Omicron Webinar AHS

Omicron (B.1.1.
529)
Tri Wibawa
Departemen Mikrobiologi FK-KMK UGM
SARS-CoV-2 Variants
01 02 03
Variants under Variants of Interest Variants of
Monitoring (VUM) (VOI) Concern (VOC)
Variant of Interest (VOI)
Pango Nextstrain Earliest documented
WHO label GISAID clade Date of designation
lineage* clade samples
Multiple countries,
Eta B.1.525 G/484K.V3 21D 17-Mar-2021
Dec-2020
United States of
Iota B.1.526 GH/253G.V1 21F America, 24-Mar-2021
Nov-2020
India, 4-Apr-2021
Kappa B.1.617.1 G/452R.V3 21B
Oct-2020
Lambda C.37 GR/452Q.V1 21G Peru, Dec-2020 14-Jun-2021
Mu Kolombia, Januari 2021 30 Agustus 2021
B.1.621 GH 21H
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
Variant of Concern (VOC)
Earliest
Pango Nextstrain Additional amino acid Date of
WHO label GISAID clade documented
lineage* clade changes monitored° designation
samples
Alpha +S:484K United Kingdom,

#
B.1.1.7 GRY 20I (V1) Sep-2020 18-Dec-2020
+S:452R
Beta B.1.351 +S:L18F South Africa,

GH/501Y.V2 20H (V2) 18-Dec-2020
May-2020
Gamma P.1 Brazil,

GR/501Y.V3 20J (V3) +S:681H 11-Jan-2021
Nov-2020
VOI: 4-Apr-2021
Delta § +S:417N India,
B.1.617.2 G/478K.V1 21A VOC: 11-May-
Oct-2020
2021
Multiple countries, VUM: 24-Nov-2021

Omicron* B.1.1.529 GRA 21K, 21L, 21M +R346K
Nov-2021 VOC: 26-Nov-2021
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
8 kasus per 23 Des 2021
Consist of 26-32 mutation in Spike gen
OMICRON Transmission:
VARIANT • As of 9 December 2021: identified in 63 countries across

all six WHO regions.
(WHO update • As of 14 December 2021: identified in 70 countries and 6
under verification
10 Dec 2021) • As of 21 December 2021: identified in 106 countries
Concern:
• (1) how transmissible the variant is;

• (2) how well vaccines and prior infection protect against
infection, transmission, clinical disease and death; and
• (3) how virulent the variant is compared to other variants.
• Based on current limited evidence Omicron
appears to have a growth advantage over
Delta
• There are still limited data on the clinical
severity of Omicron
OMICRON • There are limited available data, and no
peer-reviewed evidence, on vaccine efficacy
VARIANT or effectiveness to date for Omicron.
Preliminary data:
(WHO update 10 & • the incidence of reinfection has increased
21 Dec 2021) in South Africa→ immune evasion?
• Antibody neutralization to omicron is
lower than other variants ?
• The diagnostic accuracy of routinely used
PCR and antigen-based rapid diagnostic test
(Ag-RDT) assays does not appear to be
influenced by Omicron
COVID-19 Weekly Epidemiological Update: OMICRON
Edition 70, published 14 December 2021
Booster Vaccine – Omicron
(non peer reviewed reports)
• Pfizer:
• Preliminary laboratory studies demonstrate that three doses of the Pfizer-BioNTech
COVID-19 Vaccine neutralize the Omicron variant (B.1.1.529 lineage) while two doses
show significantly reduced neutralization titers
• Data indicate that a third dose of BNT162b2 increases the neutralizing antibody titers
by 25-fold compared to two doses against the Omicron varian
• Moderna: The Director-General of WHO
• A booster from Moderna or Pfizer's COVID-19 vaccine offers
has called for a moratorium on
a "significant increase" in protection against both the delta
booster vaccination for healthy
and new, more contagious omicron variants (Danish study).
adults until the end of 2021 to
• Asatrazeneca: counter the persisting and
• Antibody levels with booster similar to two doses profound inequity in global
against Delta vaccine access
https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-provide-update-omicron-variant
https://www.reuters.com/business/healthcare-pharmaceuticals/astrazeneca-shot-third-dose-works-against-omicron-study-2021-12-23/
medRxiv preprint doi: https://doi.org/10.1101/2021.12.20.21267966
• (Omicron) is primarily of concern due to the
large number of mutations it has in the Spike
gene.
• 60 (50 nonsynonymous, 8 synonymous, and
2 noncoding) mutations in omicron:
• 30 of which are on the S protein
Mutations • 15 in the receptor-binding domain – the part
that binds to the ACE2 receptor on human cells
through which the virus enters tissues.
• Thus, it may play key roles in ACE2 binding
and antibody recognition.
• Deletion – insertion – Point mutation
Amino acid mutations in Omicron.
Those in boxes are shared with the
respective previous variant of concern.
Mutations in blue are in the Orf1ab

(NSP) replicative transcription
complex.
Mutations in red are in the S protein.

Mutations in pink are in the structural
proteins.
There are roughly 30 unique mutations

in Omicron.
https://www.forbes.com/sites/williamhaseltine/2021/12/08/omicron-the-sum-of-all-fears/?sh=229b8c6f5b51
An immunocompromised
1 patient
The three
most likely 2 Reverse Zoonosis from animal
Omicron
origins
3 Molnupiravir-induced
William A. Haseltine, 2021, https://www.forbes.com

Risk Assessment
• The overall risk related to the new variant of
concern Omicron remains very high for several
reasons:
• The global risk of COVID-19 remains very
high overall
• Preliminary evidence suggests potential
humoral immune escape against infection
and high transmission rates, which could
lead to further surges with severe
consequences.

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Omicron (B.1.1.

Alpha +S:484K United Kingdom,

Beta B.1.351 +S:L18F South Africa,

Gamma P.1 Brazil,

Multiple countries, VUM: 24-Nov-2021

VARIANT • As of 9 December 2021: identified in 63 countries across

• (1) how transmissible the variant is;

Mutations in blue are in the Orf1ab

Mutations in red are in the S protein.

There are roughly 30 unique mutations

William A. Haseltine, 2021, https://www.forbes.com

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