SARS-CoV-2 Mutation Mechanism, Features, and Future Perspective

*Tahereh Alinejad, Danial Zareh, Zuo Hao, Tengfei Zhou and Cheng-shui Chen*

### **Abstract**

Over two years, the SARS-CoV-2 virus has evolved by producing several variants by RNA polymerase mutation. This mutation created many virus variants that five of them are designated by WHO. These are Alpha, Beta, Gamma, Delta, and Omicron, among them Alpha, Delta, and Omicron spread faster. Coronaviruses (CoVs) are enveloped in positive-sense RNA viruses and contain huge RNA virus genomes. RNA polymerase controls the replication in which the genomic material is copied, and it often makes errors that lead to create a new mutation. Most mutations create a virus that cannot replicate and spread among people. However, some mutations lead to a virus that can replicate and create a variant. This chapter will discuss the mechanism of the mutations during the last two years and the future of these mutations in SARS-CoV-2.

**Keywords:** SARS-Cov-2 mutation-biochemical mechanisms, RNA polymerase

### **1. Introduction**

To begin, most known human-associated coronaviruses have caused colds, therefore, to date, this family of viruses has not been extensively researched and is still very unknown to humanity, and only a number of severe human diseases have been attributed to this family.

However, in 2003, a virus from this family, which was responsible for severe acute respiratory syndrome (SARS) appeared and spread rapidly among humans and was the starting point for research into coronaviruses [1]. In addition to the 2003 SARS outbreak, coronaviruses (CoVs) have had two other large-scale outbreaks in the last two decades: middle eastern respiratory syndrome (MERS) and now COVID-19. Current coronavirus (COVID-19) originates from a cluster of pneumonia related to the seafood market in Wuhan City, Hubei Province, China [2]. With the occurrence of the MERS and the SARS outbreaks within the past couple of decades combined with the ongoing pandemic, coronaviruses are now considered "emerging pathogens" [1, 3–5]. In (**Figure 1**), you can have a better understanding of the types of diseases and viruses that cause the disease, as well as their relationship and year of spread.

In addition, CoVs disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an infectious disease [6]. SARS-CoV-2

#### **Figure 1.**

*History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases, MERS and SARS are classified as 1D64 and 1D65, respectively.*

belongs to the betacoronavirus genus [1]. As mentioned above, the third highly pathogenic coronavirus to enter the human population is SARS-CoV-2, which is more contagious and has a broad tissue tropism that is likely to increase the prevalence [7].

In December 2019, the SARS-CoV-2 first spread to Wuhan, China, and the rapid spread of the virus sounded the alarm around the world and all countries were on alert. The World Health Organization (WHO) declared the outbreak an epidemic, and several countries quickly confirmed several cases. By May 4, 2020, more than 3.3 million cases had been diagnosed with the disease, a staggering number. It was a concern for governments and humanity [8].

The first observations showed that the virus is transmitted from a carrier to a healthy person through close contact, such as shaking hands and kissing, and by small droplets produced during sneezing, coughing, and talking [9].

Most researchers and scientists are now focused on identifying different types of coronaviruses and in particular the regular identification of new types of mammalian coronaviruses. For example, in 2018, the HKU2-associated coronavirus of bat origin was identified as responsible for the deadly acute diarrhea syndrome in pigs **Figure 1** [5].

#### **1.1 SARS-CoV-2 genome and structure**

Coronaviruses (CoVs) of the family Coronaviridae are enveloped, positive-sense single-stranded RNA genomes ranging from 26 to 32 kilobases in length, which replicate in the cytoplasm [1, 3–5]. All of the highly pathogenic CoVs, including SARS-CoV-2, belong to the betacoronavirus genus, group 2. The SARS-CoV-2 genome sequence shares ~80% sequence identity with SARS-CoV and ~50% with MERS-CoV [3, 4]. Its genome comprises 14 open reading frames (ORFs), two-thirds of which encode 16 nonstructural proteins (nsp 1–16) that make up the replicase complex, whereas the remaining one-third encodes the structural proteins envelope (E), spike (S), nucleocapsid (N), and membrane (M). [1, 4, 5].

#### **1.2 Entry mechanism of SARS-CoV-2**

All external agents that want to enter the host cell have their entry mechanism, and the covids have their mechanism. All covids first bind to the host cell receptor by a surface glycoprotein called spike, which is encoded by themselves, and whose main job is to mediate entry into the host cell. Covids transfer their nucleocapsid to the host cell cytoplasm when their coating fuses with the host cell layer. This occurs in acidic endosomal portions or, in some cases, in the plasma membrane. The route of infection is driven by the spike glycoprotein (S), which is also a major determinant of cellular tropism. This protein is a class I combination protein and plays a key role in binding the virus to the corresponding receptor at the surface of the host cell, also the role of interference between the host membrane and the virus in the cycle is driven by critical structural changes in the spike protein. For beta-coronaviruses, there is a receptor-binding region (RBD) in the spike protein that is involved in binding to the host cell receptor. This occurs when the spike is cleaved by the proximal host protease, then the spike combination peptide is released to facilitate virus entry. ACE2 for SARS-CoV and dipeptidyl peptidase-4 (DPP4) for MERS-CoV have identified receptors. Past investigations have announced that RBDs from the heredity B of beta covids can be arranged into practically distinct clades. Those from clade 1, which incorporates SARS-CoV-2 can enter cells expressing ACE2. This has been tentatively approved by a few investigations exhibiting the crystal construction of the RBD of the spike protein with that of ACE2. ACE2 is enhanced in the ciliated bronchial epithelial cells, which have all the major targets of being significant focuses of SARS-CoV-1 and -2, though DPP4 is advanced in the unciliated epithelial cells, which act as target cells for MERS disease. The two receptors are expressed in the sort II pneumocytes, which are contaminated by both infections. Aside from the ACE2 receptor, neuropilin-1 has been as of late distinguished as an entry factor that functions in concert with ACE2 to facilitate SARS-CoV-2 entry. In any case, expression of ACE2 in the mix with a host transmembrane serine protease has been displayed to confer susceptibility to SARS-CoV-2 [1].

Like other covids, the SARS-CoV-2 section happens by means of a multi-step interaction of cell surface connection, receptor commitment, proteolytic cleavage, and membrane combination that includes a few particular domains on the spike protein [1], which is shown clearly in (**Figure 2**).

As mentioned, the function of the RBD receptor plays the most important role in the virus entering the host cell. Researchers have also recently realized that protease plays a key role in facilitating virus entry, processing covid results, and as a potential barrier to species. Research shows that the entry of the virus SARS-CoV-2 is increased following the external expansion of trypsin. The most colorful role among host proteases is the serine transmembrane protease Tmprss2, although it should be noted that different types of this family, as well as certain cathepsins, are involved. Although the spike protein has been shown to be cleaved by host proteases, there is further evidence that this protease acts on the receptor and activates it [1].

SARS-CoV-2 is different from SARS-CoV-1 and other SARS-related types due to the presence of a furin cleavage (FCS) site containing the PRRAR multi-basic amino acid in the S1/S2 convergence of the viral spike protein (S). Although FCS is present in other relatives of CoVs, such as HKU1-CoV, MERS-CoV, and OC43-CoV. However, SARS-CoV-2 has a growth-enhancing function and it is assumed that other vital factors accompany it and the rate of infection and contagion in these factors is higher [10].

#### **Figure 2.**

*Schematic of the intracellular lifecycle of SARS-CoV-2 and related immunopathology.*

FCS is a known factor in influenza infections and appears to increase destruction and infection. Of course, it should be noted that it has not yet been determined whether this pathogenic function is also present in the SARS-CoV-2 virus [10].

Although various proteases, such as TMPRSS2 and cathepsin-B or -L (CTS-B or -L), cause cleavage at the S1/S2 site of the SARS-CoV-2 virus, the presence of FCS can have benefits for the SARS-CoV-2 virus, although research is needed to prove this. A new report by Johnson et al. shows that a SARS-CoV-2 virus that mutates and lacks FCS in its spike protein reduces the proliferation of Calu3 cells in a human respiratory cell line, thus weakening the disease in the hamster pathogenesis model. Preliminary observations suggest that FCS in the SARS-CoV-2 virus may play an important role in degradation [10].

Observations show that the ACE2 receptor and the TMPRSS2 serine protease are the main factors determining the entry of SARS-CoV-2 into cell tropism. It should be noted that the cells that express these two proteins are always defending against the SARS-CoV-2 virus [1].

Taking into account all the mentioned cases and points, we find that the SARS-CoV-2 virus has higher infectivity and higher transmissibility than previous types of coronavirus, and escapes from the host's immune system and delayed its function, for example, by disabling the system of long-term antibody formation against the virus. They control and direct subatomic pathways in host cells that reduce cell growth and damage in lung epithelial cells. These new discoveries are very large and effective in helping to interpret the basic pathomechanisms in Covid-19 and in particular cause immune disorders **Figure 2** [10].

The cells encoding TMPRSS2 and the angiotensin-converting enzyme 2 (ACE2) are infected by the SARS-CoV-2 virus (severe acute respiratory syndrome

#### *SARS-CoV-2 Mutation Mechanism, Features, and Future Perspective DOI: http://dx.doi.org/10.5772/intechopen.106905*

coronavirus 2), which causes it to pass into the host cell through endocyte machinery or fuse into the plasma membrane. The genetic material (genome) of the virus is released into the cytosol of the host cell and transcription, replication, assembly, and translation. Viral progenies are produced and released into the extracellular space through undiscovered mechanisms. Arrival and amplification of the viral lead to cell pyroptosis and arrival of harm-related atomic examples, including ASC oligomers, ATP, and nucleic acids. This is joined by the discharge of supportive pro-inflammatory cytokines and chemokines culminating in a cytokine storm. Then again, MHC-I limited antigen releasing is downregulated in all probability by binding of the viral Orf8 protein, bringing about lessened T-cell activation.

#### **1.3 The origin and evolution of SARS-CoV-2**

Researchers have identified and sequenced the complete sequence of the SARA-CoV-2 genome and other beta-coronavirus genomes. The results show that SARS-CoV-2 is 96% similar to covid strain bat Cov RaTG13. And this research clearly shows that SARA-CoV-2 may have originated in bats, and may also have evolved from bat Cov RaTG13 [11].

The genomic RNA of SARS-CoV-2 encodes four driving structural proteins which are known as spike (and which likewise contains the receptor-binding domain [RBD] through which the infection ties to its natural receptor at have cell surface), the envelope (E) protein, the membrane (M) protein, and the nucleocapsid (N) protein. The genome of SARS-CoV-2 likewise contains extra genes, like that encoding for the RNA-dependent RNA polymerase (RdRP). This enzyme is fundamental for replicating viral RNA and for transcription of all RNA virals, both bearing negative and positive-sense RNA. In positive-sense single strand RNA virals, for example, SARS-CoV-2, the enzyme straightforwardly transcribes the positive-sense RNA, which acts precisely like a messenger RNA, yet additionally twofold convert positive-sense RNA into negative-sense RNA and then again in positive-sense RNA, to be gathered in the last viral particle [12].

Researchers demonstrate that an isolate numbered EPI\_ISL\_403928 shows different hereditary distances of the entire length genome and different phylogenetic trees, the coding sequences of nucleoprotein (N), spike protein (S), and polyprotein (P) from other SARS-CoV-2, with 2, 4, and 22 varieties in N, S, and P at the level of amino acid residues respectively. The outcomes show that at least two SARS-CoV-2 strains are involved in the outbreak [11].

Among the 103 strains, a sum of 149 mutations is distinguished and populace hereditary investigations demonstrate that these strains are predominantly isolated into two kinds. Results recommend that 101 of the 103 SARS-CoV-2 strains show considerable linkage between the two single nucleotide polypeptides (SNPs). The main kinds of SARS-CoV-2 (L sort and S type) are distinguished by two SNPs which situate at the destinations of 8,782 and 28,144. L sort contains 70% of the 103 strains and S type contains 30%, showing that L sort is more prevalent than the S type. Notwithstanding, the S type is the ancestral version of SARS-CoV-2. Until today, 13 mutations in the spike protein have been recognized [11].

#### **1.4 Emergence of SARS-CoV-2 variants and how they mutate**

Changes and causes of created virus types are caused by nucleotide changes that usually occur in the virus genome sequence during replication. It should be noted

that these changes are faster in RNA viruses than in DNA viruses. However, the rate of nucleotide changes in CoVs is usually slower than in other RNA viruses, due to the presence of an enzyme that plays a role in correcting defects created during replication. This enzyme is called non-structural protein 14 (nsp14) which has the function exoribonuclease (ExoN) which causes it to play a role in "editing." It is also detrimental to the replication of SARS-CoV-2 and MERS-CoV if this function is inactivated. Nucleotide changes in the genome sequence increase with respect to viral replication, transmission, and escape from the immune system due to natural selection in a population. For example, when a virus is detected by the immune system and its chances of survival are reduced, it is naturally eliminated, so the virus in which the nucleotide change occurred and caused it to escape the immune system and be safe has a better chance of survival. In general, genomic changes that affect viral health can randomly increase or decrease the frequency. Various treatments, such as monoclonal antibodies (mAb), convalescent plasma and vaccines, and even environmental factors, are important factors that have a significant impact on the genomic changes of viruses and cause the continuation of these changes and the emergence of new strains. In the event that variations evidently change the phenotype (transmission and virulence) of a viral, they are alluded to as a strain [13].

Of course, it should be noted that not only the changes that occur during replication and the specified host stresses, not only the formation of different species but also RNA editing or RNA modification can cause the formation of new types of SARA-CoV-2 Be. For example, the replacement of cytosine nucleotides by uracil and adenosine by inosine has been observed in SARS-CoV-2 genome sequence research. These events occur by RNA-editing enzymes, which include apolipoprotein B mRNA editing catalytic polypeptide-like enzyme (APOBEC) and adenosine deaminase RNA specific 1 enzyme (ADAR1) respectively. Host cells have enhanced these editing enzymes as innate viral sensory defense mechanisms; however, viruses can use these mechanisms to evolve. In Covid-19 patients, alterations in the structure of viruses have been observed within the host and are likely to occur by the same RNA-editing enzymes, but how exactly is SARS-CoV-2 altered and manipulated using these enzymes to nucleotide changes is not yet known [13].

Another factor in the development of the new SARS-CoV-2 species is recombination, which occurs in infected cells where the inherited substance of the two types is packaged in a single virion and causes different changes in the sequence of the virus genome. Recently, evidence has shown that a person can be infected with two different types of SARA-CoV-2 at the same time. In this case, the new species resulting from recombination can each have different pathogenic properties and have serious consequences for SARS-CoV-2 interactions, especially when this new species can move away from normal and stimulated antibody resistance. Overall, CoVs have a high recombination rate, and so far, conflicting data on SARS-CoV-2 recombination have been reported and its exact nature is still unclear [13].

An increase in the rate of viral evolution and a decrease in the rate of repulsion of the replicable virus has been observed in immunocompromised individuals with SARS-CoV-2 disease. Several studies during the treatment of this disease with plasma recovery method and mAb treatment have shown that the emergence of various viruses is associated with reduced sensitivity to neutralizing antibodies. However, in patients infected with the human immunodeficiency virus (HIV), an increase in changes in the genomic sequence of the virus has been observed. Single nucleotide polymorphism (SNP) examination distinguished a few varieties, frequently bringing about amino acid changes in the S protein related to immune evasion tracked down

#### *SARS-CoV-2 Mutation Mechanism, Features, and Future Perspective DOI: http://dx.doi.org/10.5772/intechopen.106905*

in variations of concern. Beta, for example, was first seen in South Africa and was thought to have evolved through the evolution of a virus within at least one host with delayed viral replication, such as in a person with HIV or immunodeficiency. Intrahost evolution is by all accounts more articulated in immunocompromised populaces, which could act as a drawn-out wellspring of new SARS-CoV-2 variations, but it stays unclear whether basic co-morbidities assume the main part in the development of viral variations [13]. All in all, various factors change the genome and create a new type of virus and disease, as mentioned above, not only the structure and editing enzymes and proteins involved in replication but also the host's immune system and the host body's enzymes and antibodies, which are injected through vaccines, can also be effective in mutation.

#### **1.5 Currently circulating SARS-CoV-2 variants**

SARS-CoV-2 variations are classified by the CDC (Center for Disease Control and Prevention) and the WHO into two sorts: variants of concern (VOC) and variants of interest (VOI). A few VOC have emerged from the first wild-type strain detached in Wuhan since the outbreak initially started in December 2019. As indicated by the Center for Disease Control (CDC), a VOC is one that has expanded contagiousness, expanded destructiveness, resistance to the vaccine, or acquired immunity from the previous infection, and can escape symptomatic recognition. The VOCs are classified by the WHO as Beta (B.1.351), Alpha (B.1.1.7), Delta (B.1.617.2), and Gamma (P.1) [13, 14].
