What are the reasons that Omicron, the latest SARS-CoV-2 VOC, is so concerning?

1. Introduction

Although this work is about the emergence of a new pathogen, the appearance of novel causes of human infections in the third millennium was quite certain and expected. These manifested as the consequence of global changes on our planet, disrupting otherwise balanced relationships in nature.  However,  the world was still surprised by the sudden emergence of a new viral pathogen (Zhu et al., 2019). Since emerging from Wuhan, China, in  December  2019, the novel coronavirus has caused devastating severe respiratory infections in humans worldwide. A new coronavirus named SARS-CoV-2 was isolated from a cluster of pneumonia patients and spread rapidly worldwide (Xu et al., 2022). The World Health Organization (WHO) declared a coronavirus disease 2019 (COVID-19) global pandemic on March 11, 2020 (WHO, 2020). The pandemic resulted in more than 670 million confirmed cases and more than 6.5 million deaths, making it one of the most serious public health disasters in history (https://www. worldometers.info/coronavirus/).

Despite the slow evolutionary rate of SARS-CoV-2 compared with other RNA viruses, its increased transmission fitness  and/or  immune  evasion,  as well as a long persistence among humans, enabled it to acquire significant genetic diversity  since  it first entered the human population (Parczewski & Ciechanowicz, 2020). Today, it has been a little over three years since the COVID-19 outbreak surged with five global waves caused with several SARS- CoV-2 variants of concern (VOC).

The first identified VOC was  Alpha  in  the United Kingdom by December 2020, which suggested that the evolution of SARS-CoV-2 had changed unpredictably. The leading factors of virus evolution include accidental epidemiological effects, mutations connected with increased transmission and infectivity, severe clinical presentations, immune escape and excellent adaptability to the new host.

Soon after, the second VOC – Beta, the third VOC – Gamma and the fourth – Delta, were identified in South Africa, Brazil and India successively. VOCs were found in areas with high infection rates, which is probably related to the high mutation frequency promoted by the adaptive evolution of the virus. Today, Omicron, the fifth and last SARS-CoV-2 variant of concern, was initially detected in samples obtained in  Botswana and South Africa in mid- and late-November 2021, respectively (Jung et al., 2022). The last variant caused a new global wave, with faster transmission during the past eight months. It shows different characteristics than previous-ancestral variants: very high infectivity, high spreading rate, minimal pathogenicity, and vaccine and antibody-tolerant (Rana et al.,  2022).  Omicron has evolved into five main lineages, including BA.1, BA.2, BA.3, BA.4, and BA.5. BA.2 sublineage was the dominant strain all over the world for several months with a very high rate of propagation (Le Page, 2022; Callaway, 2021). This subvariant has lower virulence but greater transmissibility than previous variants and predominantly affects the upper respiratory tract, meaning less lung or other organ involvement (WHO, 2021).

In early 2023, a new rising Omicron subvariant XBB.1.5 (unofficially nicknamed “Kraken” by some scientists online) appears to be the most transmissible strain so far (https://www.yalemedicine.org/news/omicron-xbb-kraken-subvariant). It circulates with two other continuously circulating subvariants recently, such as BQ 1.1 and BA.5. The last identified subvariant shows enhanced transmissibility, which comes from their ability to evade immune responses, especially in people who were  previously  infected, but not vaccinated (https://www.yalemedicine.org/news/5-things-to-know-omicron).

1.1. The evolution of SARS-CoV-2

Coronaviruses were first isolated in the 1930s as causative agents of respiratory (RT) and gastro- intestinal (GIT) infections in animals. Thirty years later, the first human coronaviruses were discovered and were long associated with mild self-limiting RT and GIT infections in humans until the emergence of two new highly pathogenic coronaviruses during the first two decades of the 21st century (Song et al., 2022). It was the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus  (MERS  Co-V), in 2002 and 2012, in the countries where they were registered for the first time (China and Saudi Arabia) caused severe acute infections of the lower parts of the respiratory tract in humans with a high fatality rate of 10% and 35%, respectively (Zhong et al., 2003; Zaki et al., 2012).

The last three emerging coronaviruses have undergone a long evolution, and their  origins  are still unknown. It was about animal coronaviruses whose natural reservoirs are certain species of bats. Before jumping over the species barrier and entering the human population, they were highly adapted to another intermediated host (Zhang et al., 2020; Lam et al., 2020). Although in the recent past, the entry of highly pathogenic emerging coronaviruses  into the human population  occurred  twice  according to an identical scenario, these events were still not a sufficient warning for humans that they could be repeated. This is what exactly happened, and the new coronavirus made a third jump, by which it entered the world of humans just like the previous two times, from the animal world, having previously been very well prepared in the intermediate host to continue its survival in human hosts as efficiently as possible (Wong et al., 2021).

Analysis of the genomes of the last three identified coronaviruses indicates a high degree of genomic homology between them: ~79% between SARS- CoV-2 and SARS-CoV, slightly less (~50%) between the new SARS-CoV-2 and MERS-CoV. However, despite the high genomic homology of SARS-CoV-2 and SARS-CoV, the difference at the level of the receptor binding domain (RBD) in the spike protein makes the new coronavirus more transmissible, with a stronger binding affinity for target cell receptors and higher replicative fitness (Lu et al., 2020). Nevertheless, the highest genome homology of 96% between SARS-CoV-2 and CoV of a specific type, the horseshoe bats RaTG13 Rhinolophus affinis, clearly indicates the origin of SARS-CoV-2 (Zhou et al., 2020).

Phylogenetic analyses show that the last SARS- CoV-2 VOC probably did not emerge from other VOCs and suggested that the Omicron VOC evolved independently by convergent evolution. The key question  is  how  Omicron  came  into   existence and why it differs from ancestral variants. Today, researchers are trying to explain the evolution of the origin of Omicron by the existence of three possible scenarios. The first theory is its efficient replication in an immunocompromised person over a long period. The possibility of this scenario which has been reported is that the SARS-CoV-2 last variant replicated in a young HIV/AIDS female from South Africa for more than six months. In that way, the virus accumulated many new and unique mutations (Karim et al., 2021). Another theory is that Omicron has been  circulating  among  humans  unnoticed  for a while, especially in countries with suboptimal surveillance of COVID-19, with a low frequency of sequencing of emerging variants compared to South Africa. The last possibility is that the Omicron may have evolved in a nonhuman species, from which it went back to humans (Wei et al., 2021). Besides that, the fact that Omicron shows an expanded host range and an increased capacity to generate new animal natural reservoirs suggests that SARS-CoV-2 can be detected, e.g., in household pets as well as in farm and wildlife animals, which is of particular importance for the evolution of the virus (Sharun et al., 2021).

1.2. The main properties of the coronaviruses: SARS-CoV-2 genom organisation and composition of the spike protein

SARS-CoV-2 belongs to the family of coronaviruses, to the order Nidovirales, subfamily Orthocoronavirinae and genus ß-coronavirus.  Coronaviruses  are spherical particles 80-120  nm  in  diameter.  Due to vertical projections in the  form  of  spikes  from the outer surface, the viral  particles  appear  like the solar corona or crown, which determines their name (Lazarevic et al., 2021). The genome of the coronavirus is in the form of single-stranded positive RNA (“+”ssRNA) and represents one of the longest genomes among RNA viruses, consisting of ~30,000 nucleotides. The first two-thirds of the genome, starting from the 5¢non-transcriptional UTR end, comprises the ORF1a  and  ORF1ab  genes  known as replicase complexes, which encode polyproteins pp1a and pp1ab. These are cleaved by autocatalytic degradation into 16 non-structural proteins (nsp 1-16) that have multiple roles in the transactivation of other viral  genes,  transcription  and  replication of the genome. Also, nonstructural  gene  products are involved in  immune  modulation  and  evasion of innate immunity mechanisms (Kim et al., 2020). The last third of the viral genome consists of genes encoding four structural proteins of the virus: S (glycoprotein outgrowths of the virus  envelope  in the form of spikes named spike protein), E (envelope proteins), M (transmembrane glycoprotein) and N (nucleocapsid protein), as well as a set of accessory genes (Wu et al., 2020; Tortorici & Veesler, 2019). The S gene encodes the S protein, the most prominent part of the viral particle that ensures the virus attaches to and enters the target cell. M and E proteins, products of the M and E genes, are responsible for forming the viral envelope during the final stages of the virus life cycle, assembly and release of the virions. The E protein, which is the most conserved, has an essential role  in  the  pathogenesis  of  COVID-19  because  it binds the human PALS1 protein, which is crucial in the biogenesis of  adherence  and  the  establishment of polarity in epithelial cells. Finally, the N protein product of the N structural gene participates forming of helical ribonucleocapsid (Teoh  et  al.,  2010).  A set of accessory genes encodes proteins, disrupting signalling ways in  the  cell  and  avoiding  the  effect of interferon, as one of the first lines of defence of the activated innate immunity during early virus- induced infection. (Michel et al., 2020)

The spike is a transmembrane  glycoprotein  on the virus’s surface of a homotrimer comprising three identical units. There is a high degree of similarity in the amino acid composition of the S protein of human- infecting CoV and coronaviruses of other animal species  (civet  cat  ~77%,  bat  75-98%  and  pangolin ~92%) (Zhang et al., 2020; Zhou et al., 2020). It consists of S1 and S2 subunits. The S1 subunit is composed of the N terminal domain (NTD) and the RBD, which plays a crucial role in binding to a specific cell receptor- angiotensin-converting enzyme 2  (ACE2)  (Huang et al., 2020; Song et al., 2018). Also, RBD targets the immune system (humoral and T-cell response) and antiviral drugs. Within the RBD is a region designated as the receptor binding motif (RBM), representing a highly variable structure within the splice, which is particularly important for binding with ACE2 (Walls et al., 2020). The second S2 subunit consists of several parts: fusion protein (FP), heptapeptide domains-1 and -2, and transmembrane and cytoplasmic domains (Hoffmann et al., 2020). S protein exists in open and closed forms. When the RBM is closed, it is hidden. At the same time, in the open conformation, the RBM, as part of the RBD, protrudes above the homotrimeric units of the spike, which enables the virus to bind to ACE2 as an initial step in the initiation of infection. The next step is entering the virus by fusing the envelope with the cell membrane, utilising the S2 subunit (Xu et al., 2022). Spike, in its native form, exists as an inactive precursor of S1 and S2 subunits, which are joined by non-covalent bonds in the pre-fusion phase. Upon binding to the receptor on the target cell, the S protein is cleaved by the activity of cellular protease enzymes: furin and transmembrane serine protease (TMPRSS2). This cleavage results in irreversible conformational changes in the junction crucial for virus entry into the cell (Hoffmann  et  al.,  2020).  The  uniqueness of the genomic organisation of SARS-CoV-2 is the existence of a short RRAR sequence, which precisely at the site of very precise polybase cleavage of the S protein conditions, the insertion of four amino acids that make up the motif recognised by the furin protease. This cleavage is thought to destabilise SARS- CoV-2, leading to conformational changes necessary for the RBD to bind to the receptor (Lan et al., 2020).

Comparative analyses of the genome of SARS-CoV-2 and other related animal coronaviruses point to the uniqueness of this event only in the case of human SARS-CoV-2, except the coronavirus of one species of bats, Rhinolophus malazanus (RmYN02), where also at the site of polybase cleavage three amino acids are inserted (Wrobel et al., 2020). It is this similarity that clearly shows that the S protein is not only a key player in the pathogenesis of infection but also in the evolution of the coronaviruses, ensuring that it infects different species, evolves to adapt to a new host and is relatively easy to pass from species to species (Dhama et al., 2020).

2. Genetic variability and major variants of SARS-CoV-2 VOC

The emergence of new virus variants results from mutations in the viral genome. It is known that the mutation rate of RNA viruses is significantly higher than viruses with DNA genomes, mainly due to uncorrectable errors made by RNA-dependent RNA polymerase during RNA replication (Parczewski et al., 2020).

Although with about 30,000 base pairs, SARS- CoV-2 has the largest genome of all known RNA viruses, the integrity of its genome is retained by the proofreading function of the viral polymerase (Jung et al., 2022; Gorbalenya et al., 2006). Specifically, the nonstructural protein 14 (Nsp14) and its cofactor Nsp10 perform exonuclease activity, substantially reducing the accumulation of mutations in the viral genome (Saramago et al., 2021). This event is crucial in limiting SARS-CoV-2 mutation rates, registered with a frequency of 1:1000 substitutions per place/ year (Buchan & Yao, 2021). However, the appearance of a large number of SARS-CoV-2 variants is a consequence of the accumulation of mutations that affect many properties such as virus transmissibility, its cellular tropism and pathogenicity, virulence, infectivity, which poses a serious challenge to the effectiveness of current vaccines, antiviral therapy and diagnostic tests (Lazarevic et al., 2021). Initially, the evolution of SARS-CoV-2 was relatively slow until the emergence of the D614G variant, whose increased transmissibility resulted in it becoming the globally dominant variant (Korber et al., 2021). Since then, the speed at which new variants of SARS-CoV-2 have continued to emerge has steadily increased.

2.1. Alpha VOC – B.1.1.7 (20I/501Y.V1, VOC 202012/01)

Alpha subtype or B.1.1.7 (20I/501Y.V1, VOC- 202012/01) represents the first identified VOC in the United Kingdom (UK) during September 2020. Compared with pre-existing variants, the Alpha variant is associated with increased transferability and risk of death in hospitalised patients. So many studies reported that the mortality rate was 61% (42– 82%), much higher than other variants (Davies et al., 2021a; Davies et al., 2021b).

Alpha subtype has nine mutations (169–70 deletion, 1144 deletion, N501Y, A570D, P681H, T716I,  S982A,  D1118H,  and  D614G)  in  the  S protein and some with significant biological impact. Mutation N501Y is associated with enhanced RBD affinity to human ACE2. The second one, also in the spike, represents a deletion at position 69/70, related to avoiding the immune response. The third P681H is connected with the conformational changes nearby of the furin polybase cleavage site in S protein into S1/S2 subunits (Graha et al., 2021).

2.2. Beta VOC – B.1.351 (20H/501Y.V2)

The next SARS-CoV-2 VOC, the Beta variant, was first detected in South Africa in October 2020 and resulted in the second wave of COVID-19 infections (Cascella et al., 2022). Beta, as the previous Alpha variant, contains nine mutations in the S protein (L18F, D80A, R246I, K417N, D215G, N501Y, E484K,

D614G, and A701V). Three mutations (N501Y, E484K, and K417N) on the RBD of S protein raise its binding affinity  for  ACE  receptors  (Mwenda et al., 2021) and increase the risk of transmission but decrease its susceptibility to neutralisation by postvaccination sera, monoclonal antibody therapy, and convalescent sera (Cascella et al., 2022).

2.3. Gamma VOC -P1 (B.1.1.28 ; GR/501Y.V3)

Gamma VOC was identified for the first time in four travellers from Brazil, who were tested at an airport in Japan (Fujino et al., 2021), also termed the Brazilian variant. This subtype possesses 17 unique mutations, including three K417T, E484K, and N501Y, located in the RBD of the S protein (Wang et al., 2021). Some of this variant’s mutations affect the virus’s transmissibility and antigenic profile. They also significantly impact the reduction of neutralising roles of antibodies.

2.4. Delta VOC – B.1.617

Variant B.1.617, known as Delta, was identified for the first time at the end of 2020 in India and rapidly spread worldwide from April 2021. There are three sublineages: B.1.617.2, B.1.617.1 and B.1.617.3, with different mutation profiles (Mlcochova et al., 2021). The Delta variant contains ten mutations (T19R, G142D*,156del,  157del,  R158G,  L452R,  T478K, D614G, P681R, and D950N) in the S  protein  – only two in the RBD, while the rest are located in N terminal domain (NTD). All sublineages possess the P681R  mutation  in  the  spike  protein,  which is crucial for increased transmissibility. Also, the P681R mutation stimulates the polybase cleavage of S protein by the cellular furin protease by extension in RRAR motive, which results in significantly higher replicative fitness and “viral load” (Singh et al., 2021). Sublineage B.1.617.2, soon after identification, was recognised as a variant with a high transmission capacity, even more than 60% compared to the Alpha variant. It has four mutations within RBD associated with a significantly increased virus ability for efficient and rapid transmission and immune evasion. Still, it is believed  that  they  also  impact the severity of clinical outcomes. The Delta variant causes more severe disease than the previous four VOCs. Mutation T478K in RBD of the B.1.617.2 variant shows reduced neutralisation by monoclonal antibodies and antibodies from convalescents’ sera.

3. What makes Omicron, the latest SARS- CoV-2 VOC, so concerning?

Omicron VOC, the fifth SARS-CoV-2  variant, was reported for the first time in mid-November 2021 in Botswana and South Africa and immediately raised global concern because of its high transmissibility (Le Page, 2022). A short while later, it became known that the Omicron comprises multiple sublineages: BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), BA.3 (B.1.1.529.3), BA.4 (B.1.1.529.4), and BA.5 (B.1.1.529.5) (Rana et al., 2022). Compared with the Wuhan viral genomes of ancestral COVID-19, Omicron has approximately 60 mutations predominantly located in the S gene. Twelve of the 31 changes in the S1 region of the Omicron spike are located in the N-terminal domain (NTD); 15 in the ACE2 receptor-binding domain (RBD), (DH69/V70, T95I, DY144, K417N, T478K, N501Y, D614G, H655Y, and P681H) where 10 of 15 alterations are located in the receptor-binding motif (RBM) and finally five at the C terminus (Kannan et al., 2021; Ingraham & Ingbar, 2021)

Significant mutations in the S1 subunit affect spike affinity for ACE2 (Q498R and N501Y), phenotypic effects such as increased transmission and immune evasion (E484A), increased viral infectivity and spike processing DH69/V70 (Meng et al., 2021), but also may be associated with negative results of PCR based S-assays. Another six mutations are found in the S2 subunit of the S protein. Three of the six are in the heptapeptide repeat 1 (HR1) region required for fusion as the virus entry mechanism into the cell.

The critical question is: what role do these mutations play in the phenotypic characteristics of Omicron?

According to the CDC, the Omicron variant spreads faster than the original SARS-CoV-2 and the Delta variant. In the first months of 2022, the Omi- cron subvariant named BA.2 began to spread even quicker than other subvariants, followed by BA.4 and BA.5, only to be outdone by the BQ and recently re- ported XBB.1.5 subvariants. Omicron VOC favours infection of the upper respiratory tract and reduces the risk of invasion of the lung (Willet et al., 2022). Consequently, Omicron replicates less efficiently in the lower part of the respiratory tract. Additional- ly, Omicron is often mild but will still cause severe COVID-19 and death in certain patient risk groups, including the elderly with comorbidities or unvacci- nated individuals (Cele et al., 2022). Also, numerous recent studies show that the Omicron VOC evades many, but not all, neutralising antibodies induced by vaccination or previous SARS-CoV-2 infection. The mutations known as D405N, F486V and 69-70 del in BA.2, BA.4 and BA. 5, the last three Omicron sub- variants, are associated with immune escape, and it is possible that these mutations were selected during the prolonged virus survival in the human popula- tion (Willett et al., 2022). Moreover, Omicron VOC causes significantly more vaccine breakthrough in- fections than pre-existing Alpha and Delta variants (Cele et al., 2022). Still, Omicron is showing sensi- tivity to antiviral therapy, such as remdesivir, mol- nupiravir, nirmatrelvir, hydroxycytidine, Paxlovid, and Acriflavine (Vangeel et al., 2022).

4. Perspective – Should we learn to live with SARS-CoV-2 in future?

The answer to this question is yes, we should learn to live with SARS-CoV-2 in the coming times. The appearance of Omicron or future new emerging variants of SARS-CoV-2 is not surprising. On the contrary, this is the expected natural process of virus evolution. Just as all ancestral SARS-CoV-2 variants were never the last ones, likely, Omicron will not be the ultimate variant either.

The hope and expectation are that severe forms of the disease with fatal outcomes will become rare, that COVID-19 will become an endemic  disease, that the virus will have a seasonal character, and that the global  level of  immunity against COVID-19  is sufficiently protective. Should it come to pass, all of this is highly encouraging for future times.

Funding: This research received no external funding.

Informed Consent Statement: Not applicable.

Data Availability Statement: Not applicable. Acknowledgments:   This  review  was  supported by the Ministry of Education and Science of the Republic of Serbia (grant no. OI175073).

Conflicts   of   Interest:   The  authors  declare  no conflicts of interest.

References

1. Buchan, W.B, & Yao, D. J. (2021). Severe Acute Respiratory Syndrome Coronavirus 2: The Emergence of Important Genetic Variants and Testing Options for Clinical Laborato Clinical Microbiology Newsletter, 43(11), 89-96.
2. Callaway, (2021). Heavily mutated Omicron variant puts scientists on alert. Nature, 600(7887), 21.
3. Cascella, , Rajnik, M., Aleem, A., Dulebohn, S.C., Di Napoli, R. (2022). Features, Evaluation, and Treatment of Coronavirus (COVID-19). StatPearls. Treasure Island,FL: StatPearls Publishing. Copyright © 2022, StatPearls Publishing LLC.
4. Cele, , Jackson, L., Khoury, D.S., Khan, K., Moyo- Gwete, T., Tegally ,H., San, J.E., et al. (2022). Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, 602(7898), 654-656.
5. Davies, G., Abbott, S., Barnard, R.C., Jarvis, C.I., Kucharski, A.J., Munday, J.D., et al. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372, 6538.
6. Davies, G., Jarvis, C.I., Edmunds, W.J., Jewell, N.P., Diaz-Ordaz, K., & Keogh RH. (2021). Increased mortality in community-tested cases of SARS-CoV-2 lineage B. 117 Nature, 593(7858), 270-274.
7. Dhama, , Patel, K.S., Sharun, K., Pathak, M., Tiwari, R., Yatoo, I.M., et al. (2020). SARS-CoV-2 jumping the species barrier: Zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus. Travel Medicine and Infectious Disease, 37, 101830.
8. Fujino, T., Nomoto, , Kutsuna, S., Ujiie, M., Suzuki, T., Sato, R., et al. (2021). Novel SARS-CoV-2 variant in travelers from Brazil to Japan. Emerging Infectious Disease, 27(4), 1243–1245.
9. Gorbalenya, E., Enjuanes, L., Ziebuhr, J., & Snijder, E.J. (2006). Nidovirales: evolving the largest RNA virus genome. Virus Research, 117(1), 17-37.
10. Graha, , Seow, J., Huettner, I., Khan, H., Kouphou, N., Acors, S., et al. (2021). Neutralization potency of monoclonal  antibodies  recognizing  dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant. Immunity, 54(6), 1276- 1289.
11. Hoffmann, , Kleine-Weber, H., Schroeder, S., Kruger, N., Herrler, T., Erichsen S, et al. (2020). SARS- CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271-280.
12. https://www.worldometerinfo/coronavirus/.  Accessed on: 24.02.2023
13. https://www.yalemedicine.org/news/5-things-to- know-omicron Omicron and its Subvariants: A Guide to What We Know. Accessed on: 02.2023
14. https://www.yalemedicine.org/news/omicron-xbb- kraken-subvarian Accessed on: 24.02.2023
15. Huang, Y., Yang, , Xu, X.F., Xu, W., & Liu, S.W. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141-1149.
16. Ingraham, E., & Ingbar, D.H. (2021). The omicron variant of SARS-CoV-2: Understanding the known and living with unknowns. Clinical and Translation Medicine, 11(12), e685.
17. Jung, , Kmiec, D., Koepke, L., Zech, F., Jacob, T., Sparrer, K.M.J., et al. (2022). Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? Journal of Virology, 96(6), e0207721.
18. Kannan, , Shaik Syed Ali, P., & Sheeza, A. (2021). Omicron (B.1.1.529) – variant of concern – molecular profile and epidemiology: a mini review. European Review for Medical Pharmacological Sciences, 25(24), 8019-8022.
19. Karim, F., Gazy, , Cele, S., Zungu, Y., Krause, R., Bernstein, M., et al. (2021). HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV -2 infection wave. eLife, 10, e67397.
20. Kim, D., Lee, J.Y., Yang, J.S., Kim, J.W., Kim, V.N., & Chang,  (2020).  The  architecture  of  SARS  CoV-2 transcriptome. Cell, 181(4), 914-921.
21. Korber, B., Fischer, W.M., Gnanakaran, , Yoon, H., Theiler, J., Abfalterer, W., et al. (2020). Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 Virus. Cell, 182(4), 812- 27.e19.
22. Lam, T.T., Jia, , Zhang, Y.W., Shum, M.H., & Jiang, J.F. (2020). Identifying SARSCoV-2-related coronaviruses in Malayan pangolins. Nature, 583, 282–285.
23. Lan, J., Ge, J., Yu, .J, Shan, .S, Zhou, , Fan, S., et al. (2020). Structure of the SARS-CoV-2 spike receptor binding domain bound to the ACE2 receptor. Nature, 581(7807), 215-220.
24. Lazarevic, , Pravica, V., Miljanovic, D., Cupic, M. (2021). Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Viruses, 13(7), 1192.
25. Le Page, , (2022). Understanding omicron. New Scientist, 253(3369), 8-9.
26. Lu, R., Zhao, , Li, J., Niu, P., Yang, B., Wu, H., et al. (2020). Genomic cha¬racterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet, 395(10224), 565- 574.
27. Meng, B., Kemp, A., Papa, G., Datir, R., Ferreira, I.A.T.M., Marelli, S, et al. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35, 109292.
28. Michel,  J.,   Mayer,   C.,   Poch,   O.,   &   Thompson, J.D.  (2020).  Characterization  of  accessory  genes  in coronavirus genomes. Virology Journal, 17(1), 131.
29. Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira I, et al. (2021) SARS-CoV-2 B. 16172 Delta variant replication and immune evasio Nature, 599, 114–119.
30. Mwenda, , Saasa, N., Sinyange, N., Busby, G., Chipimo, P.J., Hendry, J.,  et  al.  (2021).  Detection of B.1.351 SARS-CoV-2 Variant Strain – Zambia. Morbidity Mortality Weekly Reports, 70(8), 280-282.
31. Parczewski, , & Ciechanowicz, A. (2020). Molecular epidemiology of SARS-CoV-2: A review of current data on genetic variability of the virus. Polish Achieves of Internal Medicine, 131(1), 63-69.
32. Rana, R., Kant, R., Huirem, R.S., Bohra, D., & Ganguly, N.K. (2022).  Omicron  variant:  Current  insights  and future direction Microbiology Research, 265, 127204.
33. Saramago, , Bárria, C., Costa, V.G., Souza, C.S., Viegas, S.C, Domingues, S., et al. (2021). New targets for drug design: importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2. FEBS J, 288(17), 5130–5147.
34. Sharun, , Dhama, K., Pawde, A.M., Gortázar, C., Tiwari, R., Bonilla-Aldana, D.K., et al. (2021). SARS- CoV-2 in animals: potential for unknown reservoir hosts and public health implications. Vet Q, 41(1), 181- 201.
35. Singh, .J, Rahman, S., Nasreen, Z., Ehtesham, Z.N., Hira, S., & Hasnain, S. E. (2021).SARS-CoV-2 variants of concern are emerging in India. Nature Medicine, 27(7), 1131-1133.
36. Song, , Li, Z., Li, C., Huang, M., Liu, J., Fang, Q., et al. (2022). SARS-CoV-2: The Monster Causes COVID-19. Frontiers in Cellular and Infection Microbiology, 8(12), 835750.
37. Song, W.,  Gui,  ,  Wang,  X.,  &  Xiang,  Y.  (2018). Cryo-EM structure of the SARS coronavirus spike glycoprotein  in  complex  with  its  host  cell  receptor ACE2. PLoS Pathogens, 14, e1007236.
38. Team von Gottberg, , Bhiman, J.N., Lessells, R.J., Moosa, M.S. Davenport, M.P., de Oliveira, T., et al. (2022). Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, 602(7898), 654-656.
39. Teoh, T., Siu, Y.L., Chan, W.L., Schlüter, M.A., Liu, C.J., Peiris, J.S., et al. (2010). The SARS coronavirus E protein interacts with PALS1 and alters tight junction formation and epithelial morphogenesis. Molecular Biology of the Cell, 21(22), 3838-3852.
40. Tortorici, A., & Veesler, D. (2019). Structural insights into coronavirus entry. Advances in Virus Research, 105, 93-116.
41. Vangeel, , Chiu, W., De Jonghe, S., Maes, P., Slechten, B., Raymenants, J., et al. (2022). Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern. Antiviral Research, 198, 105252.
42. Walls, C., Park, Y.J., Tortorici, M.A., Wall, A., McGuire, & A.T, Veesler, D. (2020). Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, 181(2), 281-292.
43. Wang, P., Casner, R.G., Nair, S., Wang, M., Yu, J., Cerutti, G., et al. (2021). Increased resistance of SARS- CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe, 29, 747–751.
44. Wei, , Shan, K.J., Wang, W., Zhang, S., Huan, Q., & Qian W. (2021). Evidence for a mouse origin of the SARS-CoV-2 Omicron variant. Journal of Genetics and Genomics, 8(12), 1111-1121.
45. Willett, B.J., Grove, J., MacLean, O.A., Wilkie, , De Lorenzo, G., Furnon, W., et al. PITCH Consortium; COVID-19 Genomics UK (COG-UK) Consortium; Haughney, J., Robertson, D.L., Palmarini, M., Ray, S., &, Thomson, E.C. (2022b). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), 1161-1179.
46. Willett, B.J., Grove, J., MacLean, O.A., Wilkie, , Logan, N., Lorenzo, G.D., I. The COVID-19 DeplOyed VaccinE (DOVE) Cohort Study investigators, The COVID-19 Genomics UK (COG-UK) Consortium, The G2P-UK National Virology Consortium, The Evaluation of Variants Affecting Deployed COVID-19 Vaccines (EVADE) investigators, Haughney, J., Robertson, D.L., Palmarini, M., Ray, S., & Thomson, E.C. (2022a). The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism. medRxivpreprint
47. Wong, C.P.,  Lau,  S.K.P.,  &  Woo,  P.C.Y.  (2021). Interspecies Jumping of Bat Coronaviruses. Viruses, 13(11), 2188.
48. World Health Organization (WHO). (2020). https:// www.who.int/europe/emergencies/situations/covid-19. Accessed on: 02.2023
49. World  Health    Organization.     2021.     Classification of Omicron (B.1.1.529): SARSCoV-2  variant  of concern. https://www.who.int/news/item/26-11-2021- classification-of-omicron- (b.1.1.529)-sars-cov-2- variant-of-concern. Accessed on: 02.2023
50. Wrobel, G., Benton, D.J., Xu, P., Roustan, C., Martin, S.R., Rosentha, P.B., et al. (2020). SARS-CoV-2 and bat RaTG13spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nature Structural and Molecular Biology, 27(8), 763-767.
51. Wu, , Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., et al. (2020). Genome composition and divergence of the novel coronavirus (2019- nCoV) originating in China. Cell Host Microbe, 27(3), 325-328.
52. Xu, R., Wang, W., & Zhang W. (2022). As the SARS- CoV-2 virus evolves, should Omicron subvariant B2 be subjected to quarantine, or should we learn to live with it? Front Public Health, 10, 1039123.
53. Zaki, M., van Boheemen, S., Bestebroer, T.M., Osterhaus, A.D., Fouchier, R.A. (2012). Isolation of a novel coronavirus from  a  man  with  pneumonia in Saudi Arabia. New England Journal of Medicine, 367(19), 1814-1820.
54. Zhang, T., Wu, Q., Zhang, (2020) Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Current Bioogyl, 30, 1346–51.
55. Zhong, S., Zheng, B.J., Li, Y.M., Poon, L.L.M., Xie, Z.H., Chan, K.H, et al. (2003).  Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. Lancet, 362(9393), 1353-1358.
56. Zhou, P., Yang, L., Wang,  X.G.,  Hu,  B.,  Zhang, L., Zhang, W., et al. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270-273.
57. Zhu, , Zhang, D., Wang, W., Li, X., Yang, B., Song, J., et al. (2020). China Novel Coronavirus Investigating and Research Team. A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727-733.