Omicron - A Covid 19 variant

A brief information Omicron a Covid variant. found in South Africa.

1. Omicron By Manash Kumar Mondal Research Scholar University of Kalyani

2. Introduction The  SARS-CoV-2 Omicron variant  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 On 26 November 2021, the WHO designated it as a variant of concern and named it after omicron , the fifteenth letter in the Greek alphabet.

3. Introduction 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 T he variant was quickly designated as being "of concern", and travel restrictions were introduced by several countries to limit or slow its international spread.

4. 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. The WHO skipped the preceding letters nu and xi in the Greek alphabet to avoid confusion with the similarities of the English word "new" and the Chinese surname Xi The World Health Organization reserves the Omicron designation for "variants of concern The GISAID project has assigned it the clade identifier GR/484A and the Nextstrain project has assigned it the clade identifier 21K

5. Mutations The variant has a large number of mutations, of which some are concerning. 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. The variant is characterized 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. Additionally, the variant has three mutations at the furin cleavage site. The furin cleavage site increases SARS-CoV-2 infectivity.

6. Mutations The mutations by genomic region are the following : Spike protein: A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F Half (15) of these 30 changes are located in the receptor binding domain-RBD (residues 319-541)

7. Treatment Corticosteroids and IL6 receptor blockers are known to be effective for managing patients with severe COVID-19 . The impact on the effectiveness of other treatments is currently being assessed.

8. Mutations ORF1ab nsp3: K38R, V1069I, Δ1265, L1266I, A1892T nsp4: T492I nsp5: P132H nsp6: Δ105-107, A189V nsp12: P323L nsp14: I42V

9. Mutations Envelope protein: T9I Membrane protein: D3G, Q19E, A63T Nucleocapsid protein: P13L, Δ31-33, R203K, G204R

10. Public Health Reactions to Mutations The WHO is concerned that the large number of mutations may reduce immunity in people who were previously infected and in vaccinated people. Then again, the omicron variant might be more ineffective in this regard than prior variants. The effects of the mutations, if any, are unknown as of late November 2021. The WHO warns that health services could be overwhelmed especially in nations with low vaccination rates where mortality and morbidity rates are likely to be much higher, and urges all nations to increase COVID vaccinations.

11. Public Health Reactions to Mutations Professor Paul Morgan, immunologist at Cardiff University, also recommends vaccination. Morgan said, "I think a blunting rather than a complete loss [of immunity] is the most likely outcome. The virus can't possibly lose every single epitope on its surface, because if it did that spike protein couldn't work any more.

12. Public Health Reactions to Mutations So, while some of the antibodies and T cell clones made against earlier versions of the virus, or against the vaccines may not be effective, there will be others, which will remain effective. (...) If half, or two-thirds, or whatever it is, of the immune response is not going to be effective, and you're left with the residual half, then the more boosted that is the better.

13. Symptoms No unusual symptoms have yet been associated with the variant and, as with other variants, some individuals are asymptomatic. Angelique Coetzee, chair of the South African Medical Association, said she had first encountered the variant in patients who had fatigue, aches and pains, but no cough or change in sense of smell or taste. Fergus Walsh wrote, "South Africa has a young population and it is encouraging that doctors there are reporting that Omicron is causing mild symptoms with no increase in hospital admissions. But we need to see what happens when the variant moves into older age groups who are the most vulnerable to Covid.

14. Symptoms However the World Health Organization in an update on the variant stated Preliminary data suggests that there are increasing rates of hospitalization in South Africa, even if it has not been determined that this is attributed to this specific variant.

15. 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 . 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.

16. Prevention 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."

17. Diagnosis 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. Rapid antigen tests are most likely not affected

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. 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.

19. Characteristics As of November 2021, it is unknown how the variant will spread in populations with high levels of immunity, it is also unknown if the omicron variant causes a milder or more severe COVID infection. According to pharmaceutical companies, vaccines could be updated to combat the variant "in around 100 days" if necessary.

20. References "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". World Health Organization. 26 November 2021. Archived from the original on 26 November 2021. Retrieved 26 November 2021. 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. Archived from the original on 26 November 2021. Retrieved 26 November 2021. 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. Archived from the original on 26 November 2021. Retrieved 26 November 2021. Patel, Vimal (27 November 2021). "How Omicron, the New Covid-19 Variant, Got Its Name". The New York Times. ISSN 0362-4331. Archived from the original on 28 November 2021. Retrieved 28 November 2021. "There are several COVID-19 variants you haven't heard of". NewsNation Now. 27 November 2021. Archived from the original on 27 November 2021. Retrieved 27 November 2021. "Countries are scrambling to stop a new covid variant". The Economist. 26 November 2021. Archived from the original on 26 November 2021. Retrieved 26 November 2021. "In focus". gisaid.org. GISAID. 28 November 2021. Archived from the original on 21 January 2021. Retrieved 28 November 2021. The unique mix of spike amino acid changes in Omicron GR/484A (B.1.1.529) is of interest as it comprises several that were previously known to affect receptor binding and antibody escape. "Variant: 21K (Omicron)". covariants.org. CoVariants . 28 November 2021. Archived from the original on 28 November 2021. Retrieved 28 November 2021. Variant 21K (Omicron) appears to have arisen in November 2021, possibly in South Africa.

21. References "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. Archived (PDF) from the original on 26 November 2021. Retrieved 26 November 2021. Hurst, Luke (26 November 2021). "What we know so far about the B.1.1.529 'Omicron' COVID variant causing concern". Euronews . Archived from the original on 26 November 2021. Retrieved 26 November 2021. Cookson, Clive; Barnes, Oliver (26 November 2021). "What we know about Omicron variant that has sparked global alarm". Financial Times. Archived from the original on 26 November 2021. Retrieved 26 November 2021. Callaway, Ewen (25 November 2021). "Heavily mutated coronavirus variant puts scientists on alert". Nature. doi:10.1038/d41586-021-03552-w. PMID 34824381. Archived from the original on 26 November 2021. Retrieved 26 November 2021. Zimmer, Carl (26 November 2021). "New Virus Variant Stokes Concern but Vaccines Still Likely to Work". New York Times. Archived from the original on 26 November 2021. Retrieved 26 November 2021. 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.

22. References 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. Walls, Alexandra C.; Park, Young-Jun; Tortorici , M. Alejandra; Wall, Abigail; McGuire, Andrew T.; Veesler , David (April 2020). "Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein". Cell. 181 (2): 281–292.e6. doi:10.1016/j.cell.2020.02.058. Gregory, Andrew (29 November 2021). "Omicron Covid variant poses very high global risk, says WHO". The Guardian. London. Retrieved 29 November 2021. Geddes, Linda (29 November 2021). "What does appearance of Omicron variant mean for the double-vaccinated?". The Guardian. London. Retrieved 29 November 2021. "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. Archived from the original on 26 November 2021. Retrieved 27 November 2021. "Covid: Sajid Javid defends 'swift action' on Omicron variant". BBC. BBC. 28 November 2021. Archived from the original on 28 November 2021. Retrieved 28 November 2021. Covid: Third case of Omicron variant detected in the UK Archived 28 November 2021 at the Wayback Machine BBC https://www.who.int/news/item/28-11-2021-update-on-omicron

23. References Nebehay , Stephanie; Winning, Alexander (26 November 2021). "WHO names new COVID variant omicron, cautions against travel measures". Reuters. Archived from the original on 26 November 2021. Retrieved 26 November 2021. " BioNTech says it could tweak Covid vaccine in 100 days if needed". The Guardian. 26 November 2021. Archived from the original on 27 November 2021. Retrieved 27 November 2021. " Sinovac and world's Covid-19 vaccine makers 'ready' to produce Omicron jab". South China Morning Post. 29 November 2021. Retrieved 29 November 2021. "Sputnik V maker: Vaccine could be adapted to fight omicron". ABC News. Moscow. Associated Press. 29 November 2021. Retrieved 29 November 2021. "Omicron poses very high global risk, world must prepare -WHO". Reuters. Geneva. 29 November 2021. Retrieved 30 November 2021. "Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern". www.who.int. Archived from the original on 26 November 2021. Retrieved 26 November 2021. "Update on Omicron". World Health Organization. 28 November 2021. Retrieved 30 November 2021. New Covid variant: Will new measures against Omicron work? Archived 28 November 2021 at the Wayback Machine BBC