Variants of SARS-CoV-2

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are or have been believed to be of particular importance. This article deals with such notable variants.

The sequence WIV04/2019 is thought likely to be the original sequence infecting humans, known as "sequence zero".[1]

Nomenclature

SARS-CoV-2 corresponding nomenclatures[2]
Rambaut et al. () lineages Notes to Rambaut et al.[3] Nextstrain () clades, 2020 GISAID clades Notable variants or mutations
A.1–A.6 19B S
B.3–B.7, B.9, B.10, B.13–B.16 19A L
O[lower-alpha 1]
B.2 V
B.1 B.1.5–B.1.72 20A G Lineage B.1 in the Rambaut et al. () system includes variants with mutation D614G[citation needed]
B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 GH
B.1.3–B.1.66 20C Includes 501.V2 aka 20C/501Y.V2 or B.1.351 lineage
B.1.1 20B GR Includes VOC-202012/01 aka 20B/501Y.V1 or lineage B.1.1.7, B.1.1.207, and B.1.1.284
B.1.177 20A.EU1[4], 20E (EU1)[5] GV[lower-alpha 1]

While there are many thousands of variants of SARS-CoV-2,[7] there are also much larger groupings called clades. Several different clade nomenclatures for SARS-CoV-2 have been proposed.

  • As of December 2020, GISAID—referring to SARS-CoV-2 as hCoV-19[8]—identified seven clades (O, S, L, V, G, GH, and GR).[9]
  • Also as of December 2020, Nextstrain identified five (19A, 19B, 20A, 20B, and 20C).[10]
  • In an article in the November 2020 issue of International Journal of Infectious Diseases, Guan et al. identified five global clades (G614, S84, V251, I378 and D392).[11]
  • Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN) software team proposed that lineages be used for subtypes of SARS-CoV-2 in a 2020 article in Nature Microbiology;[12] as of December 2020, there have been five major lineages (A, B, B.1, B.1.1, and B.1.177) identified.[13]

As of January 2021, the World Health Organization is working on "standard nomenclature for variants that does not reference a geographical location".[14]

Notable variants

Lineage B.1.1.207

First sequenced in August 2020,[15] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[16] Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with UK's VOC-202012/01. It shares no other mutations with VOC-202012/01 and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.[15]

Variant of Concern 202012/01

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Main article: Variant of Concern 202012/01

First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month,[17] Variant of Concern 202012/01 (VOC-202012/01),[18] was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[19] and also as lineage B.1.1.7 or 20B/501Y.V1.[3][20][21] Since then, its prevalence odds have doubled every 6.5 days, the presumed generational interval.[22][23] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation.

Cluster 5

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Main article: Cluster 5

In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[24] was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[25]

The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".[26] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[27]

501.V2 variant

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Main article: 501.V2 variant

On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20C/501Y.V2 or lineage B.1.351,[21] was first detected in South Africa and reported by the country's health department.[28] Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases.[29][30] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[28][29]

Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[28][31] K417N, and E484K.[32][33] The N501Y mutation has also been detected in the United Kingdom.[28][34]

Lineage B.1.1.248

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Main article: Lineage B.1.1.248

Lineage B.1.1.248[35] was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new variant isolate was found in four people who arrived in Tokyo having travelled from the Amazonas state on 2 January 2021.[36] The Brazilian state-run Oswaldo Cruz Foundation has confirmed its belief that the variant had been circulating in the Amazon rain forest.[37] This variant of SARS-CoV-2 has 12 mutations in its spike protein, including N501Y and E484K.[38]

A preprint of a paper by Carolina M Voloch et al. identified a novel lineage of SARS-CoV-2, 'B.1.1.248', in circulation in Brazil, which originated from B.1.1.28. It describes it as first emerging in July and first detected by themselves in October, but as of publishing (December 2020), although significantly increased in frequency, still largely confined to the state capital of Rio de Janeiro.[39] In May the majority of their samples had been of lineage B.1.1.33 whereas by September there was significant spread of B.1.1.28, and during October and November the novel variant lineage (B.1.1.248) predominated over respectively 3 and 4 other classifications using the Pangolin tool.[40] The paper identifies the change E484K (present in both B.1.1.28 and B.1.1.248) as "widely spread" across the samples (for example, 36 out of the 38 samples in one set).[40]

Notable mutations

D614G

D614G is a mutation that affects the spike protein of SARS-CoV-2. The frequency of this mutation in the viral population has increased during the pandemic. G (glycine) has replaced D (aspartic acid) in many countries, especially in Europe though more slowly in China and the rest of East Asia, supporting the hypothesis that G increases the transmission rate, which is consistent with higher viral titers and infectivity in vitro.[1] In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic.[41][42][43][44] PHE confirmed that the D614G mutation had a "moderate effect on transmissibility" and was being tracked internationally.[45]

The global prevalence of D614G correlates with the prevalence of loss of smell (anosmia) as a symptom of COVID-19, possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.[46]

Variants containing the D614G mutation are considered to be part of the G clade by GISAID[1] and the B.1 clade by the PANGOLIN tool.[47]

E484K

E484K has been reported to be an "escape mutation" from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a "possible change in antigenicity".[35] B.1.1.248 (Brazil/Japan) and 501.V2 (South Africa) both exhibit this mutation.[35] The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[48]

N501Y

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[45] This change is believed by Public Health England to increase binding affinity because of its the position inside the spike glycoprotein's receptor-binding domain, which binds ACE2 in human cells;[49] data also support the hypothesis of increased binding affinity from this change.[49] Variants with N501Y include B.1.1.248 (Brazil/Japan),[35] Variant of Concern 202012/01 (UK), 501.V2 (South Africa), and COH.20G/501Y (Columbus, Ohio). This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.[50][51]

Summary

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First detection Rambaut et al. () classification Other names GISAID clade Notable mutations Clinical changes Spread
Location Date Transmissibility Virulence Antigenicity
 Nigeria August 2020 B.1.1.207 GR P681H[16] No No evidence of change No No evidence of change No No evidence of change
 United Kingdom October 2020 B.1.1.7 VOC-202012/01;
20B/501Y.V1		 GR N501Y[52]
69–70del[52]
P681H[52]		 Yes Evidence of increased transmissibility (PHE) No No evidence of change No No evidence of change Global
 Denmark October 2020 Cluster 5;
ΔFVI-spike (SSI)[24]		 Y453F[24]
69–70deltaHV[24]		 No No evidence of change No No evidence of change Yes "Moderately decreased sensitivity to neutralising antibodies"[26] Likely extinct[27]
 South Africa December 2020 B.1.351 501.V2; 20C/501Y.V2 GH N501Y; K417N; E484K[33] Yes Evidence of increased transmissibility (SADoH) No No evidence of change Undergoing investigation (E484K mutant) Global
 Japan
 Brazil		 January 2021 B.1.1.248 N501Y; E484K[38][40] Undergoing investigation (N501Y mutant) No No evidence of change Undergoing investigation (E484K mutant) Global

See also

  • RaTG13, the closest known relative to SARS-CoV-2

References

Explanatory notes
  1. ↑ 1.0 1.1 In another source, GISAID name a set of 7 clades without the O clade but including a V clade.[6]
Sources
  1. ↑ 1.0 1.1 1.2 Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ This table is an adaptation and expansion of Alm et al. (), figure 1.
  3. ↑ 3.0 3.1 Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  6. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ Lua error in package.lua at line 80: module 'strict' not found. Cited in Alm et al. ().
  11. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  12. ↑ Lua error in package.lua at line 80: module 'strict' not found. Cited in Alm et al. ()
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ 15.0 15.1 Lua error in package.lua at line 80: module 'strict' not found.
  16. ↑ 16.0 16.1 Lua error in package.lua at line 80: module 'strict' not found.
  17. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  18. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  19. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  20. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  21. ↑ 21.0 21.1 Lua error in package.lua at line 80: module 'strict' not found.
  22. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  23. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  24. ↑ 24.0 24.1 24.2 24.3 Lua error in package.lua at line 80: module 'strict' not found.
  25. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  26. ↑ 26.0 26.1 Lua error in package.lua at line 80: module 'strict' not found.
  27. ↑ 27.0 27.1 Lua error in package.lua at line 80: module 'strict' not found.
  28. ↑ 28.0 28.1 28.2 28.3 Lua error in package.lua at line 80: module 'strict' not found.
  29. ↑ 29.0 29.1 Lua error in package.lua at line 80: module 'strict' not found.
  30. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  31. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  32. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  33. ↑ 33.0 33.1 Lua error in package.lua at line 80: module 'strict' not found.
  34. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  35. ↑ 35.0 35.1 35.2 35.3 Lua error in package.lua at line 80: module 'strict' not found.
  36. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  37. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  38. ↑ 38.0 38.1 Lua error in package.lua at line 80: module 'strict' not found.
  39. ↑ Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil (Abstract) Carolina M Voloch et al. via www.medrxiv.org, accessed 15 January 2021 doi.org/10.1101/2020.12.23.20248598
  40. ↑ 40.0 40.1 40.2 Voloch, Carolina M.; et al. (2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil" full text (see figure 5). Retrieved 15 January 2021. doi:10.1101/2020.12.23.20248598 – via Medarxiv.
  41. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  42. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  43. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  44. ↑ SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo "an emergent Asp614→Gly (D614G) substitution in the spike glycoprotein of SARS-CoV-2 strains that is now the most prevalent form globally" 18 December 2020 science.sciencemag.org, accessed 14 January 2021 DOI: 10.1126/science.abe8499
  45. ↑ 45.0 45.1 Lua error in package.lua at line 80: module 'strict' not found.
  46. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  47. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  48. ↑ Michael Greenwood (15 January 2021). "What Mutations of SARS-CoV-2 are Causing Concern?". News Medical. Retrieved 16 January 2021.
  49. ↑ 49.0 49.1 Chand et al. (), "Potential impact of spike variant N501Y" (p. 6).
  50. ↑ Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio 13 January 2021, wexnermedical.osu.edu, accessed 16 January 2021
  51. ↑ Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio Huolin Tu, et al. 15 January 2021 via www.biorxiv.org, accessed 16 January 2021, doi.org/10.1101/2021.01.12.426407
  52. ↑ 52.0 52.1 52.2 Chand et al (), p. 6.
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