The Omicron variant was first reported to the WHO from South Africa in November 2021. It has over 30 mutations in the spike protein and is highly transmissible. While initial cases showed mild symptoms, there are increasing hospitalization rates in South Africa. Vaccines may need to be updated due to Omicron's ability to evade immunity. The WHO warns Omicron poses a very high global risk and increased vaccination is urged.

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
• The 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
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from the original on 26 November 2021. Retrieved 26 November 2021.
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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
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22. References
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23. References
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