COVID-19 Variants

SARS-CoV-2, which causes COVID-19, is a virus from the Coronavirus family. Coronaviruses are named after the Latin word, “corona”, meaning “crown” because they express spike proteins on their surface which resembles the ‘thrones of a crown’. The spike protein is comprised of three domains: a short cytoplasmic tail, a transmembrane domain, and an ectodomain. The ectodomain is arguably the most critical structure of the virus because of its role in facilitating the entry of SARS-CoV-2 into host cells. The ectodomain has two general subunits which can be denoted as S1 and S2. To infect host cells, SARS-CoV-2 uses its spike S1 unit to bind to the host entry receptor, angiotensin-converting enzyme 2 (ACE2). Once bound, SARS-CoV-2 then uses the spike S2 unit to fuse its viral envelope with the cellular outermembrane in order to enter the host cell.

Viruses including SARS-CoV-2 can undergo change by acquiring genetic mutations to generate new variants of the virus. As these new variants emerge, some will persist if their mutations improve their virulence and/or transmissibility. As a result, a major concern about the ongoing genetic evolution of SARS-CoV-2 is that the virus could acquire mutations to its spike protein that will improve the virus’ transmissibility and/or disguise its detection from the immune system.

As of February 23, 2021, there have been 3  SARS-CoV-2 Variants of concern (VOC) that have emerged and undergone transmission around the world. A variant becomes a concern when it exhibits features of increased infectivity and/or transmissibility.

Updated February 23, 2021
Authored and maintained by Toby Le

Variant of Concern:  B.1.1.7

Other Names: 202012/01

Location of Origin: UK

Initial Emergence: September, 2020

Impact on Vaccine Efficacy

  • January 19, 2021: Pfizer and BioNTech constructed a pseudovirus with the B1.1.7 variant mutation, N501Y. The company tested their vaccine, BNT162b2, against the pseudovirus and found the protective efficacy to remain unaffected [1]
  • January 25, 2021: Moderna Inc. announced their vaccine, mRNA-1273, was able to induce similar levels of neutralizing antibodies against the B.1.1.7 variant as prior variants [2,3]
  • January 28, 2021: Novavax announced results from their phase 3 clinical trials in the United Kingdom showing their vaccine, NVX-CoV2373, had a protective efficacy of 89.3% against SARS-CoV-2[4]. About 50% of PCR-confirmed symptomatic cases from their placebo group, who did not receive the vaccine, were infected by the B.1.1.7 variant. Thus, these results suggest that the NVX-CoV2373 vaccine can still confer protection against the B.1.1.7 variant

Impact on Transmission

  • December 18, 2021:  UK’s New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) released a report suggesting that B.1.1.7 exhibits a higher rate of transmission than previous SARS-CoV-2 strains [5]. Within three months of its emergence (September), the B.1.1.7 variant has become the predominant circulating strain in the UK [6]
  • January 7, 2021: One peer-reviewed study detected a 75% increase in transmissibility of the B.1.1.7 variant than the original strain  [7]

Arrival to Canada

  • December 26, 2020: Ontario confirmed Canada’s first cases of the B.1.1.7 variant in two individuals from Toronto [8–10]
  • December 27, 2020: British Columbia confirms first positive case of the B.1.1.7 variant from an individual that returned from the UK on December 15th [11] 
  • December 25, 2020: Alberta confirmed first positive case of the B.1.1.7 variant from an individual that recently travelled to the UK [12,13]
  • December 29, 2020: Quebec confirmed first case of the B.1.1.7 variant from an individual whose family member travelled to the UK and returned on December 11. The traveller was then tested positive for COVID-19 on December 13th. The traveller continued follow quarantine rules and remained at home with three members of their immediate family. The B.1.1.7 variant was later confirmed in a member of this family. Further testing revealed all three members to be infected with COVID-19 [14–17]
  • January 22, 2021: Nova Scotia confirmed first two variant cases of COVID-19, B.1.1.7 and B.1.351. Both cases were associated with international travel and did not result in community transmission [18,19]
  • February 2, 2021: Saskatchewan confirmed first two positive cases of the B.1.1.7 variant infection in two residents from Regina [20,21].  Two days later, Saskatchewan confirmed first case of B.1.1.7 variant infection in Saskatoon [22]
  • February 2, 2021: New Brunswick confirmed first three cases of the B.1.1.7 variant; 2 from the St. John area and 1 one from the Miramichi area. Two of the cases were linked to international traveling, whereas the one case was linked to travel within Canada [23]
  • February 9, 2021: Manitoba confirmed first case of the B.1.1.7 variant from a sample that was collected on January 22, 2021. The case has been linked to international travel. Further reports revealed the infected individual was in contact with 5 other people, all of whom remained negative for COVID-19  to date [24,25].
  • February 12, 2021: Newfoundland and Labrador confirmed an outbreak of the B.1.1.7 variant in St John’s Metro region. Pre-liminary testing of 19 cases sent by the Newfoundland and Labrador government found all samples to be positive for the B.1.1.7 variant [26]
  • February 13, 2021: Prince Edward Island confirmed first case of B.1.1.7 variant which has been linked to international travel. The individual was reported to be their 20s and had no close contacts upon their return to Canada [27,28].

Risk to Canadians

  • December 12, 2020: Public Health England releases a report suggesting that the B.1.1.7 variant can evade detection by PCR assays which use the ‘S’ gene as the amplification target, also known as a S gene target failure (SGTF) [29–31]
  • January 8, 2021: Long-term care home, Roberta House, from Barrie Ontario was deemed to be in a COVID-19 outbreak
    • January 2: preliminary testing detected 6 positive cases were from the B.1.1.7 variant. This variant was believed to have spread onto at least 21 household members of staff and those that visited the facility [32]
    • January 26, 2021: The Simcoe Muskoka District Health Unit discovered over 100 cases of the B.1.1.7 variant which were linked to the Roberta House outbreak [33]
    • February 8, 2021: Reports found 129 residents at Roberta House to be positive for COVID-19 in which 69 have died [34,35]
    • February 9, 2021: 65 cases of  infected residents were confirmed to be from the B.1.1.7 variant. 18 additional cases have been screened positive for presence of mutation and will require further validation of the variant [36].
  • January 25, 2021: Alberta confirmed its first case of B.1.1.7 variant without links to travel exposure. Alberta’s Minister of Health, Tyler Shandro, shares the concern that the variant may have begun circulating inside the community [37].
  • February 11, 2021: Scientific experts predict that the B.1.1.7 variant will eventually become the dominant strain of SARS-CoV-2 in Ontario. Cases of the B.1.1.7 variant are believed to increase in late February [38]
  • February 12,2021: According to a pre-print study, the B.1.1.7 variant was able to accelerate its transmission in the Greater Toronto Area by 1.8 fold per week during the month of January [39]
  • February 12, 2021: Newfoundland and Labrador government declared outbreak in St. John area due to a spike in positive cases for SARS-CoV-2. The province has transitioned to Alert Level 5 with the assumption that the variant B.1.1.7 is responsible for the outbreak. Pre-liminary testing of 19 cases sent by the Newfoundland and Labrador government found all samples to be positive for the B.1.1.7 variant [26]
  • February 13, 2021: In a modeling study by epidemiologist Caroline Colijn, researcher shows that failure to contain and prevent transmission of the B.1.1.7 variant can lead to an outbreak in March with more than 5,000 cases per day in British Columbia, Ontario, and Saskatchewan [40]

Disease Severity

January 21, 2021: NERVTAG published a report suggesting that B.1.1.7 was linked to a 30% increase in risk of death compared to previous strains [41]. The same report also identified several limitations in their conclusion including their small sample size

Critical Mutations

  • N501Y: Mutation at genomic position 501 in the receptor binding domain (RBD) of the spike protein. This resulted in an amino acid change from asparagine (N) to tyrosine (Y)
  • P681H: Mutation at the cleavage site of the spike protein [42]

Variant of Concern   P.1

Other Names: B.1.1.248

Initial Date of Emergence: December 2020

Initial Location: Brazil

Impact Vaccine Efficacy

  • January 25, 2021: Due to its mutation similarities with the B.1.1.7 variant, researchers predict that the Moderna vaccine will be equally protective against both variants [39]

Impact on Transmission

  • December 16-23: Researchers discovered 13 out of 31 (42%)  RT-PCR tests in Manaus, Brazil to be positive for the new P.1 variant. Data were published onto a public domain on January 12, 2021 [43]
  • January 25, 2021: Minnesota confirmed America’s first case of the P.1 variant [44].
  • January 12, 2021: The Center for Arbovirus Discovery, Diagnostics, Genomics, and Epidemiology (CADDE) Genomic Network reported 85% of genotyped samples from Manaus Brazil to be from the P.1 variant [45]
  • January 27, 2021: Researchers declared the P.1 variant as the dominant SARS-CoV-2 strain in Manaus Brazil [46,47]

Arrival to Canada

  • February 8, 2021: Ontario confirmed Canada’s first case of the P.1 variant in Toronto, Ontario. The case was linked to international travel to Brazil [49].

Risk to Canadians

No Data (2021-02-14)

Disease Severity

No Data (2021-02-14

Notable Mutations

  • Three mutations in the receptor binding domain (RBD) of the spike protein: N501Y, K417T and E484K
  • Consists of 3 deletions and 17 unique changes in amino acid sequence [42]

Variant Lineage:  B.1.351

Other Names: 501Y.V2

Initial Date of Emergence: October 2020

Initial Location: South Africa

Impact Vaccine Efficacy

  • January 25, 2021: Moderna Inc. found a six-fold reduction in the neutralizing titer induced by their vaccine, mRNA-1273,  in response to the B.1.351 variant. Despite the reduced efficacy, the neutralizing titers remained above levels required for protection against SARS-CoV-2 infection [2,3]. Moderna Inc. is looking to study how an additional booster of its vaccine can impact the level of neutralizing titers against the B.1.351 variant. Additionally, the company is also seeking to develop a booster vaccine, mRNA- 1273.351, against the B.1.351 variant [2]
  • January 28, 2021: Novavax shared interim results from its clinical trial in South Africa, revealing reduced protective efficacy (40-60%) of its vaccine against the variant B.1.351 [4]
  • January 29, 2021: Johnson & Johnson, also the only drug corporation that is developing a one-shot vaccine, released results from its phase 3 vaccine trials in the United States, Latin America, and South Africa. Analysis of the results found the vaccine efficacy to be 72%, 66%, and 57% in the United States, Latin America, and South Africa,  respectively. The reduced vaccine efficacy found in the South African clinical trial has been attributed to the B.1.351 variant [50,51]. The study data is currently peer-review.
  • February 7, 2021: AstraZeneca released vaccine trial results in South Africa showing reduced vaccine efficacy against the B.1.351 variant [52]. The study is currently under peer-review.

Impact on Transmission

  • December 23, 2020: Professor Salim Abdool Karim, Chairperson of the COVID-19 Ministerial Advisory Committee, suggests there is evidence that the B.1.351 variant is 50% more infectious than previous strains [53]. This study is currently under peer-review (2021-02-14)
  • January 28, 2021: The United States’ first two cases of B.1.351 variant was detected in South Carolina [54,55]

Arrival to Canada

  • January 8, 2021: Alberta confirmed Canada’s first case of the B.1.351 variant [56]
  • January 14, 2021: British Columbia confirmed first case of B.1.351 variant [57,58]
  • January 22, 2021: Nova Scotia confirmed first two variant cases of COVID-19, B.1.1.7 and B.1.351. Both cases were associated with international travel and did not result in community transmission [18]
  • February 2,2021: Ontario confirmed first case of B.1.351 in the Peel region of Southern Ontario [59]
  • February 9, 2021: Quebec confirmed first two cases of the B.1.351 variant in Abitibi-Témiscamingue of Western Quebec. Both cases had no history of international travel [60–62]

Risk to Canadians

  • January 28, 2021: Novavax Inc. releases findings from their phase 3 and 2b clinical trials in the United Kingdom and South Africa, respectively. In their preliminary analysis, they have provided data suggesting that patients who were previously infected with the original SARS-CoV-2 strain can still be re-infected with the B.1.351 strain [4]. Data was later published in the following report [63]
  • February 9, 2021: According to Quebec’s Public Health Director, Dr. Horacio Arruda, the B.1.351 may have been responsible for two COVID-19 outbreaks in Abitibi-Témiscamingue during January, 2021. According to Abitibi-Témiscamingue’s medical officer, Dr. Omobola Sobanjo, preliminary results suggest  that up to 30 cases can be directly linked back to the two first cases of B.1.351 in Quebec  [60–62]

Disease Severity

No Data (2021-02-14)

Notable Mutations

  • Acquired several mutations in the spike proteins: N501Y, E484K, K417N, D614G, and A701V [42]

Updates about Vaccine Development

  • January 25, 2021: Moderna Inc. is looking to study how an additional booster of its vaccine can impact the level of neutralizing titers against the B.1.351 variant. Additionally, the company is also seeking to develop a booster vaccine, mRNA- 1273.351, against the B.1.351 variant [2,3].
  • February 4, 2021: Johnson & Johnson is pursuing Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for its single-dose vaccine, Janssen [64]
  • February 7, 2021: AstraZeneca is developing a 2nd generation vaccine that is effective against the B.1.351 variant. This is a response to its recent clinical trials in South Africa where researchers deemed the AstraZeneca to be ineffective against the B.1.351 variant [52]
  • February 7, 2021: South Africa halted their rollout of the AstraZeneca vaccines due to its reduced efficacy against the B.1.351 variant [65]
  • February 10, 2021: South Africa replaced its original vaccine candidate, AstraZeneca, with the Johnson & Johnson vaccine, which has not yet been approved by the U.S. Food and Drug Administration and the South Africa’s regulatory authority. The South African government intends to provide this vaccine to its front-line health workers in the following week [66,67].
  • February 19, 2021: Pfizer submits vaccine stability data to the Food and Drug Administration (FDA) revealing that their vaccine, BNT162b2, can be stored at higher temperatures between -25 to -15 °C. This current label requires that the vaccine be stored between -80 to -60 °C. New storage conditions is currently pending approval from the FDA [68,69] 

Key Events

  • September, 2020: Emergence of B.1.1.7 variant in the United Kingdom
  • October, 2020: Emergence of B.1.351 variant in South Africa
  • December 2020: Emergence of P.1 variant in Brazil
  • December 26, 2020: Ontario confirmed Canada’s first cases of the B.1.1.7 variant in two individuals from Toronto [8–10]
  • January 8, 2021: Alberta confirmed Canada’s first case of the B.1.351 variant [56].
  • January 25, 2021: Moderna Inc. is looking to study how an additional booster of its vaccine can impact the level of neutralizing titers against the B.1.351 variant. Additionally, the company is also seeking to develop a booster vaccine, mRNA- 1273.351, against the B.1.351 variant [2,3].
  • January 27, 2021: Researchers declared the P.1 variant as the dominant SARS-CoV-2 strain in Manaus Brazil [47,48]
  • February 7, 2021: South Africa halted their rollout of the AstraZeneca vaccines due to its reduced efficacy against the B.1.351 variant [65]
  • February 7, 2021: AstraZeneca is developing a 2nd generation vaccine that is effective against the B.1.351 variant. This is a response to its recent clinical trials in South Africa where researchers deemed the AstraZeneca to be ineffective against the B.1.351 variant [52]
  • February 8, 2021: Ontario confirmed Canada’s first case of the P.1 variant in Toronto, Ontario. The case was linked to international travel to Brazil [49].
  • February 10, 2021: South Africa replaced its original vaccine candidate, AstraZeneca, with the Johnson & Johnson vaccine, which has not yet been approved by the U.S. Food and Drug Administration and the South Africa’s regulatory authority. The South African government intends to provide this vaccine to its front-line health workers in the following week [66,67]. 
  • February 19, 2021: The Public Health Agency of Canada (PHAC) released modeling predicting a high resurgence in COVID-19 cases if stringent public health measures are not implemented as vaccine programs expand [70]

COVID-19 Variant Cases in Canada

For up-to-date tracking of COVID-19 variants by province, visit CTV News.

Global COVID-19 Variant Trackers

NextStrain

This phylogeny shows evolutionary relationships of SARS-CoV-2 viruses from the ongoing COVID-19 pandemic. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of specific transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred geographic transmission patterns and temporal estimates are only a hypothesis.

GSAID

GSAID obtained COVID-19 virus sequence data from several sources in Saudi Arabia (CDC, Hospitals) and worldwide. They process genome isolates to first obtain a fingerprint of mutations appearing in sampled populations across different locations, which helps to understand COVID-19 virus variants and their infection track.

Additional GSAID COVID-19 variant tracker featuring relative variant genome frequency per region.

More Information on Variants

https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm?s_cid=mm7003e2_e
https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.ht
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html
https://cov-lineages.org/global_report.html
https://www.nytimes.com/interactive/2021/health/coronavirus-variant-tracker.html

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