11/11) 100% (58/58) Health Kingston, Frontenac and Lennox 80.0% (4/5) 88.9% (8/9) 100% (4/4) 100% (4/4) 90.9% (20/22) & Addington Public Health Leeds, Grenville & Lanark 100% (16/16) 100% (9/9) 100% (3/3) 100% (1/1) 100% (29/29) District Health Unit Renfrew County and District 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) 0.0% (0/0) Health Unit TOTAL EASTERN 91.4% (127/139) 96.8% (179/185) 98.2% (160/163) 100% (21/21) 95.9% (487/508) Durham Region Health 97.5% (79/81) 97.6% (120/123) 100% (127/127) 95.7% (67/70) 98.0% (393/401) Department Haliburton, Kawartha, Pine 100% (10/10) 100% (14/14) 100% (3/3) 100% (3/3) 100% (30/30) Ridge District Health Unit Peel Public Health 96.6% (281/291) 99.5% (378/380) 100% (326/326) 99.0% (189/191) 98.8% (1,174/1,188) Peterborough Public Health 100% (5/5) 100% (10/10) 100% (8/8) 100% (9/9) 100% (32/32) Simcoe Muskoka District Health 100% (79/79) 99.1% (111/112) 100% (75/75) 100% (47/47) 99.7% (312/313) Unit

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Week 32 Week 33 Week 34 Week 35 Total Public Health Unit (August 8 – August (August 15 – August (August 22 – August (August 29 – (August 8 – 14) 21) 28) September 4) September 4) York Region Public Health 94.7% (180/190) 98.7% (308/312) 99.3% (300/302) 98.4% (184/187) 98.1% (972/991) TOTAL CENTRAL EAST 96.6% (634/656) 98.9% (941/951) 99.8% (839/841) 98.4% (499/507) 98.6% (2,913/2,955) Toronto Public Health 97.6% (569/583) 99.6% (696/699) 99.2% (527/531) 99.2% (249/251) 98.9% (2,041/2,064) TOTAL TORONTO 97.6% (569/583) 99.6% (696/699) 99.2% (527/531) 99.2% (249/251) 98.9% (2,041/2,064) Chatham-Kent Public Health 93.3% (14/15) 100% (21/21) 100% (34/34) 100% (16/16) 98.8% (85/86) Grey Bruce Health Unit 100% (16/16) 100% (13/13) 100% (10/10) 100% (5/5) 100% (44/44) Huron Perth Public Health 100% (11/11) 100% (15/15) 100% (13/13) 100% (3/3) 100% (42/42) Lambton Public Health 100% (10/10) 100% (16/16) 100% (6/6) 100% (3/3) 100% (35/35) Middlesex-London Health Unit 98.6% (72/73) 99.4% (169/170) 100% (101/101) 100% (41/41) 99.5% (383/385) Southwestern Public Health 92.0% (23/25) 96.0% (24/25) 100% (16/16) 100% (4/4) 95.7% (67/70) Windsor-Essex County Health 100% (195/195) 100% (266/266) 100% (206/206) 100% (103/103) 100% (770/770) Unit TOTAL SOUTH WEST 98.8% (341/345) 99.6% (524/526) 100% (386/386) 100% (175/175) 99.6% (1,426/1,432) Brant County Health Unit 100% (42/42) 100% (36/36) 100% (31/31) 96.7% (29/30) 99.3% (138/139) City of Hamilton Public Health 98.3% (227/231) 99.7% (334/335) 98.3% (118/120) 100% (10/10) 99.0% (689/696) Services Haldimand-Norfolk Health Unit 100% (5/5) 100% (17/17) 100% (10/10) 100% (2/2) 100% (34/34) Halton Region Public Health 94.7% (89/94) 98.0% (99/101) 100% (46/46) 100% (19/19) 97.3% (253/260) Niagara Region Public Health 94.9% (56/59) 95.9% (71/74) 96.9% (62/64) 100% (45/45) 96.7% (234/242) Region of Waterloo Public 95.9% (70/73) 96.3% (78/81) 98.4% (61/62) 96.7% (29/30) 96.7% (238/246) Health and Emergency Services Wellington-Dufferin-Guelph 95.8% (23/24) 100% (40/40) 100% (52/52) 100% (25/25) 99.3% (140/141) Public Health TOTAL CENTRAL WEST 97.0% (512/528) 98.7% (675/684) 98.7% (380/385) 98.8% (159/161) 98.2% (1,726/1,758) UNKNOWN 0.0% (0/0) 0.0% (0/0) 100% (1/1) 0.0% (0/0) 100% (1/1) TOTAL ONTARIO 97.0% (2,203/2,271) 99.0% (3,035/3,066) 99.4% (2,312/2,326) 98.9% (1,114/1,126) 98.6% (8,664/8,789) 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. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4a. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, North West Region, August 8 to September 4, 2021

Pango lineage (WHO label) Northwestern Health Unit Thunder Bay District Health Unit Total Variant of concern Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 1 (7.7%) 0 (0.0%) 1 (4.0%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.2 (Delta) 12 (92.3%) 12 (100%) 24 (96.0%) Variant of interest Blank Cell Blank Cell Blank Cell A.23.1 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.1.318 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%) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.526 (Iota) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.3 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 0 (0.0%) 0 (0.0%) 0 (0.0%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.3 (Theta) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 0 (0.0%) 0 (0.0%) Total sequenced 13 (100%) 12 (100%) 25 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4b. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, North East Region, August 8 to September 4, 2021

North Bay Parry Public Health Algoma Public Porcupine Health Timiskaming Pango lineage (WHO label) Sound District Sudbury & Total Health Unit Health Unit Health Unit Districts Variant of concern Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.2 (Delta) 12 (100%) 12 (100%) 12 (100%) 10 (100%) 0 (0.0%) 46 (100%) Variant of interest Blank Cell 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%) 0 (0.0%) B.1.1.318 0 (0.0%) 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%) 0 (0.0%) B.1.525 (Eta) 0 (0.0%) 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%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 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%) 0 (0.0%) B.1.621 (Mu) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 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%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Total sequenced 12 (100%) 12 (100%) 12 (100%) 10 (100%) 0 (0.0%) 46 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used it patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4c. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, Eastern Region, August 8 to September 4, 2021

Kingston, Leeds, Renfrew Eastern Hastings Frontenac and Grenville & Ottawa Public County and Pango lineage (WHO label) Ontario Health Prince Edward Lennox & Total Lanark District Health District Health Unit Public Health Addington Health Unit Unit Public Health Variant of concern Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 7 (11.5%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 5 (1.5%) 0 (0.0%) 12 (2.4%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 1 (1.6%) 0 (0.0%) 1 (4.5%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 2 (0.4%) B.1.617.2 (Delta) 52 (85.2%) 58 (100%) 20 (90.9%) 29 (100%) 328 (97.0%) 0 (0.0%) 487 (95.9%) Variant of interest Blank Cell Blank Cell 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%) 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%) 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%) 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%) 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%) 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%) 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%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 1 (1.6%) 0 (0.0%) 1 (4.5%) 0 (0.0%) 5 (1.5%) 0 (0.0%) 7 (1.4%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 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%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Total sequenced 61 (100%) 58 (100%) 22 (100%) 29 (100%) 338 (100%) 0 (0.0%) 508 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4d. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, Central East Region, August 8 to September 4, 2021

Haliburton, Simcoe Pango lineage (WHO label) Durham Kawartha, Peel Public Peterborough Muskoka York Region Region Health Pine Ridge Total Health Public Health District Health Public Health Department District Health Unit Unit Variant of concern Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 4 (1.0%) 0 (0.0%) 3 (0.3%) 0 (0.0%) 1 (0.3%) 4 (0.4%) 12 (0.4%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 2 (0.2%) 2 (0.1%) B.1.617.2 (Delta) 393 (98.0%) 30 (100%) 1,174 (98.8%) 32 (100%) 312 (99.7%) 972 (98.1%) 2,913 (98.6%) Variant of interest Blank Cell Blank Cell 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%) 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%) 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%) 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%) 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%) 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%) 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%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 4 (1.0%) 0 (0.0%) 11 (0.9%) 0 (0.0%) 0 (0.0%) 13 (1.3%) 28 (0.9%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 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%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Total sequenced 401 (100%) 30 (100%) 1,188 (100%) 32 (100%) 313 (100%) 991 (100%) 2,955 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4e. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, Toronto Region, August 8 to September 4, 2021

Pango lineage (WHO label) Toronto Public Health Total Variant of concern Blank Cell Blank Cell B.1.1.7 (Alpha) 3 (0.1%) 3 (0.1%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 1 (0.0%) 1 (0.0%) B.1.617.2 (Delta) 2,041 (98.9%) 2,041 (98.9%) Variant of interest Blank Cell Blank Cell A.23.1 0 (0.0%) 0 (0.0%) B.1.1.318 0 (0.0%) 0 (0.0%) B.1.427/B.1.429 (Epsilon) 0 (0.0%) 0 (0.0%) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) B.1.526 (Iota) 0 (0.0%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 0 (0.0%) B.1.617.3 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 17 (0.8%) 17 (0.8%) C.37 (Lambda) 1 (0.0%) 1 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) P.3 (Theta) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 1 (0.0%) 1 (0.0%) Total sequenced 2,064 (100%) 2,064 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4f. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, South West Region, August 8 to September 4, 2021

Chatham- Grey Bruce Huron Perth Lambton Middlesex- Windsor- Southwestern Pango lineage (WHO label) Kent Public Health Public Public London Essex County Total Public Health Health Unit Health Health Health Unit Health Unit Variant of concern Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 3 (4.3%) 0 (0.0%) 3 (0.2%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.2 (Delta) 85 (98.8%) 44 (100%) 42 (100%) 35 (100%) 383 (99.5%) 67 (95.7%) 770 (100%) 1,426 (99.6%) Variant of interest Blank Cell Blank Cell Blank Cell 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%) 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%) 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%) 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%) 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%) 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%) 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%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 1 (1.2%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 2 (0.5%) 0 (0.0%) 0 (0.0%) 3 (0.2%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 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%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Total sequenced 86 (100%) 44 (100%) 42 (100%) 35 (100%) 385 (100%) 70 (100%) 770 (100%) 1,432 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 4g. Number and percentage of cases by VOC/VOI Pango lineage and public health unit (PHU), representative surveillance, Central West Region, August 8 to September 4, 2021

City of Region of Wellington- Halton Niagara Brant Hamilton Haldimand- Waterloo Public Dufferin- Pango lineage (WHO Region Region County Public Norfolk Health and Guelph Total label) Public Public Health Unit Health Health Unit Emergency Public Health Health Services Services Health Variant of concern Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (0.4%) 2 (0.8%) 4 (1.6%) 1 (0.7%) 8 (0.5%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 1 (0.1%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (0.1%) B.1.617.2 (Delta) 138 (99.3%) 689 (99.0%) 34 (100%) 253 (97.3%) 234 (96.7%) 238 (96.7%) 140 (99.3%) 1,726 (98.2%) Variant of interest Blank Cell Blank Cell Blank Cell 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%) 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%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.427/B.1.429 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) (Epsilon) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 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%) 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%) 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%) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 1 (0.7%) 5 (0.7%) 0 (0.0%) 6 (2.3%) 6 (2.5%) 4 (1.6%) 0 (0.0%) 22 (1.3%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) 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%) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 1 (0.1%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (0.1%) Total sequenced 139 (100%) 696 (100%) 34 (100%) 260 (100%) 242 (100%) 246 (100%) 141 (100%) 1,758 (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. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Case counts for these weeks may increase in subsequent reports. Public health unit was assigned based on diagnosing health unit in CCM. If a case did not link to CCM (3.3%), OCGN patient postal code was used or ordering provider postal code was used if patient postal code was missing. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program, CCM

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Table 5. Number and percentage (row %) of outbreak-associated and non outbreak- associated cases by VOC/VOI Pango lineage, representative surveillance, Ontario, August 8 to September 4, 2021

Pango lineage (WHO label) Outbreak-associated Non outbreak-associated Total cases Variant of concern Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 2 (5.9%) 32 (94.1%) 34 (100%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 0 (0.0%) 5 (100%) 5 (100%) B.1.617.2 (Delta) 891 (10.6%) 7,494 (89.4%) 8,385 (100%) Variant of interest Blank cell Blank Cell Blank Cell A.23.1 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.1.318 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%) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.526 (Iota) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.3 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 9 (12.0%) 66 (88.0%) 75 (100%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.3 (Theta) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 0 (0.0%) 2 (100%) 2 (100%) Total sequenced 902 (10.6%) 7,599 (89.4%) 8,501 (100%) Note: VOC/VOI designations include descendant lineages as defined by PHAC, ECDC, and WHO. Cases include only those that linked to CCM (96.7%). ‘Outbreak-associated cases’ include cases linked to a confirmed outbreak as declared by the local medical officer of health or their designate. The proportion of eligible samples sequenced by the Ontario COVID-19 Genomics Network (OCGN) decreased from 100% to 50% on August 27. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Data Sources: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Hamilton Regional Laboratory Medicine Program, The Shared Hospital Laboratory, CCM (outbreak Indicator)

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Table 6. Number and percentage (row %) of ever hospitalized and deceased cases by VOC/VOI Pango lineage, representative surveillance, Ontario, August 8 to September 4, 2021

Pango lineage (WHO label) Ever hospitalized Deceased Total cases Variant of concern Blank cell Blank cell Blank cell B.1.1.7 (Alpha) 2 (5.9%) 0 (0.0%) 34 (100%) B.1.351 (Beta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.1 (Gamma) 1 (20.0%) 0 (0.0%) 5 (100%) B.1.617.2 (Delta) 432 (5.2%) 47 (0.6%) 8,385 (100%) Variant of interest Blank cell Blank cell Blank Cell A.23.1 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.1.318 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%) B.1.525 (Eta) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.526 (Iota) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.1 (Kappa) 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.617.3 0 (0.0%) 0 (0.0%) 0 (0.0%) B.1.621 (Mu) 1 (1.3%) 0 (0.0%) 75 (100%) C.37 (Lambda) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.2 (Zeta) 0 (0.0%) 0 (0.0%) 0 (0.0%) P.3 (Theta) 0 (0.0%) 0 (0.0%) 0 (0.0%) Non-VOC/VOI 2 (100%) 0 (0.0%) 2 (100%) Total sequenced 438 (5.2%) 47 (0.6%) 8,501 (100%) Note: VOC/VOI designations include descendant lineages as defined by PHAC, ECDC, and WHO. Cases include only those that linked to CCM (96.7%). Hospitalized cases include cases that reported hospitalization at time of data extraction. Deceased cases include cases that reported a “Fatal” outcome at the time of data extraction. Hospitalized cases and deceased cases are not mutually exclusive. Results may not be representative of Ontario overall. The proportion of eligible samples sequenced by the Ontario COVID-19 Genomics Network (OCGN) decreased from 100% to 50% on August 27. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Not all sequencing and bioinformatics analyses for recent weeks were complete at the time of data extraction. Data Sources: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Hamilton Regional Laboratory Medicine Program, The Shared Hospital Laboratory, CCM (hospitalization and death indicators)

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Cumulative Whole Genome Sequencing Results

Table 7. Number of cases by VOC/VOI Pango lineage, cumulative counts, Ontario, January 1, 2021 to September 4, 2021

Pango lineage (WHO label) January 1 – August 7 August 8 – September 4 Total Variant of concern (VOC) Blank Cell Blank Cell Blank Cell B.1.1.7 (Alpha) 11,797 39 11,836 B.1.351 (Beta) 1,238 0 1,238 P.1 (Gamma) 3,921 6 3,927 B.1.617.2 (Delta) 7,795 8,927 16,722 Variant of interest (VOI) Blank Cell Blank Cell Blank Cell A.23.1 96 0 96 B.1.1.318 1,728 0 1,728 B.1.427/B.1.429 (Epsilon) 21 0 21 B.1.525 (Eta) 389 0 389 B.1.526 (Iota) 116 0 116 B.1.617.1 (Kappa) 89 0 89 B.1.617.3 3 0 3 B.1.621 (Mu) 148 81 229 C.37 (Lambda) 7 1 8 P.2 (Zeta) 46 0 46 P.3 (Theta) 1 0 1 Non-VOC/VOI 3,695 2 3,697 Total sequenced 31,090 9,056 40,146 Note: VOC/VOI designations include descendant lineages as defined by PHAC, ECDC, and WHO. Results do not represent all Ontario cases. Includes results from PHO since January 1, 2021, The Hospital for Sick Children since April 21, 2021, Kingston Health Sciences Centre since January 1, 2021, Shared Hospital Laboratory since March 26, 2021, and Hamilton Regional Laboratory Medicine Program since April 11, 2021. Past testing algorithms have led to preferential sequencing of samples with N501Y and/or E484K mutations detected by PCR, which has biased the results toward lineages with these mutations. Pango lineage assignments may change over time, which may impact cumulative totals. Results should be interpreted with caution as frequencies do not reflect prevalence. Sample date represents the earliest date available for the sample. If more than one sample was sequenced for a case, the most recent sample was included. Data source: PHO, The Hospital for Sick Children, Kingston Health Sciences Centre, Shared Hospital Laboratory, Hamilton Regional Laboratory Medicine Program

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Technical Notes

Data Sources Public Health Ontario (PHO)

 Data were extracted from the PHO Laboratory Information Management System on September 16 at approximately 5:00 a.m.

 Data were extracted from the PHO SARS-CoV-2 Whole Genome Sequencing Database on September 16 at approximately 9:00 a.m.

The Hospital for Sick Children (HSC)

 Data were received by PHO on September 15, 2021 at approximately 1:30 p.m.

Kingston Health Sciences Centre (KHSC)

 Data were received by PHO on September 15, 2021 at approximately 12:00 p.m.

Shared Hospital Laboratory (SHL)

 Data were received by PHO on September 15, 2021 at approximately 2:00 p.m.

Hamilton Regional Laboratory Medicine Program (HRLMP)

 Data were received by PHO on September 15, 2021 at approximately 6:20 p.m.

Public Health Case and Contact Management Solution (CCM)

 Data were extracted from the Public Health Case and Contact Management Solution on September 15 at approximately 1:00 p.m.

Ontario SARS-CoV-2 Whole Genome Sequencing Strategy  At the beginning of 2021, Ontario’s whole genome sequencing strategy was to sequence samples with specific mutations identified from VOC PCR testing to confirm they were variants of concern. From February 3, 2021 this included sequencing samples with the N501Y detected (initially associated with the B.1.1.7 [Alpha] lineage) and from March 22, 2021, samples with the E484K mutation detected (initially associated with the P.1 [Gamma] and B.1.351 [Beta] lineages).

 Ontario’s strategy has recently shifted to representative surveillance with VOC PCR testing laboratories being asked to send 10% of eligible samples (Ct ≤ 30 and sufficient volume remaining) to Ontario COVID-19 Genomics Network (OCGN) sequencing laboratories. PHO began sequencing a 10% systematic sample of eligible samples on May 2; 50% on May 30; 100% on June 14; 50% on August 27; and 10% on September 10. Other VOC PCR testing laboratories were asked to begin submitting a 10% systematic or random sample of eligible samples to OCGN laboratories on May 26; 50% on June 2; 100% on June 14; 50% on August 27; and 10% on

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September 10. The proportion of samples sequenced may change over time with changes in provincial case trends.

Data Caveats and Methods  Whole genome sequencing sample logistics are complex and require samples to be transferred across a large network of laboratories. Samples are initially sent to one of 73 diagnostic testing laboratories. If the diagnostic PCR cycle threshold is ≤ 35 and there is sufficient volume remaining, samples are submitted for testing at one of 11 VOC PCR testing laboratories. If the VOC PCR cycle threshold is ≤ 30 and there is sufficient volume remaining, VOC PCR testing laboratories have been asked to submit a proportion of their eligible samples to one of five OCGN laboratories for sequencing according to the surveillance strategy.

 The dates associated with samples submitted by network laboratories vary due to sample logistics and different laboratory information systems. Dates associated with WGS samples were assigned based on a hierarchy: sample collection date > SARS-CoV-2 diagnostic received date > SARS-CoV-2 diagnostic reported date > VOC PCR received date > VOC PCR reported date > WGS received date > WGS reported date. Weeks were created to align with surveillance weeks used by the Public Health Agency of Canada for influenza reporting.

 Samples from the same case were linked if they had the same health card number or if they had the same first name, last name, and date of birth. If more than one sample was sequenced for a case, the most recent sample was used. This may shift a case to a more recent week if a subsequent sample was sequenced from the same case. A small proportion of cases may have samples that were not linked due to inconsistencies or data entry errors.

 Lineage nomenclature is dynamic. Pango lineage naming and assignment may change as more samples are sequenced and analyzed globally. Similarly, VOC and VOI classifications may change.

Data Caveats and Methods: Representative Surveillance  Results may not be representative of Ontario overall. Samples selected include a proportion of eligible samples received by OCGN laboratories according to the whole genome sequencing strategy. Individual VOC PCR laboratories may have implemented the strategy and/or increased the proportion of samples selected on different dates.

 PHO is unable to confirm whether VOC PCR testing laboratories have submitted eligible samples.

 Results for recent weeks are incomplete as not all sequencing and bioinformatics analyses were complete at the time of data extraction.

 Public health unit was assigned using diagnosing health unit in CCM. If the case did not link to CCM (3.3%), then public health unit was assigned using OCGN patient postal code or ordering provider postal code if patient postal code was missing.

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Data Caveats and Methods: Public Health Case and Contact Management Solution (CCM)  CCM is a dynamic disease reporting system, which allows ongoing updates to data previously entered. As a result, data extracted from CCM represent a snapshot at the time of extraction and may differ from previous or subsequent reports.

 Methods for processing the CCM case data are described in the Technical Notes of the COVID- 19 Daily Epidemiological Summary

 Data corrections or updates can result in case records being removed and/or updated from past reports.

 Dates associated with COVID-19 cases in Ontario were assigned using a hierarchy to best align with the sample date used for representative surveillance: sample collection date > test reported date > case reported date. As a result, the number of cases may differ from other reports which use different dates.

 Case were linked to CCM if they had the same health card number or if they had the same first name, last name, and date of birth. Cases may not have linked to CCM due to discrepancies in patient identifiers or if they were not residents of Ontario (diagnosing health unit was reported as MOH).

 Tables for outbreak, hospitalized, and deceased indicators include only cases that linked to CCM (96.7% of cases).

 ‘Outbreak-associated cases’ include cases linked to a confirmed outbreak as declared by the local medical officer of health or their designate in accordance to the Health Protection and Promotion Act and criteria outlined in Ministry guidance documents.

 Outbreaks in settings outside of Ontario are excluded from all outbreak counts.

 Data on hospital admissions and deaths are likely under-reported as these events may occur after the completion of public health follow up of cases. Cases that were admitted to hospital or died after follow-up was completed may not be captured in CCM.

 Hospitalization includes all cases for which a hospital admission date was reported or hospitalization/ICU admission was reported as ‘Yes’ at the time of data extraction. It includes cases that have been discharged from hospital as well as cases that are currently hospitalized. Emergency room visits are not included in the number of reported hospitalizations.

 Deaths are determined by using the outcome field in CCM. Any case marked ‘Fatal’ is included in the deaths data. The CCM field Type of Death is not used to further categorize the data.

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Data Caveats and Methods: Cumulative Whole Genome Sequencing Results  The data included do not reflect all whole genome sequencing conducted in Ontario. Data from the OCGN laboratories cover different time periods: PHO since January 1, 2021, HSC since April 21, 2021, KHSC since January 1, 2021, SHL since March 26, 2021, and HRLMP since April 11, 2021.

 Past testing algorithms have led to preferential sequencing of samples with N501Y and/or E484K mutations detected by VOC PCR. This has created a sampling bias reflected in the distribution of lineage results. Data submitted to PHO from other laboratories in the OCGN have not been independently verified.

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References 1. Public Health Agency of Canada. SARS-CoV-2 variants: national definitions, classifications and public health actions [Internet]. Ottawa, ON: Government of Canada; 2021 [modified 2021 August 26; cited 2021 August 27]. Available from: https://www.canada.ca/en/public- health/services/diseases/2019-novel-coronavirus-infection/health-professionals/testing- diagnosing-case-reporting/sars-cov-2-variants-national-definitions-classifications-public-health- actions.html 2. World Health Organization. Tracking SARS-CoV-2 variants [Internet]. Geneva, Switzerland; 2021 [modified 2021 September 2; cited 2021 September 3]. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ 3. European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern as of 8 July 2021 [Internet]. Stockholm, Sweden; 2021 [modified 2021 August 26; cited 2021 August 27]. Available from: https://www.ecdc.europa.eu/en/covid-19/variants-concern 4. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7. Available from: https://doi.org/10.1038/s41564-020-0770-5 5. cov-lineages. pangolin [Internet]. 2020 [cited 2021 May 29]. GitHub. Available from: https://github.com/cov-lineages/pangolin

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Citation Ontario Agency for Health Protection and Promotion (Public Health Ontario). Epidemiologic summary: SARS-CoV-2 whole genome sequencing in Ontario, September 21, 2021. Toronto, ON: Queen’s Printer for Ontario; 2021. Disclaimer This document was developed by Public Health Ontario (PHO). PHO provides scientific and technical advice to Ontario’s government, public health organizations and health care providers. PHO’s work is guided by the current best available evidence at the time of publication. The application and use of this document is the responsibility of the user. PHO assumes no liability resulting from any such application or use. This document may be reproduced without permission for non-commercial purposes only and provided that appropriate credit is given to PHO. No changes and/or modifications may be made to this document without express written permission from PHO. For Further Information For more information, email [email protected]. Public Health Ontario Public Health Ontario is an agency of the Government of Ontario dedicated to protecting and promoting the health of all Ontarians and reducing inequities in health. Public Health Ontario links public health practitioners, front-line health workers and researchers to the best scientific intelligence and knowledge from around the world.

For more information about PHO, visit publichealthontario.ca.

©Queen’s Printer for Ontario, 2021

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