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SARS-CoV-2 Omicron variant

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The Omicron variant, also known as lineage B.1.1.529, is a variant of SARS-CoV-2, the coronavirus that causes COVID-19. The first known case was in Botswana, dated 9 November 2021. On 26 November 2021 the World Health Organisation ("WHO") designated it a variant of concern and named it for the Greek letter Omicron.[1][2][3]

The variant has an unusually large number of mutations, several of which are novel and several 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 "of concern" and travel restrictions were introduced by several countries to limit or slow its international spread.

History

The first known specimen was collected on 9 November 2021 from Botswana.[4] It was also detected in South Africa;[5] one case had travelled to Hong Kong,[6][7] one confirmed case was identified in Israel in a traveler returning from Malawi,[8] along with two who returned from South Africa and one from Madagascar.[9] One confirmed case in Belgium had apparently acquired it in Egypt before 11 November.[10]

All four initial cases reported from Botswana occurred among fully vaccinated individuals.[11] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals. [12]

On 24 November 2021, the variant was first reported to the WHO from South Africa.[1] On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution designated B.1.1.529 a variant of concern and gave it the designation Omicron,[1][2][3] rather than Nu which was the next available letter in the Greek alphabet.[13][14]

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" due to the lack of firm conclusions by the medical community.[15]

Mutations

The variant has a large number of mutations, of which some are concerning.[16] 32 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.[17][4]

The omicron variant is characterised by 30 amino acid changes, three small deletions and one small insertion in the spike protein compared to the original virus (A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F). Out of these changes, 15 are located in the receptor binding domain (residues 319-541). The variant also carries a number of changes and deletions in other genomic regions (NSP3 – K38R, V1069I, Δ1265, L1266I, A1892T; NSP4 – T492I; NSP5 – P132H; NSP6 – Δ105-107, A189V; NSP12 – P323L; NSP14 – I42V; E – T9I; M – D3G, Q19E, A63T; N – P13L, Δ31- 33, R203K, G204R).[18]

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.[4]

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.[19][1]

Epidemiology

The number of cases in the B.1.1.529 lineage is increasing in all areas of South Africa, mainly in Gauteng.[16] Some evidence shows that this variant has an increased risk of reinfection. Studies are underway to evaluate the exact impact on transmissibility, mortality, and other factors. Evidence regarding the implications of this variant and vaccine efficacy is still being investigated.[19][20]

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

International response

On 26 November, the WHO advised countries not to impose new restrictions on travel and instead recommended a "risk-based and scientific" approach to travel measures.[22]

Countries that announced travel bans from southern Africa in response to the identification of the variant include Japan, Canada, the European Union, Israel, the United Kingdom, and the United States.[23][24] The Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[25]

In response, South African Minister of Health Joe Phaahla defended his country's handling of the pandemic and claimed that travel bans went against the "norms and standards" of the World Health Organization.[26]

See also

References

  1. ^ a b c d "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)
  2. ^ 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.
  3. ^ a b Meyer, David (16 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)
  4. ^ a b c Callaway, Ewen (25 November 2021). "Heavily mutated coronavirus variant puts scientists on alert". Nature. doi:10.1038/d41586-021-03552-w.
  5. ^ "outbreak.info". outbreak.info. Retrieved 26 November 2021.{{cite web}}: CS1 maint: url-status (link)
  6. ^ Covid: New heavily mutated variant B.1.1.529 in South Africa raises concern, 25 November 2021, BBC News, accessed 25 November 2021
  7. ^ 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
  8. ^ @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.
  9. ^ 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
  10. ^ 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)
  11. ^ Four cases of the new COVID-19 variant recorded in Botswana, 25 November 2021, Mmegi Online, accessed 26 November 2021
  12. ^ @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.
  13. ^ 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.
  14. ^ Meyer, David (16 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)
  15. ^ 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.
  16. ^ 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.
  17. ^ Cookson, Clive; Barnes, Oliver (26 November 2021). "What we know about Omicron variant that has sparked global alarm". Financial Times. Retrieved 26 November 2021.
  18. ^ "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.
  19. ^ a b Nebehay, Stephanie; Winning, Alexander (26 November 2021). "WHO names new COVID variant omicron, cautions against travel measures". Reuters. Retrieved 26 November 2021.
  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. ^ "WHO cautions against imposing travel restrictions due to new variant". Geneva. Reuters. 26 November 2021. Retrieved 26 November 2021.
  23. ^ 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.
  24. ^ 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.
  25. ^ https://agenciabrasil.ebc.com.br/saude/noticia/2021-11/anvisa-recomenda-restricoes-de-voo-diante-de-nova-variante-de-covid-19
  26. ^ 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.
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