SARS-CoV-2 Omicron variant

SARS-CoV-2 Omicron variant Jump to navigationJump to search Graphic of a globe with a red analog clock This article documents a current event. Information may change rapidly as the event progresses, and initial news reports may be unreliable. The latest updates to this article may not reflect the most current information. Please feel free to improve this article (but note that updates without valid and reliable references will be removed) or discuss changes on the talk page. (November 2021) (Learn how and when to remove this template message) Part of a series on the COVID-19 pandemic Scientifically accurate atomic model of the external structure of SARS-CoV-2. Each "ball" is an atom. COVID-19 (disease)SARS-CoV-2 (virus) CasesDeaths Timeline Locations International response Medical response Variants Economic impact and recession Impacts SARS-CoV-2 (Wikimedia colors).svg COVID-19 portal vte 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 first known case was detected in Botswana, dated 9 November 2021.[2] On 26 November 2021, the World Health Organization (WHO) designated it as a variant of concern and named it after the Greek letter Omicron.[3][4][5] 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. Contents 1 Classification 1.1 Nomenclature 1.2 Mutations 2 Symptoms 3 Prevention 4 Diagnosis 5 Characteristics 6 Epidemiology 7 Statistics 8 History 8.1 Reported cases 8.2 Market reactions 8.3 International response 9 See also 10 References Classification Nomenclature On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution designated PANGO lineage B.1.1.529 a variant of concern and gave it the designation Omicron[3][4][5] (skipping Nu or Xi, the next letters in the Greek alphabet).[6][5] The World Health Organization reserves the Omicron designation for "variants of concern".[7][5] 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 The variant has a large number of mutations, of which some are concerning.[8] 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.[9][10] 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.[11] The furin cleavage site increases SARS-CoV-2 infectivity.[12] The mutations by genomic region are the following:[13][14] 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 been associated with the variant, and as with other variants, some individuals are asymptomatic.[15] 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.[3][16] On 26 November, BioNTech said it will 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.[17] 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 VOC 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 VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics."[18] 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.[3] Rapid antigen tests are likely not affected.[15] 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.[10] 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.[14] 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.[8] 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.[16][19] 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.[20] There is still vast uncertainty about the transmissibility with respect to the Delta variant, with a possible 100% increase (2x)[21][22] to 500% increase (6x).[23] Statistics GISAID data as of 27 November, unless otherwise stated:[24] Confirmed cases by country Country Confirmed cases South Africa 83 Botswana 17 Hong Kong 2 United Kingdom 2[25] Germany 2[25] Israel 1 Belgium 1 World (7 countries) Total: 108 History Reported cases On 24 November 2021, the variant was first reported to the WHO from South Africa.[3] The first known specimen was collected on 9 November 2021 from Botswana.[10] It was also detected in South Africa;[26] one case had traveled to Hong Kong,[27][28] and one confirmed case was identified in Israel in a traveler returning from Malawi,[29] along with two who returned from South Africa and one from Madagascar.[30] One confirmed case in Belgium had apparently acquired it in Egypt before 11 November.[31] All four initial cases reported from Botswana occurred among fully vaccinated individuals.[32] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals,[29] as did the single suspected case in Germany.[33] On 27 November, two cases were detected in the United Kingdom and another two in Munich, Germany.[25] 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.[34] Market reactions 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 one market analyst[who?] due to the lack of firm conclusions by the medical community.[35] Cryptocurrency markets were also routed.[36][37] 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.[38] 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.[14] 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, and Malaysia.[39][40][41][42] The Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[43] 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.[44] 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.[45] See also Variants of SARS-CoV-2 SARS-CoV-2 Beta variant COVID-19 pandemic in Africa COVID-19 vaccination in Africa COVID-19 vaccination in Botswana COVID-19 vaccination in South Africa References "Tracking SARS-CoV-2 variants". www.who.int. 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