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SARS-CoV-2 Omicron variant

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The Omicron variant, also known by the PANGO lineage identifier B.1.1.529, GISAID clade identifier GR/484A, and Nextstrain clade identifier 21K,[1] is a variant of SARS-CoV-2, the virus that causes COVID-19. The variant was first reported to the World Health Organization (WHO) from South Africa on 24 November 2021.[2] On 26 November 2021, the WHO designated it as a variant of concern and named it after the Greek letter omicron.[3][4]

The variant has an unusually large number of mutations, several of which are novel, and several of which affect the spike protein used for most vaccine targeting at the time of its discovery. This level of variation has led to concerns regarding transmissibility, immune system evasion, and vaccine resistance. As a result, the variant was rapidly designated as being "of concern", and travel restrictions were introduced by several countries to limit or slow its international spread.

Classification

Nomenclature

On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution declared PANGO lineage B.1.1.529 a variant of concern and designated it with the Greek letter omicron.[2][3][4] The WHO skipped nu and xi, the next letters in the Greek alphabet, to avoid confusion with the English word "new" and the common Chinese surname Xi.[5][4][6][7] The World Health Organization reserves the Omicron designation for "variants of concern".[8][4]

The GISAID project has assigned it the clade identifier GR/484A[1] and the Nextstrain project has assigned it the clade identifier 21K.[1]

Mutations

  • Genomic sequence
    Genomic sequence

The variant has a large number of mutations, of which some are concerning.[9] Thirty-two mutations affect the spike protein, the main antigenic target of antibodies generated by infections and of many vaccines widely administered. Many of those mutations had not been observed in other strains.[10][11] The variant is characterised by 30 amino acid changes, three small deletions and one small insertion in the spike protein compared with the original virus, of which 15 are located in the receptor binding domain (residues 319-541). It also carries a number of changes and deletions in other genomic regions. Of note, the variant has three mutations at the furin cleavage site.[12] The furin cleavage site increases SARS-CoV-2 infectivity.[13] The mutations by genomic region are the following:[14][15]

  • Spike protein: A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K[clarification needed], G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
  • ORF1ab
    • nsp3: K38R, V1069I, Δ1265, L1266I, A1892T
    • nsp4: T492I
    • nsp5: P132H
    • nsp6: Δ105-107, A189V
    • nsp12: P323L
    • nsp14: I42V
  • Envelope protein: T9I
  • Membrane protein: D3G, Q19E, A63T
  • Nucleocapsid protein: P13L, Δ31-33, R203K, G204R

Symptoms

Main article: Symptoms of COVID-19

No unusual symptoms have yet been associated with the variant, and as with other variants, some individuals are asymptomatic.[16]

Prevention

See also: COVID-19 § Prevention

As with other variants, the WHO recommended that people continue to keep enclosed spaces well ventilated, avoid crowding and close contact, wear well-fitting masks, clean hands frequently, and get vaccinated.[2][17]

On 26 November, BioNTech said it would know in two weeks whether the current vaccine is effective against the variant and that an updated vaccine can be shipped in 100 days if necessary. AstraZeneca, Moderna and Johnson & Johnson were also studying the variant's impact on the effectiveness of their vaccines.[18]

WHO asked nations to do the following:

  • "Enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • Report initial cases/clusters associated with virus-of-concern infection to WHO through the IHR mechanism.
  • Where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the virus of concern on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics."[19]

Diagnosis

See also: COVID-19 testing

Current PCR tests can detect the variant. Some laboratories have indicated that a widely used PCR test does not detect one of the three target genes. Just as with the Alpha variant, this partial detection ("S gene target failure") can serve as a marker for the variant, however.[2] Rapid antigen tests are likely not affected.[16]

Characteristics

Many of the mutations to the spike protein are present in other variants of concern and are related to increased infectivity and antibody evasion. Computational modeling suggests that the variant may also escape cell-mediated immunity.[11]

On 26 November, the ECDC wrote that an evaluation of the neutralizing capacity of convalescent sera and of vaccines is urgently needed to assess possible immune escape, saying these data are expected within two to three weeks.[15]

Epidemiology

The number of cases in the B.1.1.529 lineage is increasing throughout South Africa, mainly in the South Africa province of Gauteng.[9] Some evidence shows that this variant has an increased risk of reinfection. Studies are underway to evaluate the impact on transmissibility, mortality, and other factors. Evidence regarding the implications of this variant and vaccine efficacy is under investigation.[17][20]

In 2020, South African infection rates reached a low on 11 November. Cases peaked in mid-January 2021. Similarly in 2021, cases bottomed out on 11 November, before again rising rapidly, growing four-fold by 25 November.[21]

There is still vast uncertainty about Omicron's transmissibility compared to the Delta variant, with speculations of possible 100% increase (twice as transmissible)[22][23] to 500% increase (six times as transmissible).[24] Due to the background of low case rates in South Africa, it is not known whether Omicron is any more transmissible than Delta.[11]

Statistics

Map of countries with confirmed SARS-CoV-2 Omicron variant cases

GISAID data as of 27 November 2021, unless otherwise stated:[25]

Confirmed cases by country
Country Confirmed cases
South Africa 99
Botswana 17
Hong Kong 2
United Kingdom 2[26]
Germany 2[26]
Australia 2[27]
Italy 1[26]
Israel 1
Belgium 1
Czech Republic 1[28]
World (10 countries) Total: 128

As of 28 November, all known cases outside of South Africa and Botswana have been travel related. The Belgium case appears related to Egypt (or Turkey). Recent travelers have been subject to more testing, biasing the results.[citation needed]

History

Reported cases

On 24 November 2021, the variant was first reported to the WHO from South Africa.[2] The first known specimen was collected on 9 November 2021 from Botswana.[11] It was also detected in South Africa;[29] one case had traveled to Hong Kong,[30][31] and one confirmed case was identified in Israel in a traveler returning from Malawi,[32] along with two who returned from South Africa and one from Madagascar.[33] One confirmed case in Belgium had apparently acquired it in Egypt before 11 November.[34]

All four initial cases reported from Botswana occurred among fully vaccinated individuals.[35] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals,[32] as did the single suspected case in Germany.[36]

On 27 November, two cases were detected in the United Kingdom, another two in Munich, Germany and one in Milan, Italy.[26] The Dutch health ministry estimated that 61 of the around 600 passengers on two flights from South Africa that had landed at Amsterdam Airport Schiphol on 26 November (which had taken off just before the Netherlands had banned travel from South Africa) tested positive for COVID-19 of as yet unknown variants. Entry into the Netherlands (and thus getting on the flight) generally required having been vaccinated or PCR-tested, or having recovered. One of the flights originated from Johannesburg, Gauteng. Gauteng is where the Omicron variant appears to be dominant already. The passengers of both flights had been tested and quarantined upon arrival because of the newly imposed restrictions.[37]

On 28 November, two cases were detected in Sydney, Australia. Both people landed in Sydney the previous day, and have travelled from southern Africa to Sydney via Doha, Qatar. The two people, who are fully vaccinated, entered isolation; 12 other travellers from southern Africa also entered quarantine for fourteen days, while about 260 other passengers and crew on the flight have been directed to isolate.[27]

Market reactions

Main article: Financial market impact of the COVID-19 pandemic

Worry about the potential economic impact of the Omicron variant led to a drop in global markets on 26 November, including the worst drop of the Dow Jones Industrial Average in 2021, led by travel-related stocks. The price of Brent Crude and West Texas Intermediate oil fell 10% and 11.7%, respectively. This reaction was described as "overblown" by Wayne Wicker of MissionSquare Retirement due to the lack of firm conclusions by the medical community.[38] Cryptocurrency markets were also routed.[39][40]

International response

On 26 November, WHO advised countries not to impose new restrictions on travel, instead recommending a "risk-based and scientific" approach to travel measures.[41] On the same day the European Centre for Disease Prevention and Control (ECDC) reported modeling indicating that strict travel restrictions would delay the variant's impact on European countries by two weeks, possibly allowing countries to prepare for it.[15]

Also on the same day, several countries announced travel bans from southern Africa in response to the identification of the variant, including Japan, Canada, the European Union, Israel, Australia, the United Kingdom, Singapore, the United States, Malaysia, Indonesia and New Zealand.[42][43][44][45][46][47] The Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[48] The state of New York declared a state of emergency ahead of a potential Omicron spike, though no cases had yet been detected in the state or the rest of the United States.[49] On 27 November, Switzerland introduced obligatory tests and quarantine for all visitors arriving from countries where the variant was detected, which originally included Belgium and Israel.[50]

In response, South African Minister of Health Joe Phaahla defended his country's handling of the pandemic and said that travel bans went against the "norms and standards" of the World Health Organization.[51]

See also

References

  1. ^ a b c "Tracking SARS-CoV-2 variants". www.who.int. Retrieved 27 November 2021.
  2. ^ a b c d e "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". World Health Organization. 26 November 2021. Retrieved 26 November 2021.{{cite web}}: CS1 maint: url-status (link)
  3. ^ a b Parekh, Marcus; Platt, Poppie; Team, Global Health Security; Barnes, Joe (26 November 2021). "Coronavirus latest news: EU suspends all flights to southern Africa over omicron Covid variant fears". The Telegraph. ISSN 0307-1235. Retrieved 26 November 2021.
  4. ^ a b c d Meyer, David (26 November 2021). "What's Omicron? Here's what we know and don't know about the new COVID variant that's roiling markets and air travel". Fortune. Retrieved 26 November 2021.{{cite web}}: CS1 maint: url-status (link)
  5. ^ Parekh, Marcus; Platt, Poppie; Team, Global Health Security; Barnes, Joe (26 November 2021). "Coronavirus latest news: EU suspends all flights to southern Africa over omicron Covid variant fears". The Telegraph. ISSN 0307-1235. Retrieved 26 November 2021.
  6. ^ Patel, Vimal (27 November 2021). "How Omicron, the New Covid-19 Variant, Got Its Name". The New York Times. ISSN 0362-4331. Retrieved 28 November 2021.
  7. ^ "There are several COVID-19 variants you haven't heard of". NewsNation Now. 27 November 2021. Retrieved 27 November 2021.
  8. ^ "Countries are scrambling to stop a new covid variant". The Economist. 26 November 2021. Retrieved 26 November 2021.
  9. ^ a b Hurst, Luke (26 November 2021). "What we know so far about the B.1.1.529 'Omicron' COVID variant causing concern". Euronews. Retrieved 26 November 2021.
  10. ^ Cookson, Clive; Barnes, Oliver (26 November 2021). "What we know about Omicron variant that has sparked global alarm". Financial Times. Retrieved 26 November 2021.
  11. ^ a b c d Callaway, Ewen (25 November 2021). "Heavily mutated coronavirus variant puts scientists on alert". Nature. doi:10.1038/d41586-021-03552-w. PMID 34824381.
  12. ^ Zimmer, Carl (26 November 2021). "New Virus Variant Stokes Concern but Vaccines Still Likely to Work". New York Times. Retrieved 26 November 2021.
  13. ^ Zhang, Liping; Mann, Matthew; Zulfeqhar, Syed; Reynolds, Hayley; Tian, E; Samara, Nadine; Zeldin, Darryl; Tabak, Lawrence (23 November 2021). "Furin cleavage of the SARS-CoV-2 spike is modulated by O-glycosylation". Proceedings of the National Academy of Science of the United States of America. 118 (47): e2109905118. doi:10.1073/pnas.2109905118. PMID 34732583. S2CID 242937417.
  14. ^ SARS-CoV-2 variants of concern and variants under investigation in England, technical briefing 29 (PDF) (Briefing). Public Health England. 26 November 2021. GOV-10481. Archived (PDF) from the original on 26 November 2021. Retrieved 26 November 2021. {{cite tech report}}: |archive-date= / |archive-url= timestamp mismatch; 27 November 2021 suggested (help)
  15. ^ a b c "Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA" (PDF). ecdc.europa.eu. Retrieved 26 November 2021.
  16. ^ a b "Frequently asked questions for the B.1.1.529 mutated SARS-CoV-2 lineage in South Africa". NICD. National Institute for Communicable Diseases. 26 November 2021. Retrieved 27 November 2021.
  17. ^ a b Nebehay, Stephanie; Winning, Alexander (26 November 2021). "WHO names new COVID variant omicron, cautions against travel measures". Reuters. Retrieved 26 November 2021.
  18. ^ "BioNTech says it could tweak Covid vaccine in 100 days if needed". The Guardian. 26 November 2021. Retrieved 27 November 2021.
  19. ^ "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". www.who.int.
  20. ^ Sample, Ian (24 November 2021). "Scientists warn of new Covid variant with high number of mutations". The Guardian. Retrieved 24 November 2021.
  21. ^ "COVID-19 Data Explorer". Our World in Data. Retrieved 26 November 2021.
  22. ^ "Omicron variant spreads to Europe as UK announces countermeasures". the Guardian. 26 November 2021. Retrieved 27 November 2021.
  23. ^ Health Department briefs media about a new so-called super-variant, retrieved 27 November 2021
  24. ^ "New COVID variant possibly 500 percent more infectious than Delta". Newsweek. 26 November 2021. Retrieved 27 November 2021.
  25. ^ "Tracking of Variants". GISAID. Updated frequently.
  26. ^ a b c d "UK, Germany and Italy detect Omicron coronavirus variant cases". Reuters. 27 November 2021. Retrieved 27 November 2021.
  27. ^ a b "Travellers test positive to Omicron COVID-19 strain after arriving in Sydney from southern Africa, NSW Health says". ABC News. 28 November 2021. Retrieved 28 November 2021.
  28. ^ "Variantu covidu omikron potvrdila sekvenace v Liberci. Výsledek prověří Národní referenční laboratoř". iROZHLAS.
  29. ^ "Lineage: Mutation Tracker: s:S371L Mutation Report". outbreak.info. Retrieved 26 November 2021.{{cite web}}: CS1 maint: url-status (link)
  30. ^ Covid: New heavily mutated variant B.1.1.529 in South Africa raises concern, 25 November 2021, BBC News, accessed 25 November 2021
  31. ^ Tracking SARS-CoV-2 variants (Tables: Currently designated Variants Under Monitoring -describes 529 variant as present in 'Multiple countries'- and 'Formerly monitored variants'- B.1.523 & B.1.619 Reclassified Nov 2021). www.who.int, accessed 25 November 2021
  32. ^ a b @BNODesk (26 November 2021). "Statement from Israel's health ministry reporting 1 confirmed case of new coronavirus variant B.1.1.529" (Tweet). Retrieved 26 November 2021 – via Twitter.
  33. ^ 14:30 4 מאומתים לווריאנט החדש התגלו בארץ, רה"מ יקיים מסיבת עיתונאים translated: "...Verified for the new strain 4 verified for the new variant were discovered in the country...", m.ynet.co.il, accessed 26 November 2021
  34. ^ Reuters (26 November 2021). "Belgium detects first case of new COVID-19 variant in Europe". Reuters. Retrieved 26 November 2021. {{cite news}}: |last= has generic name (help)
  35. ^ Four cases of the new COVID-19 variant recorded in Botswana, 25 November 2021, Mmegi Online, accessed 26 November 2021
  36. ^ Kerstin Kesselgruber (27 November 2021). "Flughafen Frankfurt: Person mit Omikron-Verdacht war vollständig geimpft" [Frankfurt airport: Person suspected to be infected with omicron variant was fully vaccinanted]. Frankfurter Rundschau (in German). Archived from the original on 27 November 2021. Retrieved 27 November 2021.
  37. ^ "61 travellers from South Africa in Netherlands positive for COVID-19 -authorities". Reuters. Amsterdam. 27 November 2021. Retrieved 27 November 2021.
  38. ^ Gregg, Aaron (26 November 2021). "Dow plunges more than 900 points as new coronavirus variant sends global markets reeling". Washington Post. Retrieved 26 November 2021.
  39. ^ "Bitcoin and other crypto plunge as fear of new COVID variant routs markets". Fortune.
  40. ^ Davies, Pascale (26 November 2021). "Bitcoin's price has slumped after a new COVID variant was found. Why?". euronews.
  41. ^ "WHO cautions against imposing travel restrictions due to new variant". Reuters. Geneva. 26 November 2021. Retrieved 26 November 2021.
  42. ^ Yong, Clement (26 November 2021). "Singapore bans travellers from 7 African countries; no cases of new Covid-19 variant here". The Straits Times. Singapore. Retrieved 26 November 2021.
  43. ^ Linskey, Annie (26 November 2021). "U.S. to restrict travel from South Africa and other countries as it assesses risks of new omicron variant". Washington Post. Retrieved 26 November 2021.
  44. ^ Walsh, Marieke; Stone, Laura (26 November 2021). "COVID-19 variant of concern Omicron causes Canada to impose restrictions on travel from southern parts of Africa". The Globe and Mail. Retrieved 26 November 2021.
  45. ^ Daim, Nuradzimmah; Harun, Hana (26 November 2021). "Temporary entry ban on foreign travellers following discovery of heavily mutated Covid-19 variant". New Straits Times. Archived from the original on 26 November 2021. Retrieved 27 November 2021. {{cite news}}: |archive-date= / |archive-url= timestamp mismatch; 27 November 2021 suggested (help)
  46. ^ "New Zealand bans travel from 9 southern African countries". Radio New Zealand. 28 November 2021. Archived from the original on 28 November 2021. Retrieved 28 November 2021.
  47. ^ "Covid Omicron: RI larang masuk pendatang yang baru dari sejumlah negara Afrika, Afsel kecewa 'dihukum' banyak negara". BBC News Indonesia (in Indonesian). 28 November 2021. Retrieved 28 November 2021.
  48. ^ Anvisa recomenda restrições de voo diante de nova variante de covid-19 26 November 2021 agenciabrasil.ebc.com.br, accessed 27 November 2021
  49. ^ Kennedy, Mark; Price, R. Darren. "'It's Coming': NY Declares State of Emergency Ahead of Potential Omicron Spike". NBC New York. Retrieved 27 November 2021.
  50. ^ "Switzerland announces new restrictions for Israelis after the discovery of Omicron". Globally 24. Retrieved 27 November 2021.
  51. ^ Winning, Alexander; Cocks, Tim (26 November 2021). "South Africa says travel bans over new variant unjustified". Reuters. Archived from the original on 26 November 2021. Retrieved 26 November 2021.

External links

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