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LETTER TO THE EDITOR
Year : 2022  |  Volume : 13  |  Issue : 2  |  Page : 138-140  

Omicron: A variant of concern not a cause of panic


Department of Chemistry, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India

Date of Submission12-Jan-2022
Date of Acceptance01-Feb-2022
Date of Web Publication07-Apr-2022

Correspondence Address:
Dr. Shefali Arora
Energy Acres, P.O. Bidholi, Via Prem Nagar, Dehradun - 248 007, Uttarakhand
India
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/japtr.japtr_14_22

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How to cite this article:
Arora S. Omicron: A variant of concern not a cause of panic. J Adv Pharm Technol Res 2022;13:138-40

How to cite this URL:
Arora S. Omicron: A variant of concern not a cause of panic. J Adv Pharm Technol Res [serial online] 2022 [cited 2022 Jun 26];13:138-40. Available from: https://www.japtr.org/text.asp?2022/13/2/138/342685



Omicron detected in November 2021, belongs to Pango Lineage B.1.1.529 with a large number of S-gene mutation in comparison to original SAR-CoV-2 virus. Thirty changes are found in this variant with three small deletions and one small insertion in the spike proteins, and out of these spike proteins, 15 are of from receptor-binding domain. Omicron is the variant of concern (VOC) in terms of marked reduction in vaccine effectiveness, enhanced transmissibility, and increased risk for reinfection and immune escape as compared to delta variant. The overall assessment of omicron is “high” to “very high.”

As per WHO reports, the five variants of coronavirus are the “Variants of concern” namely 20I (alpha, V1); 20H (beta, V2); 20J (gamma, V3); 21A (delta); and 21K (omicron). The variant 21K (omicron) now a days is creating a “very high” risk. It was first detected in November 24, 2021, in South Africa and later on detected in Botswana and Hong Kong. The first specimen of omicron or B.1.1.529 was confirmed on November 9, 2021. Analysis of global transmission reported that omicron spreading rate is faster than delta. If we compare the delta variant with omicron than delta variant is first detected in India in December 2021. It is first called as a variant of interest (VOI) on April 4, 2021, and declared as VOC on May 11, 2021. The omicron becomes VOC from variant under monitoring (VUM) in just 2 days which proves its severity as per WHO reports. The case of delta variant was confirmed in 48 countries as of May 18, 2021, 5 month after the first case in India and omicron was detected in 16 new countries across four continents in just 10 days. The case of omicron increases over 1343 vs 289 new cases between November 21, 2021, and November 28, 2021 (WHO reports). Omicron is the VOC which shows genetic changes that affects the virus properties such as severity of disease, immune escape, transmissibility, therapeutic escape, significant community transmission, detrimental changes in COVID-19 epidemiology, and changes in clinical disease presentation and all these impact creates an emerging risk to worldwide public health.

Many variants of omicron were reported from South Africa,[2] Belgium,[3] Hong Kong,[4] Botswana,[5] and Israel.[6] Previously, omicron designated as “Nu” and “X” but WHO refused both the terms as “Nu” to clear the confusion with the English word “new” and “Xi” was a common surname. The transmissibility of omicron in South Africa raises concern as it causes the super spreading events and causes high growth rate due to immune escape [Table 1]. It was investigated that the omicron has more mutation in the S-gene and shows a very significant effect on neutration. This variant carries twenty mutation in the spike protein which are resistant toward convalescent and vaccine sera.[7]
Table 1: Different variant of variant of concerns/variant of interests/variant under monitorings of SAR-CoV-2

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21K (omicron) is of primarily concern because of the detection of large number of mutation in its spike gene [Figure 1]. Most of these variants plays an important role in antibody recognition and ACE2 binding and are in the N-terminal or receptor-binding domain. Omicron showed 69/70 deletion test and gives negative result and create the S-assay within TaqPath tests called S-gene target failure or SGTF. However, in 20I (alpha, V1) and 21 I (Eta) also showed deletion at position S: H69- and S: V70- as in 21K (omicron). In omicron, 3-amino acid inserted in spike of EPE at position 214 and at the S1-S2 furin cleavage site (S: H6554, S: N679K, and S: P681H). The binding affinity to ACE2 has been increased by the mutations in S: Q498R and S: N501Y. In omicron, in spite of this, there is deletion of 3-amino acid in NSP6 from 105 to 107, namely ORF1a: L-3674-; ORF1a: S3675-; and ORF1a: G3676-. Scientist told about this mutation that it helps in compromising cell by innate immune evasion and degrade viral components. The two new mutations N: R203K and N: G204R in nucleocapsid were detected in omicron which enhanced subgenomic RNA expression and increased viral load [Figure 2].
Figure 1: Key mutation in omicron variant with deletion

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Figure 2: The proportion of cases that were the Omicron variant (blue) and Indian “Delta” variant (red) over time in Guateng province in South Africa, where the virus came into existence. It suggests that the mutant strain could outcompete delta within weeks (Source: Google image)

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Over 50 mutations are found in omicron, out of which, 32 mutations only on the spike protein. Outer part of SAR-CoV-2 virus has spike protein which form protruding knobs. These knobs facilitate the virus to adhere on the cell and ultimately virus can gain entry. On the other hand, ten mutations are found in omicron un the receptor-binding domain: The part of spike protein which interact with the ACE-2 receptor and takes entry into the cells.

Dr. Salim S. Abdool Karim, director from Centre for the Aids Program of Research in South Africa, Columbia University told that the omicron is highly transmissible, may not be clinically worse. The symptoms are extremely mild as per the report of Chairwoman of South Africa Medical Association, Angelique Coetzee. The common symptoms of omicron are head and body aches, dry cough, fever, night sweating, fatigue, scratchy throat, and occasional sore throat and vary for different age group as reported by Dr. Unben Pillay from Germany, which is the area of 81% of the new cases of omicron. With the age group of 20's and 30's generally shows milder symptoms and scientist warn that this new variant can be severe for older peoples.[8] Now the question arises that if the omicron shows mild symptoms than why this variant is called VOC. The answer is that people who contracted and recovered from COVID are more susceptible to catch it again this variant means chance of reinfection compared to other highly transmissible variant. Actually, omicron came into existence when the antibodies working a perfectly normal response means they reduce over time and not able to fight off an infection. The memory B and T cells are responsible for creating an immune response when infected by the virus so several countries have ready for the administration of booster doses to create immunity against COVID-19. Scientist is not sure that omicron could render vaccine less effective as it shows many keys mutation in comparison to beta and gamma. It has 26 unique mutations which were targeted by vaccine antibodies as per the report of Professor, John Moore from Weill Cornell Medical College in New York. Paul Burton, CMO from Moderna Inc. reported that the omicron may not effective toward current vaccine and if this is the case, the reformulate shot could be available in early 2022. WHO recommended the some medications and steroids such as IL6 receptor blockers suitable for this new strain omicron.

SGTF from PCR test is the marker of omicron detection. The mechanism for reporting the initial case/cluster associate to WHO for omicron infection is.[9]

The number of sequence of omicron/total number of sequence generated through routine surveillance [Figure 3].
Figure 3: Three-dimensional photographs of comparison of delta and omicron mutation (Sources: Google image)

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Science-based approach and risk analysis may reduce the COVID-19 circulation in worldwide. WHO is ready to provide guidance and support for fighting to this deadly disease with full of readiness and response.[10] Future studies are required to understand the escape potential against vaccine- and infection-based immunity. Geneva-based agency reported that the severity level of omicron variant will understand in “days to several weeks.” Again there is lots of pressure on health-care system with the increasing the effective reproduction in number of the variant. Definitely the outbreak of this variant infection will create high level of morbidity and mortality. Hence, be ready to fight and beat this new variant “omicron” with the same precaution and habits which we follow in the past.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
  References Top

1.
WHO Reports, Tracking SARS-CoV-2 Variants, Tracking SARS-CoV-2 Variants; 2021. Available from: http://who.int [Last accessed on 2022 Jan 06].   Back to cited text no. 1
    
2.
National Institute for Communicable Diseases - Division of the National Health Laboratory Service - South Africa. New COVID-19 Variant Detected in South Africa. NCID/NHLS; 2021. Available from: http:// www.nicd.ac.za/new-covid-19-variant-detected-in-south-africa/. [Last accessed on 2022 Jan 06].   Back to cited text no. 2
    
3.
Het Laatste Nieuws. Eén geval van Zuid-Afrikaanse Variant in Ons Land Bevestigd: "Voorzichtigheid is Nodig, Paniek Niet". HLN; November 26, 2021. Available from: http://www.hln. be/binnenland/een-geval-van-zuid afrikaanse-variant-in-ons -land-bevestigd-voorzichtigheid-is-nodig-paniek-niet ~a34621a6/. [Last accessed on 2022 Jan 06].   Back to cited text no. 3
    
4.
The Government of the Hong Kong Special Administrative Region. CHP Investigates Six Additional Confirmed Cases of COVID-19 and Provides Update on Latest Investigations on Imported Cases 12388 and 12404. Hong Kong: GovHK; 2021. Available from: http:// www.info.gov.hk/gia/general/202111/25/P2021112500379.htm. [Last accessed on 2022 Jan 06].   Back to cited text no. 4
    
5.
Botswana Government. Media Release - New COVID 19 Variant Detected in Botswana. Twitter; November 25, 2021, 03:16 pm. Available from: http://twitter.com/BWGovernment/ status/1463874240130785280. [Last accessed on 2022 Jan 06].   Back to cited text no. 5
    
6.
Ministry of Health of Israel. The Variant Discovered in South African Countries was Identified in Israel. MoH of Israel Coronavirus Information Centre; 2021. Available from: http://www.gov.il/he/ departments/news/26112021-01. [Last accessed on 2022 Jan 06].   Back to cited text no. 6
    
7.
Schmidt F, Weisblum Y, Rutkowska M, Poston D, Da Silva J, Zhang F, et al. High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature 2021;600:512-6.   Back to cited text no. 7
    
8.
Sguazzin, A. (2021) Doctor Who Saw Omicron Early Says Symptoms Different to Delta, http://www.bloomberg.com/ news/articles/2021-11-29/doctor-who-saw-omicron-early-says-symptomsdifferent-to-delta [Last access on 29th November 2021].   Back to cited text no. 8
    
9.
Enhancing Readiness for Omicron (B.1.1.529): Technical Brief and Priority Actions for Member States World Health Organization HQ 28 November 2021 (updated 29 November with minor editorial corrections). Available from: http://technical-brief-and-priority-action-on-Omicron.pdf. [Last accessed on 2022 Jan 06].   Back to cited text no. 9
    
10.


    Figures

  [Figure 1], [Figure 2], [Figure 3]
 
 
    Tables

  [Table 1]



 

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