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A mini review on omicron variant of SARS-COV: A new variant of concern (VOC)

Authors:
  • Independent Researcher
  • Independent Researcher
  • university of okara

Abstract

The Corona Virus Disease (COVID-19) is a pandemic which outbreak from Wuhan China in late 2019. It has produced serious disturbances and unprecedented problems around the whole world including in worldwide healthcare systems. Severe corona viral acute syndrome 2 (SARS-CoV-2) causing a severe viral pneumonia which began in December 2019 in Wuhan. The Omicron virus is a newly emerging variant of previously existing SARS-CoV-2. This variant is firstly reported in South Africa on November 24, 2021. The World Health Organization (WHO) identified it as a variation of concern on November 26, 2021. A large number of mutations (60 mutations) with several novel mutations, are discovered in this variant and these mutations disrupt the spike protein targeted by most COVID-19 vaccines. Higher degree of mutations in the virus makes it virus of concern in its transmission, effects on immune system and level of vaccine resistance. As a result, the variant was quickly identified as "of concern," and several countries instituted travel restrictions in an attempt to prevent the spread of the mutation throughout the world. Omicron also reported as zoonotic disease.
*Corresponding author: Muhammad Saleem Khan
Department of Zoology, Faculty of Life Sciences, University of Okara, Okara 56130 Pakistan.
Copyright © 2022 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0.
A mini review on omicron variant of SARS-COV: A new variant of concern (VOC)
Ali Umar 1, Zeeshan Ulfat 1, Muhammad Waseem Aslam 1, Ahmad Waheed 1, Nasir Ali 1, Saira Parveen 2, Neelam
Amjad 3, Muhammad Wajid 1, Azka Zafar 1, Muhammad Shoaib Akhtar 4, Kamran Jafar 1, Shabbir Ahmad 1,
Hasnain Akmal 1, Nazaket Ali 1, Warda Zafar 1, Hina Naz 1, Sadia Bashir 1, Alia Umar 1 and Muhammad Saleem
Khan 1, *
1 Department of Zoology, Faculty of Life Sciences, University of Okara, Okara 56130 Pakistan.
2 Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore Pakistan.
3 Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore Pakistan.
4 Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara 56130 Pakistan.
GSC Biological and Pharmaceutical Sciences, 2022, 19(01), 001004
Publication history: Received on 11 February 2022; revised on 28 March 2022; accepted on 30 March 2022
Article DOI: https://doi.org/10.30574/gscbps.2022.19.1.0106
Abstract
The Corona Virus Disease (COVID-19) is a pandemic which outbreak from Wuhan China in late 2019. It has produced
serious disturbances and unprecedented problems around the whole world including in worldwide healthcare systems.
Severe corona viral acute syndrome 2 (SARS-CoV-2) causing a severe viral pneumonia which began in December 2019
in Wuhan. The Omicron virus is a newly emerging variant of previously existing SARS-CoV-2. This variant is firstly
reported in South Africa on November 24, 2021. The World Health Organization (WHO) identified it as a variation of
concern on November 26, 2021. A large number of mutations (60 mutations) with several novel mutations, are
discovered in this variant and these mutations disrupt the spike protein targeted by most COVID-19 vaccines. Higher
degree of mutations in the virus makes it virus of concern in its transmission, effects on immune system and level of
vaccine resistance. As a result, the variant was quickly identified as "of concern," and several countries instituted travel
restrictions in an attempt to prevent the spread of the mutation throughout the world. Omicron also reported as
zoonotic disease.
Keywords: Omicron; Corona Virus; COVID-19; Virus recombination; Mutation; SARS-CoV-2
1. Introduction
The Corona virus Disease (COVID-19) is a pandemic which outbreak from Wuhan China in late 2019 [1-4]. It has
produced serious disturbances and unprecedented problems around the whole world including in worldwide
healthcare systems [5-7]. Severe corona viral acute syndrome 2 (SARS-CoV-2) causing a severe viral pneumonia [8]
which began in December 2019 in Wuhan, China [9] infected more than 271 million individuals and caused more than
5 million deaths worldwide till December 14, 2021. The Omicron virus is a newly emerging variant of previously existing
SARS-CoV-2. This variant is firstly reported in South Africa on November 24, 2021. The World Health Organization
(WHO) identified it as a variation of concern on November 26, 2021, and It is given the name omicron, which is a Greek
letter. A large number of mutations (60 mutations) with several novel mutations, are discovered in this variant and
these mutations disrupt the spike protein targeted by most COVID-19 vaccines. Higher degree of mutations in the virus
makes it virus of concern in its transmission, effects on immune system and level of vaccine resistance. As a result, the
variant was quickly identified as "of concern," and several countries instituted travel restrictions in an attempt to
prevent the spread of the mutation throughout the world. However, by December 7, 2021, the variation had spread to
over 50 countries [10].
GSC Biological and Pharmaceutical Sciences, 2022, 19(01), 001004
2
2. Origin of Omicron
Existing literature showed that Cells in the lungs and gastrointestinal tract have been found to be capable of harboring
both SARS-CoV-2 and common-cold coronaviruses at the same time. Virus recombination occurs when two different
viruses in the same host cell interact with one another while reproducing themselves. This results in the development
of new copies of the virus that contain genetic material from both "parents." Laut Soundararajan and colleagues'
findings, this novel mutation may have initially evolved in a person who was infected with both infections when a variant
of SARS-CoV-2 picked up the genetic sequence from the other virus. The study has not yet been subjected to peer review
[11].
Figure 1 Origination of Omicron variant from common cold virus and previously existing SARS-CoV2
Neither unusual symptoms nor asymptomatic individuals have been reported in association with the variant, as has
been the case with other variants in the previous literature. In the early stages of the variant's diagnosis, patients
complained of fatigue and aches and pains. according to Angelique Coetzee, chair of the South African Medical
Association patients with this variant had no loss of taste, change in smell and cough [12]. The presence of two Omicron
variants (Standard BA1 and Stealth Omicron BA2) has been proved by researchers. BA.2 has been called "Stealth
Omicron" because it doesn't have the deletion that PCR tests can use to find it. This makes it different from the
"standard" variety. According to computational modelling, the variant may also evade cell-mediated immunity. A
relationship to HIV infection could possibly explain the high frequency of mutations in the Omicron variant's sequence.
Indeed, in order to be affected by such a large number of changes, the virus must have evolved for a long time without
killing or eliminating its host. One example is when a person has a weaker immune system but is receiving adequate
medical care to survive. This is true for HIV patients in South Africa, where they account for more than 20% of the
population [13].
2.1. Variants of Omicron:
Figure 2 Omicron Variants
The presence of two Omicron variants (Standard BA1 and Stealth Omicron BA2) has been proved by researchers. BA.2
has been called "Stealth Omicron" because it doesn't have the deletion that PCR tests can use to find it. This makes it
different from the "standard" variety. According to computational modelling, the variant may also evade cell-mediated
GSC Biological and Pharmaceutical Sciences, 2022, 19(01), 001004
3
immunity. A relationship to HIV infection could possibly explain the high frequency of mutations in the Omicron
variant's sequence. Indeed, in order to be affected by such a large number of changes, the virus must have evolved for a
long time without killing or eliminating its host. One example is when a person has a weaker immune system but is
receiving adequate medical care to survive. This is true for HIV patients in South Africa, where they account for more
than 20% of the population [13].
2.2. Symptoms of Omicron
Neither unusual symptoms nor asymptomatic individuals have been reported in association with the variant, as has
been the case with other variants in the previous literature. In the early stages of the variant's diagnosis, patients
complained of fatigue and aches and pains. according to Angelique Coetzee, chair of the South African Medical
Association patients with this variant had no loss of taste, change in smell and cough [12].
Figure 1 Symptoms of Omicron Variant
As a result of ongoing research, it appears that Omicron may be the most contagious variant found in South Africa to
date. By the end of November, the most recent date for which data is available, Omicron was responsible for 70% of all
cases in South Africa; it is expected to have increased to more than 90% by now. The Omicron outbreak is centered in
the South African province of Gauteng, where daily COVID-19 cases are doubling every three to four days, according to
the World Health Organization. The number of active COVID-19 cases in Tshwane increased from 6,697 to 20,425 in
less than a week's time. In Gauteng, South Africa's most populous province, one out of every three tests’ results in a
positive result for HIV. With such a high positivity rate, it is likely that COVID-19 is being transmitted widely throughout
the population, and the actual number of cases is therefore likely to be higher than the official count. The Omicron
variant of the CORONA VIRUS is the fastest spreading variant of the virus solely because of the way it transmits and its
mode of transmission is air [14]. There is various vaccine available for COVID-19 [15, 16]. These vaccines may or may
not prevent the emerging variant omicron.
3. Omicron a zoonotic disease
In February 2022, Omicron was reported in a wild White tailed deer by researchers at Pennsylvania State University in
Staten Island [17].
4. Conclusion
Higher degree of mutations in the virus makes it virus of concern in its transmission, effects on immune system and
level of vaccine resistance. As a result, the variant was quickly identified as "of concern" and several countries instituted
travel restrictions in an attempt to prevent the spread of the mutation throughout the world. Omicron also reported as
zoonotic disease.
Compliance with ethical standards
Disclosure of conflict of interest
Authors have no conflict of interest.
GSC Biological and Pharmaceutical Sciences, 2022, 19(01), 001004
4
Statement of ethical approval
The present review article work does not contain any studies performed on animal’s/ humans’ subjects by any of the
authors.
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These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2. 1. Background There are a variety of human diseases with unknown etiology. A viral parentage has been purposed for numerous diseases and also has significance to search new viruses [1]. Various difficulties have been faced which scrutinize new viruses, such as some viruses do not replicate in vitro and have cytopathic effects (CPE). The viruses that are unable to replicate in vitro leads to the failure of virus discovery. The DNA-amplified restriction fragment length polymorphism (cDNA-AFLP 4) technique helps to identify the new viruses including the discovery of new coronavirus [1]. Coronaviruses, a genus of the Coronaviridae family, are enveloped viruses recognized as of large plus RNA strand genome. The size of RNA is 27-32 kb and polyadenylated. There are three groups of coronaviruses that are serologically distinct. Viruses are characterized within each group by their genomic sequence and host range [2]. Coronaviruses have been discovered in mice, turkeys, cats, horse, and humans and cause many diseases including respiratory tract and gastroenteritis [2]. Two human viruses (HCoV-229E, HCoV-OC43) were identified in the mid-1960s and are known to cause the common cold. The recently identified SARS-CoV can cause a life-threatening pneumonia and is the most pathogenic human coronaviruses identified thus far [3]. SARS-CoV is probable to occupy in animal source and recently initiated the epidemic in humans through zoonotic transmission [4]. SARS-CoV is the first membrane of a fourth group of coronaviruses [5]. In Wuhan (Hubei province, China), multiple patients associated to Hunan south China seafood market diagnosed with third zoonotic human coronavirus (CoV) of the century emerged in 31st of December 2019. CoV is similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections including fever, lung infiltration, and difficulty breathing [6]. After an extensive speculation about the causative agent of CoV, the identification of novel CoV was announced by the Chinese Center for Disease Control (CDS) on 19th of January 2020 [7]. The novel CoV, SARS-CoV-2, was insulated from a single patient and later corroborated from 16 more patients [8]. The viral pneumonia of SARS-CoV-2 was quickly predicted as the likely causative agent, while not yet confirmed. The first sequence of SARS-CoV-2 has been submitted after its conformation [9]. Later, five more sequences of SARS-CoV-2 were deposited to the GSAID database on 11th of January from Chinese institutes [10] (Supplementary 1); multiple sequence alignment of SARS-CoV, MERS-CoV, and SARS-CoV-2 carried out and conserved part in DNA, as well as protein sequence, was observed. Hundreds of human deaths were linked with infection having significant morbidities with the age>50. Various clinical symptoms have been highlighted such as dry cough, leukopenia, fever, and shortness of breath. The extracorporeal membrane oxygenation of the patients considered severe cases and need supportive care. The infection of SARS-CoV-2 in elderly patients are less virulent as compared to SARS-CoV (10% mortality) and MERS-CoV (35% mortality) [11]. 1.1. Origin The source of the SARS-CoV-2 is still unclear, although the initial cases have been associated with the Huanan South China Seafood Market. The early patients present in the Market got the virus through either human-to-human transmission or a more widespread animal source [11]. The samples from the infected market showed positive results for the novel coronavirus while no specific animal association has been identified [12]. Through codon analyses, it is suggested that the snakes might be the possible source of the viral infection [13], although the assertion has been disputed by others [14] including possible animal vectors, and the researchers are trying to discover the source of SARS-CoV-2. Coronavirus was thought to infect humans and bats more effectively as both are more related to Coronavirus lifecycle [15]. It has been evidenced that several bats are capable of infecting human cells without intermediate adaptation [16]. The human serology data shows the association of bat CoV proteins leads to zoonotic transmission of SARS-like bat coronavirus for deadliest out breaks [17]. MERS-CoV is also a zoonotic virus and have the origin from the bats [18]. The zoonotic contacts of camel has been evidenced in primary cases of MERS-CoV [19]. These lessons from SARS and MERS highlight the importance of rapidly finding source for SARS-CoV-2 in order to stem the ongoing outbreak [19]. 1.2. Susceptible Populations With low patient data, who may be most sensitive to SARS-CoV-2 is difficult to make robust resolution. Disease severity such as SARS-CoV and MERS-CoV equated strongly to host the condition including biological sex, age, and the overall health [20], and similar findings have been observed in early patients of SARS-CoV-2. The SARS- and MERS-CoV infection leads to increase the severity and death rate in people over the age of 50 years [21]. The observed patients having novel CoV had poor health conditions including diabetes, kidney or heart function issues, and hypertension that make them more susceptible for MERS-CoV outbreak, while diabetes, smoking, cardiovascular disease, hypertension, and other chronic illness have also been observed. In the majority of deaths and corresponding to findings in animal models [22], the results indicate that vigilance is essential for these weak patients following SARS-CoV-2 infection [22]. 1.3. Insights from the Sequence Dr. Zhang’s group at Fudan University and many other groups in China instance the dedication and increased the capacity of the scientific infrastructures in China by rapid sequencing of nearly 30,000 nucleotide of the (COVID) genome [23]. The whole genome analyses of SARS-CoV-2 showed ~80% nucleotide identity to the original SARS epidemic virus. The two different bat SARS-like CoVs (ZC45 and ZXC21) shared ~89% identity with the genome of SARS-CoV-2 [24]. It has been observed that the novel CoV showed recombination with previously identified bat coronaviruses through phylogenetic analyses [25]. A CoV sequence of bat (RaTG3) having 92% sequence identity with the novel virus supports the bat origins for the SARS-CoV-2 [14]. The SARS-CoV-2 spike protein has roughly 75% amino acid identity with SARS-CoV [26] while the SARS-CoV-2 receptor-binding domain (RBD) is 73% conserved with spike RBD of SARS-CoV by narrowing analysis relative to the epidemic RBD [27]. The receptor-binding domain of SARS-CoV-2 was capable of binding with ACE2 in the context of the SARS-CoV spike protein [28]. 1.4. Genomic Features and Lifecycle of the Coronavirus Coronaviruses have unique club-like spikes, and the RNA genome is larger than other virus which leads to a unique mode of replication. Coronaviruses contain ~30 kb of positive-strand RNA genome [29]. The significant features of coronavirus genomes include a 5 caped end which plays an important role in the replication of RNA, as 5 end has a leader sequence along with a UTR region, possessing essential loops. The 3 poly-A tail end has essential structures for RNA genome synthesis and replication [30]. These two modifications allow RNA viruses for translation of replication (replicase) proteins [23]. A coronavirus genome has significant parts and helps for the synthesis and replications of whole genome (Figure 1) [31].
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