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The [[World Health Organization]] (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".<ref name=":1">{{Cite news|date=2020-11-08|title=6 countries find coronavirus at mink farms; fears mutation could hinder vaccine|work=[[The Times of Israel]]|url=https://www.timesofisrael.com/6-countries-find-coronavirus-at-mink-farms-fears-mutation-could-hinder-vaccine/|access-date=2020-11-09|quote=Italy, the Netherlands, Spain and Sweden are the other nations to have discovered SARS-CoV-2 in minks, WHO said in a statement.}}</ref> SSI warned that the mutation could reduce the effect of [[COVID-19 vaccine]]s 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.<ref name=sum19nov>{{cite web|title=De fleste restriktioner læmpes i Nordjylland|trans-title=most restrictions eased in North Jutland|url=https://www.sum.dk/Aktuelt/Nyheder/Coronavirus/2020/November/De-fleste-restriktioner-lempes-i-Nordjylland.aspx|publisher=Sundheds- og Ældreministeriet|date=19 November 2020}}</ref>
The [[World Health Organization]] (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".<ref name=":1">{{Cite news|date=2020-11-08|title=6 countries find coronavirus at mink farms; fears mutation could hinder vaccine|work=[[The Times of Israel]]|url=https://www.timesofisrael.com/6-countries-find-coronavirus-at-mink-farms-fears-mutation-could-hinder-vaccine/|access-date=2020-11-09|quote=Italy, the Netherlands, Spain and Sweden are the other nations to have discovered SARS-CoV-2 in minks, WHO said in a statement.}}</ref> SSI warned that the mutation could reduce the effect of [[COVID-19 vaccine]]s 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.<ref name=sum19nov>{{cite web|title=De fleste restriktioner læmpes i Nordjylland|trans-title=most restrictions eased in North Jutland|url=https://www.sum.dk/Aktuelt/Nyheder/Coronavirus/2020/November/De-fleste-restriktioner-lempes-i-Nordjylland.aspx|publisher=Sundheds- og Ældreministeriet|date=19 November 2020}}</ref>


=== B.1.207 ===
=== B.1.1.207 ===
Sequencing by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria discovered a variant with a P681H mutation, shared in common with [[VOC-202012/01]]. First sequenced in August,<ref name=":0">{{Cite web|date=2020-12-23|title=Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria|url=https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567|access-date=2021-01-01|website=Virological|language=en-US}}</ref> the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US [[Centers for Disease Control and Prevention|Centers for Disease Control]].<ref name=":2">{{Cite web|last=CDC|date=2020-02-11|title=Coronavirus Disease 2019 (COVID-19)|url=https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html|access-date=2021-01-01|website=Centers for Disease Control and Prevention|language=en-us}}</ref> 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.<ref name=":0" /> The site of mutation is highly variable in coronaviruses.<ref name=":2" />
Sequencing by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria discovered a variant with a P681H mutation, shared in common with [[VOC-202012/01]]. First sequenced in August,<ref name=":0">{{Cite web|date=2020-12-23|title=Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria|url=https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567|access-date=2021-01-01|website=Virological|language=en-US}}</ref> the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US [[Centers for Disease Control and Prevention|Centers for Disease Control]].<ref name=":2">{{Cite web|last=CDC|date=2020-02-11|title=Coronavirus Disease 2019 (COVID-19)|url=https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html|access-date=2021-01-01|website=Centers for Disease Control and Prevention|language=en-us}}</ref> 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.<ref name=":0" /> The site of mutation is highly variable in coronaviruses.<ref name=":2" />


Revision as of 18:36, 5 January 2021

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has several notable variants that are believed or have been believed to be of particular importance. The sequence WIV04/2019 is thought likely to be the original sequence infecting humans, known as "sequence zero".[1]

Clades

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

Notable variants

Involving N501Y

N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501,[9] believed by Public Health England to increase binding affinity.[10]

501.V2

Main article: 501.V2 variant

501.V2 variant, also known as 501.V2, 20C/501Y.V2 or B.1.351 lineage,[11] was first detected in South Africa and reported by the country's health department on 18 December 2020.[12] 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.[13][14] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 pandemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[12][13]

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,[12][15] K417N, and E484K.[16][17] The N501Y mutation has also been detected in the United Kingdom.[12][18]

Variant of Concern 202012/01

Main article: Variant of Concern 202012/01

Variant of Concern 202012/01 (VOC-202012/01),[19] previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[20] and also as lineage B.1.1.7 or 20B/501Y.V1,[21][22][11] was first detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month.[23] Since then, its prevalance odds have doubled every 6.5 days, the presumed generational interval.[24][25] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom. This increase is thought to be at least partly because of change N501Y inside the spike glycoprotein's receptor-binding domain, which is needed for binding to ACE2 in human cells.

Cluster 5

Main article: Cluster 5

Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[26] 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.

The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".[27] 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.[28]

B.1.1.207

Sequencing by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria discovered a variant with a P681H mutation, shared in common with VOC-202012/01. First sequenced in August,[29] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[30] 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.[29] The site of mutation is highly variable in coronaviruses.[30]

D614G

D614G is a variant that affects the spike protein of SARS-CoV-2. The G variant (glycine at position 614) has increased in frequency during the pandemic, probably after initially arising in China and then spreading to Italy in January and globally from there. G 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.[31][32][33]

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 G variant to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.[34]

Viruses containing the G variant are considered to be part of the G clade by GISAID and the B1 clade by the Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN) tool.[1][35]

References

  1. ^ a b c Zhukova, A; Blassel, L; Lemoine, F; Morel, M; Voznica, J; Gascuel, O (2020-11-24). "Origin, evolution and global spread of SARS-CoV-2". Comptes Rendus Biologie: 1–20. doi:10.5802/crbiol.29. PMID 33274614.
  2. ^ Koyama, Takahiko; Platt, Daniel; Parida, Laxmi (June 2020). "Variant analysis of SARS-CoV-2 genomes". Bulletin of the World Health Organization. 98 (7): 495–504. doi:10.2471/BLT.20.253591. PMC 7375210. PMID 32742035. We detected in total 65776 variants with 5775 distinct variants.
  3. ^ Alm, E.; Broberg, E. K.; Connor, T.; Hodcroft, E. B.; Komissarov, A. B.; Maurer-Stroh, S.; Melidou, A.; Neher, R. A.; O’Toole, Áine; Pereyaslov, D.; The WHO European Region sequencing laboratories and GISAID EpiCoV group; et al. (2020). "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Euro Surveillance: Bulletin Europeen Sur les Maladies Transmissibles = European Communicable Disease Bulletin. 25 (32). doi:10.2807/1560-7917.ES.2020.25.32.2001410. PMC 7427299. PMID 32794443.
  4. ^ "hCoV-19 clades" (JPG). www.gisaid.org. Retrieved 24 December 2020.
  5. ^ "Nextclade". clades.nextstrain.org. Retrieved 24 December 2020. Cited in Alm et al. (2020).
  6. ^ Guan, Qingtian; et al. (2020). "A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic". International Journal of Infectious Diseases. 100: 216–223. doi:10.1016/j.ijid.2020.08.052. PMC 7443060. PMID 32841689.
  7. ^ Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMID 32669681. S2CID 220544096. Cited in Alm et al. (2020).
  8. ^ "Lineages". cov-lineages.org. Retrieved 24 December 2020.
  9. ^ COG-UK update on SARS-CoV-2 Spike mutations of special interest: Report 1 (PDF) (Report). COVID-19 Genomics UK Consortium (COG-UK). 20 December 2020. p. 7.
  10. ^ Chand et al. (2020), "Potential impact of spike variant N501Y" (p. 6).
  11. ^ a b CDC. "Emerging SARS-CoV-2 Variants". Centers for Disease Control and Prevention. Retrieved 2021-01-04.
  12. ^ a b c d "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
  13. ^ a b Wroughton, Lesley; Bearak, Max (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Retrieved 20 December 2020.
  14. ^ Mkhize, Dr Zwelini (18 December 2020). "Update on Covid-19 (18th December 2020)" (Press release). South Africa. COVID-19 South African Online Portal. Retrieved 2020-12-23. Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick.
  15. ^ Abdool Karim, Salim S. (19 December 2020). "The 2nd Covid-19 wave in South Africa:Transmissibility & a 501.V2 variant, 11th slide". www.scribd.com.
  16. ^ Statement of the WHO Working Group on COVID-19 Animal Models (WHO-COM) about the UK and South African SARS-CoV-2 new variants (PDF), World Health Organization, 2020-12-22, retrieved 2020-12-23
  17. ^ Lowe, Derek (22 December 2020). "The New Mutations". In The Pipeline. American Association for the Advancement of Science. Retrieved 23 December 2020. I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
  18. ^ "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Retrieved 2020-12-23.
  19. ^ Chand, Meera; Hopkins, Susan; Dabrera, Gavin; Achison, Christina; Barclay, Wendy; Ferguson, Neil; Volz, Erik; Loman, Nick; Rambaut, Andrew; Barrett, Jeff (21 December 2020). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 (PDF) (Report). Public Health England. Retrieved 23 December 2020.
  20. ^ "PHE investigating a novel strain of COVID-19". Public Health England. 14 December 2020.
  21. ^ Rambaut, Andrew; Loman, Nick; Pybus, Oliver; Barclay, Wendy; Barrett, Jeff; Carabelli, Alesandro; Connor, Tom; Peacock, Tom; L. Robertson, David; Vol, Erik (2020). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations (Report). Written on behalf of COVID-19 Genomics Consortium UK. Retrieved 20 December 2020.{{cite report}}: CS1 maint: multiple names: authors list (link)
  22. ^ Kupferschmidt, Kai (20 December 2020). "Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear". Science Mag. Retrieved 21 December 2020.
  23. ^ "Covid: Ireland, Italy, Belgium and Netherlands ban flights from UK". BBC News. 20 December 2020.
  24. ^ "New evidence on VUI-202012/01 and review of the public health risk assessment".
  25. ^ "COG-UK Showcase Event - YouTube". www.youtube.com. Retrieved 2020-12-25.
  26. ^ Lassaunière, Ria (11 November 2020). "SARS-CoV-2 spike mutations arising in Danish mink and their spread to humans". Statens Serum Institut. Archived from the original on 10 November 2020. Retrieved 11 November 2020.
  27. ^ "6 countries find coronavirus at mink farms; fears mutation could hinder vaccine". The Times of Israel. 2020-11-08. Retrieved 2020-11-09. Italy, the Netherlands, Spain and Sweden are the other nations to have discovered SARS-CoV-2 in minks, WHO said in a statement.
  28. ^ "De fleste restriktioner læmpes i Nordjylland" [most restrictions eased in North Jutland]. Sundheds- og Ældreministeriet. 19 November 2020.
  29. ^ a b "Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria". Virological. 2020-12-23. Retrieved 2021-01-01.
  30. ^ a b CDC (2020-02-11). "Coronavirus Disease 2019 (COVID-19)". Centers for Disease Control and Prevention. Retrieved 2021-01-01.
  31. ^ Schraer, Rachel (18 July 2020). "Coronavirus: Are mutations making it more infectious?". www.bbc.co.uk. Retrieved 3 January 2021.
  32. ^ "New, more infectious strain of COVID-19 now dominates global cases of virus: study". medicalxpress.com. Archived from the original on 17 November 2020. Retrieved 16 August 2020.
  33. ^ Korber, Bette; Fischer, Will M.; Gnanakaran, Sandrasegaram; Yoon, Hyejin; Theiler, James; Abfalterer, Werner; et al. (2 July 2020). "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus". Cell. 182 (4): 812–827.e19. doi:10.1016/j.cell.2020.06.043. ISSN 0092-8674. PMC 7332439. PMID 32697968. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  34. ^ Butowt, R; Bilinska, K; Von Bartheld, CS (2020-10-21). "Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor". ACS Chem Neurosci. 11 (20): 3180–3184. doi:10.1021/acschemneuro.0c00596. PMC 7581292. PMID 32997488.
  35. ^ "cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages". github.com. Retrieved 2 January 2021.
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