Public Health Concerns of SARS-CoV-2 Omicron Variant: What We Know So Far!

Abstract

The Omicron variant is the latest variant of the Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2), the virus that causes the Coronavirus Disease 2019 (COVID-19). The new variant is characterized by thirty (30) substitutions, three (3) small deletions and one (1) small insertion in the spike protein, of these, fifteen (15) are in the receptor binding domain (RBD). This new variant was first detected in samples collected on 11 November 2021 in Botswana and on 14 November 2021 in South Africa and was first reported to the World Health Organization (WHO) from South Africa on 24 November, 2021. As of 01 December, the variant has so far spread to at least twenty-five (25) countries around the world through international travels. So far, the Omicron variant is the most divergent variant that has been detected in significant numbers during the pandemic, which raises public health concerns that it may be associated with increased transmissibility, significant reduction in vaccine efficacy and increased risk for reinfections among those who have suffered COVID-19 before. This review takes a look at the public health concerns of the omicron variant and also highlight important interventions required to contain the variant.

Full text

Research Article Open Access
Public Health Concerns of SARS-CoV-2 Omicron Variant: What
We Know So Far!
1Department of Medical Laboratory Science, Babcock University, Ilishan-Remo, Nigeria
2Department of Medical Laboratory Science, Federal University, Laa, Nigeria
3Department of Medical Laboratory Science, University of Calabar, Calabar, Nigeria
4Department of Medical Microbiology, Federal Medical Centre, Lokoja, Nigeria
5Department of Education, Medical Laboratory Science Council of Nigeria, FCT-Abuja, Nigeria
Seyi Samson Enitan1*, Eong Joseph Eong1, Surajudeen Alim Junaid2, Ernest Chibuike Ohanu3, Grace Eleojo Itodo4, Oluyemisi Ajike
Adekunbi1, Nwachi Idume Ogbonna5, Emmanuel Ileoma1, Peace Ojonugwa Idris1 and Oluwabusolami Oluwatosin Jegede1
*Corresponding author
SS Enitan, Department of Medical Laboratory Science, Babcock University, Ilishan-Remo, Nigeria, Tel: +2348065483761,
E-mail: enitans@babcock.edu.ng
Received: December 05, 2021; Accepted: December 24, 2021; Published: January 07, 2022
Journal of Virology Research &
Reports
Keyword: COVID-19; SARS-CoV-2; Omicron variant; Public
Health Concerns, Interventions
Introduction
On November 11 and 14, 2021, a new strain of the Severe Acute
Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2),
the Omicron variant, was rst detected in samples collected in
Botswana and south Africa, respectively, and was rst reported
to the World Health Organization (WHO) from South Africa on
24 November, 2021 [1,2]. The new variant has so far spread to at
least 25 countries around the world (Brazil, Canada, Australia,
Israel, Hong Kong, Belgium, Japan, Norway, Sweden, United
Kingdom and Nigeria among others), causing rising global
concerns [3]. The United States (US) reported her rst case of
Omicron on December 01, 2021 in a person with recent travel
history to South Africa [4]. However, a few countries, including
the United States, have reported cases in individuals without
travel history to South Africa. This development has resulted in
new travel bans, economic uncertainties, scientic deliberations
among public health experts and even panic among the general
populace on the potential threats of the new variant.On the advice
of the World Health Organization’s Technical Advisory Group
on Virus Evolution (TAG-VE), the World Health Organization
designated the Omicron variant (B.1.1.529), a variant of concern
(VOC). This decision taken on November 26, 2021, was based on
the evidence presented to the TAG-VE that Omicron has several
mutations that may inuence how it behaves, for instance, its
transmissibility and the severity of illness it causes. Interestingly,
signicant spike protein substitutions have been observed in
Omicron, some of which have been previously observed in other
variants and are known to be associated with reduced susceptibility
to available therapeutics including monoclonal antibody and sera
from convalescent COVID-19 patients and vaccinees [4].
Genomic Diversity of Omicron
The Omicron variant (B.1.1.529) belongs to Pango lineage
B.1.1.529, Nextstrain clade 21K, and is characterized by at least
thirty (30) amino acid substitutions, three (3) small deletions and
one (1) small insertion in the spike protein compared to the original
virus (A67V, Δ69-70, Δ143-145, Δ211, T95I, G142D, G339D,
S371L, L212I, ins214EPE, K417N, S373P, S375F, S477N, T478K,
N440K, G446S, G496S, Q498R, E484A, Q493K, T547K, N501Y,
J Viro Res Rep, 2022
ABSTRACT
e Omicron variant is the latest variant of the Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2), the virus that causes the
Coronavirus Disease 2019 (COVID-19). e new variant is characterized by thirty (30) substitutions, three (3) small deletions and one (1) small
insertion in the spike protein, of these, een (15) are in the receptor binding domain (RBD). is new variant was rst detected in samples collected
on 11 November 2021 in Botswana and on 14 November 2021 in South Africa and was rst reported to the World Health Organization (WHO) from
South Africa on 24 November, 2021. As of 01 December, the variant has so far spread to at least twenty-ve (25) countries around the world through
international travels. So far, the Omicron variant is the most divergent variant that has been detected in signicant numbers during the pandemic,
which raises public health concerns that it may be associated with increased transmissibility, signicant reduction in vaccine ecacy and increased
risk for reinfections among those who have suered COVID-19 before. is review takes a look at the public health concerns of the omicron variant
and also highlight important interventions required to contain the variant.
Volume 3(1): 1-4
ISSN: 2755-0125

Citation: Seyi Samson Enitan, Eong Joseph Eong, Surajudeen Alim Junaid, Ernest Chibuike Ohanu, Grace Eleojo Itodo, et al (2022) Public Health Concerns of
SARS-CoV-2 Omicron Variant: What We Know So Far!. Journal of Virology Research & Reports. SRC/JVRR-138. DOI: doi.org/10.47363/JVRR/2022(2)138
Y505H, N679K, D614G, H655Y, D796Y, P681H, N764K, N969K,
L981F N856K, Q954H). Notably, fteen (15) of the thirty (30)
amino acid substitutions are in the receptor binding domain
(RBD) (residues 319-541). There are also a number of changes
and deletions in other genomic regions (V1069I, Δ1265, NSP3
– K38R, NSP4 – T492I; L1266I, A1892T; NSP6 – Δ105-107,
NSP5 – P132H; NSP14 – I42V; A189V; NSP12 – P323L; Q19E,
E – T9I; M – D3G, Δ3133, A63T; N – P13L, G204R, R203K) [3,
5]. According to the latest report by Bambino Gesu hospital in
Rome, the Omicron variant (Figure 2) has many more mutations
than the Delta variant [6].
(Image credited to: Soupvector - Own work, CC BY-SA 4.0,
https://commons.wikimedia.org/w/index.php?curid=112983798)
Figure 1: Omicron variant and other major or previous variants
of concern of SARS-CoV-2 depicted in a tree scaled radially by
genetic distance, derived from Nextstrain on 1 December 2021.
Figure 2: A rst image of the Omicron variant, compared to the
Delta variant, made by the Bambino Gesù Hospital in Rome [6].
Public Health Concerns of Omicron
The Omicron variant is the most divergent variant that has been
detected in signicant numbers during the pandemic so far,
which raises public health concerns that it may be associated
with increased transmissibility, signicant reduction in vaccine
effectiveness and increased risk for reinfections.
The emergence of the Omicron variant came has no surprise. It
would be recall that SARS-CoV-2 has been previously reported
to acquires at least one new mutation in its genome every two
weeks [7, 8]. The potential implications of this observed mutations
in terms of diagnostics, therapeutics and vaccine development is
being investigated some of which include:
Ability to spread more quickly in humans
The current emergence of Omicron as the predominant variant
in South Africa raises worries that the Omicron variant may be
more transmissible than Delta variant, but due to the low number
of cases in South Africa when Omicron emerged, it is unclear if
this variant is more transmissible than the Delta variant. Further,
the relatively small number of cases documented to date makes
it difcult to estimate transmissibility. Analysis of the changes in
the spike protein indicates that the Omicron variant is likely to
have increased transmission compared to the original SARSCoV-
2 virus, but it is difcult to infer if it is more transmissible than
Delta [4, 5].Investigations in South Africa using S-gene target
failure (SGTF) of the PCR assays as a proxy for the variant have
shown that there is a very sharp increase in incidence across most
provinces since mid-November, with the most pronounced increase
in the Gauteng province, where SGTF is observed for more than
50% of all tested specimens in the last few days. Sequencing
of 77 selected SGTF samples from Gauteng collected between
12 and 20 November 2021 conrmed all of them as Omicron.
These ndings presented in a press conference held by the South
African Ministry of Health on 25 November 2021 suggest that the
Omicron variant is already dominant in Gauteng and is present
in signicant magnitudes in most parts of South Africa. Overall,
COVID-19 case numbers are rapidly increasing in Gauteng, albeit
from low levels, and it is likely that this increase is driven by the
presence of Omicron [5].The reporting of sequencing results in
the African region is low overall. Only Botswana and South Africa
have reported sequences from samples collected within the last 30
days to a level that allows for detection of community transmission
of Omicron. This means that ongoing transmission of this variant
cannot be excluded for other countries. Since the variant is spread
across regions in South Africa and has been detected in Botswana,
some circulation in other countries is likely [5]. According to
a BBC News report [1], daily infections in South Africa were
averaging between 200 and 300 in mid-November, until the
emergence of Omicron. Some 8,500 new COVID-19 infections
were registered in the latest daily gures. That is almost double
the 4,300 cases conrmed the previous day. This is suggestive of
increased transmissibility and call for concerns. The number of
Omicron reported to GISAID EpiCoV from samples collected
since 26 October 2021 from all countries and territories in Africa
is presented in Table 1. A total of 100 sequences were reported,
of which 59 were conrmed cases of Omicron.
Table 1. Frequency of Omicron sequences in Africa [5]
Ability to cause either milder or more severe disease in humans
So far, the Omicron variant has shown signs of high frequency
of mutation and transmissibility. However, clinical manifestation
associated with it appear to be very mild. Scientists in South Africa
and around the world are conducting research to better understand
the dynamics of the new variant and will continue to share the
ndings of these studies as they become available. Initial ndings
suggest that there may be an increased risk of re-infection with
Omicron (i.e, people who have previously suffered COVID-19
could become re-infected more easily with this new variant), as
compared to other variants of concern, but the information is
scanty [3]. Currently, it is unclear if infection with the Omicron
variant causes the severe type of COVID-19 or not. More number
of cases will be needed to associate the Omicron variant with
disease severity. Initial ndings from South Africa indicates that
there are no unusual symptoms associated with Omicron variant
infection, and as with other variants. So far, some patients have
been reported to be symptom free [5].
J Viro Res Rep, 2022 Volume 3(1): 2-4

Citation: Seyi Samson Enitan, Eong Joseph Eong, Surajudeen Alim Junaid, Ernest Chibuike Ohanu, Grace Eleojo Itodo, et al (2022) Public Health Concerns of
SARS-CoV-2 Omicron Variant: What We Know So Far!. Journal of Virology Research & Reports. SRC/JVRR-138. DOI: doi.org/10.47363/JVRR/2022(2)138
J Viro Res Rep, 2022
Ability to evade detection by specic diagnostic tests
Existing SARS-CoV-2 PCR diagnostics have continue to detect
this variant. Several laboratories have indicated that for one widely
used PCR test, one of the three target genes is not detected (called S
gene dropout or S gene target failure) and this test can therefore be
used as marker for this variant, pending sequencing conrmation.
Using this approach, this variant has been detected at faster rates
than previous surges in infection, suggesting that this variant may
have a growth advantage [3]. The current Food and Drug Agency
(FDA)’s analysis has identied the following EUAauthorized
molecular tests whose performance may be impacted by other
SARS-CoV-2 viral mutations: Xpert Xpress SARS-CoV-2 DoD,
Xpert Xpress SARS-CoV-2, Xpert Omni SARS-CoV-2 (Cepheid),
Linea COVID-19 Assay Kit (Applied DNA Sciences, Inc.), TaqPath
COVID-19 Combo Kit (Thermo Fisher Scientic, Inc.), Accula
SARS-CoV-2 Test (Mesa Biotech Inc.), among others. However,
the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-
PCR Diagnostic Panel and the Multiplex Assay for Flu and SARS-
CoV-2 are expected to detect the Omicron variant. Meanwhile, the
Thermo Fisher TaqPath COVID-19 Combo Kit (3 total targets) has
signicantly reduced S-gene target sensitivity due to the deletion at
H69 and V70 in the B.1.1.529 (Omicron) spike protein. Specimens
being tested using the TaqPath COVID-19 Combo Kit that yield an
S gene target failure (SGTF) could be Omicron. Importantly, any
possible Omicron specimen must be conrmed by sequencing. It is
expected that since the TaqPath COVID-19 Combo Kit is designed
to detect multiple genetic targets, the overall test sensitivity should
not be affected negatively [9, 10].
Decreased susceptibility to therapeutic agents
Nearly all lineages designated as Delta remain susceptible to
available monoclonal antibody therapeutics and are preventable
by the current vaccines. Currently, there are no virus-specic data
available to assess whether monoclonal antibody treatments will
retain efcacy against the Omicron variant. Based on data from
other variants with signicantly fewer changes in the RBD, the
expectation is that the Omicron variant will remain susceptible
to some monoclonal antibody treatments, while others may have
less potency [4, 11].
Ability to escape vaccine-induced immunity
At the moment, there are no data available to assess the
Omicronneutralizing ability of sera from vaccinees or convalescent
patients with previous SARS-CoV-2 infection [4]. Laboratory
and epidemiological studies are needed to assess the impact
of the Omicron variant on vaccine efcacy and breakthrough
infections, including individuals who have received booster doses.
Experts are highly optimistic that vaccines will continue to play a
critical role in controlling the COVID-19 pandemic, particularly
to offer protection against hospitalization and death. Among the
possibilities mentioned above, the ability to escape vaccineinduced
immunity— would likely be the most worrisome because once
a large proportion of the population is vaccinated, there will be
immune pressure that could favor and accelerate emergence of
such variants by selecting for “Escape mutants” [12-14]. We
however, hope this is not the case with the Omicron variant.
Other concerns include: Omicron will place more pressure on
COVID-19 vaccine inequity in Africa (where under 7% of the
population is vaccinated). Besides, unless drastic measures are
taken, another broad-based lockdown is already looming with
potential economic, social and educational impacts. Nobody
want this to happen, hence the need for urgent public health
interventions to contain the new variant.
Public Health Interventions to contain Omicron
Measures to slow down or contain the virus will include among
others ravel restrictions. Active epidemiological surveillance,
early detection, isolation and case management Vigorous
testing of travelers regardless of vaccination status. Airport
Surveillance Post-Arrival Testing and Sequencing (COVID-19
viral test should be conducted for all travelers 3-5 days after
arrival. Travelers who are yet to receive the booster dose should
self-quarantine for 7 days, even if their test is negative. It is
also important for Travelers to self-isolate if they test positive
or become symptomatic).Continuous strengthen of the health
systems, especially in resource-limited countries is very critica
l. Enforcement of non-pharmaceutical measures including mask
mandate on Planes and public places. Robust contact tracing of
suspected cases. Acceleration of vaccine coverage for high-priority
groups, especially the booster doses. Prioritization of laboratory
studies to support eld ndings (Laboratory data and clinical
ndings are needed to ascertain if those who are vaccinated and
boosted are less likely to be infected with Omicron or not. Health
care professionals including the Clinical laboratory staff should
be: 1) aware that genetic variants of SARS-CoV-2 arise regularly,
and false negative test results can occur, 2) Molecular tests that
use multiple genetic targets to determine a nal result are less
likely to be impacted by increased prevalence of genetic variants
and 3) consider negative results in combination with clinical
observations, patient history, and epidemiological information and
consider repeat testing with a different EUA authorized or FDA
cleared molecular diagnostic test (with different genetic targets) if
COVID-19 is still suspected after receiving a negative test result.
International cooperation and solidarity with global partners
including WHO should be sustained especially in the area of
information sharing according to the IHR agreement. Continuous
provision of technical supports to resource-limited countries to
enable early response to this variant, as well as to aid access to
diagnostics, vaccines, and therapeutics.
Highlights of Existing knowledge
So far we now know that a new variant (Omicron) with more
signicant numbers of mutation than the Delta variant is currently
raving the world with a likely higher transmissibility rate.
• Degree of associated severity is yet to be known.
• Existing SARS-CoV-2 PCR diagnostics have continue to
detect this variant.
• Decreased susceptibility to existing therapeutic agents should
be anticipated.
• Data to support the ability of the variant to escape
vaccineinduced immunity is being anticipated.
• The variant will continue to place a strain on the already
overwhelmed fragile health care system, especially those of the
developing countries. In addition, infection with COVID-19
does not confer a long lasting immunity (Immunity to COVID
-19 does not involve long-term memory cells).
• Serum therapy is useful in less severe cases.
• Adequately treated cases do not become seronegative as
• quickly as possible.
• A lot of likely surrogates for the diagnosis of COVID-19 are
still being investigated.
Patients who had recovered from COVID 19 can be re-infected
by the Omicron variant with potential for high fatality depending
on the immune status.
Volume 3(1): 3-4

Citation: Seyi Samson Enitan, Eong Joseph Eong, Surajudeen Alim Junaid, Ernest Chibuike Ohanu, Grace Eleojo Itodo, et al (2022) Public Health Concerns of
SARS-CoV-2 Omicron Variant: What We Know So Far!. Journal of Virology Research & Reports. SRC/JVRR-138. DOI: doi.org/10.47363/JVRR/2022(2)138
Copyright: ©2022 SS Enitan, et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
J Viro Res Rep, 2022
Highlights of knowledge gaps
Identied knowledge gaps include: 1) Virological characterization,
including in-vitro infectivity studies and neutralization studies
evaluating both vaccinee and convalescent sera are still under way.
2) Lack of sequencing and screening using S-gene target failure in
many of the likely affected countries means that the true prevalence
of this variant is likely underestimated. 3) The severity of this
strain particularly with reference to impact on hospitalization and
fatality is yet to be determined. 4) Epidemiological analyses to
estimate growth rates and secondary attack rates is also not known.
5) Analyses of the vaccine effectiveness for different vaccines
against Omicron (direct and indirect effects) are currently being
investigated. 6) Cross-protection of natural immunity from other
SARS-CoV-2 variants is also not known.
Conclusion
No doubt, Omicron is here to stay with us like other variants,
enhanced genomic and epidemiological surveillances is important
to stay one-step ahead of the virus in the molecular-arm-race. At
the moment, research efforts are ongoing to learn more about the
variants to better understand how easily it might be transmitted
and whether currently authorized vaccines will protect people
against it. Information regarding the virologic, epidemiologic,
and clinical characteristics of the new variant will be emerging
in the coming days.
Competing Interests
The authors have declared that no competing interests exist.
Funding
This compilation is a review article written by its authors and
required no substantial funding to be stated.
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