Varian Omicron:

Asal Usul dan

Penyebarannya

Amin Soebandrio
PAMKI
Time-line of Omicron

2
December
24
November 29 • United Arab 4
27 November Emirates, December
4 9 • South Africa November France,
November November makes its • Scotland. Iceland, • South
first report • United Spain and Greece , Korea, Cook
• South Africa • Botswana of B.1.1.529 Kingdom Sweden. Singapore Islands

8 14–23 26 28 1 3 5
November November November November December December December
• The first • More than • PANGO • Danish, • United • Malaysia • More cases
confirmed 70 percent lineage Australia States, reported in
sample is of samples B.1.1.529 Saudi US.
collected in from designated Arabia,
South Gauteng a variant of Ghana,
Africa. province in concern South
South Africa (VOC) and Korea,
are Omicron gave it the Norway,
designation Nigeria, and
Omicron The Dutch.
Geography of SARS-CoV-2
 Variants Frequencies

https://nextstrain.org/ncov/gisaid/global
Phylogeny of SARS-CoV-2
Omicron
Variant and
Other VoCs

https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant
Omicron Genomic sequence

https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant
Clusters of Mutation

https://www.businessinsider.com/why-omicron-variant-mutations-are-concerning-2021-
11?IR=T&r=US&utm_medium=referral&utm_source=yahoo.com
Large Number • The deletion at positions S:H69- and S:V70- (see
mutations:h69-)) is also found in 20i(alpha, V1) and
of Mutation 21d(eta), along with some other variants.
Contributes in SGTF.
Many of them • Mutations at the s1-s2 furin cleavage site (s:h655y,
are in RBD and s:n679k, s:p681h) may also be associated with
increased transmissibility
N-terminal • The combination of mutations s:q498r and s:n501y
domains in in-vitro evolution studies significantly increased
the binding affinity to ace2
• 3 amino-acid deletion in orf1a at orf1a:l3674-,
orf1a:s3675-, and orf1a:g3676- could aid in innate
immune evasion.
• Two mutations in nucleocapsid, n:r203k and n:g204r
(not new) are linked to increase sub genomic rna
expression and increased viral loads.
 The novel variant Omicron is not yet
Potential Scenario detected in the country and considered
not yet present in the country.

The novel variant Omicron is considered

not yet present in the community but was
detected among the incoming travelers.

The novel variant Omicron was detected

in community, but as sporadic cases or
within a few manageable sizes of clusters

The novel variant Omicron is in the

country, and it is widespread in
communities.

Technical Brief: Enhancing Readiness for Omicron (B.1.1.529) in the WHO South-East Asia
Region. 27 November 2021
 • Enhance surveillance and sequencing efforts to
better understand circulating sars-cov-2 variants.
• Submit complete genome sequences and
associated metadata to a publicly available
COUNTRIES database, such as GISAID.
• Report initial cases/clusters associated with VOC
ARE ASKED TO infection to who through the IHR mechanism.
• Where capacity exists and in coordination with the
DO THE international community, perform field
investigations and laboratory assessments to
FOLLOWINGS: 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.

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-
variant-of-concern
SGTF testing / algorithm
• For countries with access to diagnostic tests in which at least one
gene target contains the S gene target.
• Prioritize specimens with S Gene target failure (no detection for S gene and
detection for other gene targets) for sequencing confirmation of the Omicron.
• A sudden increase in S gene target failures may be indicative of circulation of
the Omicron in light with reducing prevalence of Alpha variant, however,
confirmation by sequencing is recommended.
• For countries without access to diagnostic tests with S gene target,
enhanced surveillance and sequencing is recommended to
characterize the circulating SARS-CoV-2 variants.
 Current knowledge about Omicron
• Transmissibility
• It is not yet clear whether Omicron is more transmissible

• Severity of disease
• It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants,
including Delta.

• Effectiveness of prior SARS-CoV-2 infection

• Preliminary evidence suggests there may be an increased risk of reinfection with Omicron

• Effectiveness of vaccines
• WHO is working with technical partners to understand the potential impact of this variant on our existing countermeasures,
including vaccines.

• Effectiveness of current tests

• The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other
variants as well.

• Effectiveness of current treatments

• Corticosteroids and IL6 Receptor Blockers will still be effective for managing patients with severe COVID-19.
https://www.who.int/news/item/28-11-2021-update-on-omicron
Thank you.