The COVID-19 virus has emerged as a significant pathogen in recent years, causing a global pandemic of unprecedented proportions. The disease first appeared on December 8th, 2019, in Wuhan, China. This report pertained to patients afflicted with severe pneumonia symptoms (1). Researchers identified the virus in China on January 7th, 2020 (2). The World Health Organization subsequently classified it as nCoV-2019. Ultimately, they named this disease COVID-19 (3). Coronaviruses, such as COVID-19 (SARS-CoV-2), pertain to the category of ssRNA viruses that possess an envelope and display a size variation between 80 and 120 nanometers. The distinguishing feature of the virus is its positive-sense ssRNA (4), which means the virus genome is being directly translated within the cellular environment of the host ( Figure 1 ). The fundamental nature of the virus’s genetic material is such that it comprises a single-stranded ribonucleotide chain. This chain encodes four distinct structural proteins, including N, M, E, and S. Alongside these, encoding sixteen non-structural proteins that are identified as NSP 1–16 (5–7). Researchers acknowledge that coronaviruses, on the whole, are pathogenic microorganisms capable of infecting both human and animal hosts. The classification of these viruses is based on the order Nidovirales, which include Coronaviridae, Roniviridae, and Arteriviridae families (8).

The Coronaviridae family has two subfamilies, Coronavirinae and Torovirinae. The Coronavirinae subfamily causes respiratory infections, while the Torovirinae subfamily in animals leads to intestinal infections (9). The Coronavirinae family includes four genera: Alpha, Beta, Gamma, and Delta (10). In terms of pathogenicity in humans, the two genera of Alpha and Beta play a crucial role. The Alpha genus includes 229E and NL-63, and the Beta genus includes HKU-1, MERS, SARS, and OC43. Scientists have placed the SARS-CoV-2 virus in the Beta genus after identifying its genome sequence. In this way, the number of human coronaviruses reached seven, of which two are in the Alpha genus and five are in the Beta genus (11). The coronavirus genome has a cap at the 5’ end and a poly(A) tail at the 3’ end. After the COVID-19 virus enters the cell and releases its genome, the replication process begins by translating ORF1a and ORF1b (12). The Long Replicase Gene (ORF1ab Gene) is over 21 Kb in size and encodes sixteen unstructured proteins (NSP 1 -> 16), which translates as Pp1ab polyprotein. In addition, next to this gene (late genes) are four structural proteins S, E, M, N, and 6 non-structural proteins that are also encoded by subgenomic mRNAs (NS 3a -> 14). ORF1a encodes the immediate early genes, while ORF1b can encode the early genes. However, ORF1a must repress the native immune response of the host, whereas ORF1b has a duty to replication and synthesis of RNA (13, 14). Virus NSPs use the target cell membrane to collect transcription and replication complexes which take part in negative-strand RNA synthesis (15). The NSP1 protein binds to the 40S subunit of the ribosome in the cell, inhibiting translation in the host cell. This complex induces endonucleolytic cleavage of the 5’UTR region in host mRNAs, eventually degrading them. The presence of an end-conductor sequence in the 5’ region protects viral mRNAs from endonucleolytic cleavage. By suppressing gene expression in the host cell, the NSP1 protein facilitates viral gene expression and evades the host immune response (16). The NSP2 protein interacts with host PHB1 and PHB2 molecules to regulate the cell survival transmission pathway. These two proteins play a crucial role in stabilizing mitochondrial function and protecting cells from stress (17). The NSP3 protein is involved in the N-terminal cleavage of polyproteins. Additionally, this protein, PL-PRO, exhibits deubiquitinating or DeISGylating activity that inhibits the immune response and targets lys63 and 48Lys polyubiquitin chains on cellular substrates (18). Alongside the NSP4 protein, it participates in forming membrane vesicles essential for virus replication. Moreover, it inhibits induction of type I interferon innate immunity by blocking phosphorylation, dimerization, and translocation between cell nuclei while also suppressing NF-kappa-B signaling (19, 20). In its coding gene region resides a SUD domain sequence unique to SARS-type coronaviruses which binds to G4 mRNA to inhibit apoptotic signaling and promote cell survival (21). NSP5 (Proteinase 3 CL) is responsible for cleaving the C-terminal end sequence of replicase polyprotein at eleven different regions. Known substrates for this enzyme contain [ILMVF]-Q-|-[SGACN] sequences. It also interacts with ADRP (22). The NSP6 protein initiates host endoplasmic reticulum autophagosome formation but limits their expansion while facilitating transmission of virus components to lysosomes (23). The NSP7 protein forms a hexadecamer with NSP8 acting as a primase during virus replication (24). As an ssRNA binding protein, the NSP9 protein is also involved in virus replication (25). Finally, the NSP10 protein plays a crucial role in the viral translation system by synchronizing the 3’-5’ exoribonuclease activities of the NSP14 protein and the 2’-O-methyltransferase activity of the NSP16 protein. It is also involved in the cap methylation of viral mRNAs sequences (26). The NSP12 comprises 932 amino acids. The NSP12 form consists of a NiRAN domain and an RNA-dependent RNA polymerase (RDRP) domain, which are connected by a connector domain (27). NSP12 functions as an RDRP. NSP12 proteins, together with NSP7 and NSP8 cofactors, participate in the replication and translation of the RNA virus genome (28). NSP13 (helicase or Hel) is a multifunctional protein with a binding domain located at the N-terminal region. This protein is responsible for unwinding the double helix structure of RNA and DNA from the 5’ to 3’ direction. The helicase activity of this protein relies on magnesium ions (Mg2+) (29, 30). The E (envelope) protein plays a central role in virus morphogenesis and formation. Acting as a viroporin, this protein facilitates ion passage through protein-lipid pentameric pores. Additionally, it contributes to apoptosis induction. Comparative alignment studies have identified genomic sequences of this coronavirus protein in bats and scaly anteaters. Structural modifications observed in the E protein include substitutions at position 69 (R69N/D/E), deletion at position 70 (70G/C), and substitutions at positions 55 and 56 (T, V -> S, F). These alterations highlight the significant role played by this small but crucial protein during virus infection and replication stages (31). The glycoprotein M (Membrane) helps orchestrate virus morphogenesis by facilitating proper juxtapositioning of different viral components while also playing an important role in virus germination.

HE is involved in a component of envelope proteins in some (but not all) coronaviruses. Some coronaviruses, such as human coronavirus OC43, contain the glycoprotein HE, which has hemagglutination and acetyl esterase activity. HE has a similar function to both the influenza virus receptor-binding protein (HA) and receptor-destructive enzyme (NA). The virus binds to the mucous membranes of the respiratory tract by HE. Type C influenza also contains this enzyme.

The protein on the surface of the virion is called HE. Scientists do not consider this protein an essential structural component of the virus because not all Coronaviruses express HE. However, HE may play an important role in binding coronaviruses to the target cell and facilitating the release of the virus from the cell surface.

The S region of the virus genome encodes the glycoprotein spike, which is located on the surface of the virus and plays an important role in binding to host cells and determining pathogenicity. The S protein is responsible for infection and transmission in patients (32, 33). Spike stimulates the immune system and stands as one of the crucial immunogenic antigens for this virus. By triggering antibody production, it effectively neutralizes viral activity (34). The total length of glycoprotein S is 1273 amino acids and includes a guide peptide (amino acids 1–13) in the part of the N-terminus. This part has two sub-groups, one S1 (14–685) and the other S2 (686–1273). S1 is responsible for receptor binding, and S2 is responsible for the fusion of the virus membrane with the host cell membrane. On the other hand, Spike is a homotrimeric glycoprotein that binds to the type I integral membrane in ACE2. The glycoprotein S at the furin cleavage site contains several base amino acids (PRRA) at the junction of the S1 and S2 subunits, which increase the infectivity of the virus. The S1 protein has a receptor-binding domain (RBD) that is involved in binding to the ACE2 receptor and virus entry into the host cell and induces structural changes in glycoprotein S (35), while the S2 domain mainly contains the HR (Heptad Repeat). However, HR1 and HR2, which are closely related to them, have virus membrane fusion (34, 36) ( Figure 2 ). This protein causes the virus to enter human lung cells using TMPRSS2. The acidic pH of lysosomes and endosomes activates the enzymes cathepsin B and L. The virus also requires an acidic environment with a pH of about 3 to enter the cell cytosol. Proteolysis of glycoprotein S by CatB/L cathepsin activates the S2 fusion peptide and activates virus membrane integration into endosomes. Also, host cells express the spike protein at their surface, causing membrane attachment of adjacent cells to each other and forming syncytium. Syncytium formation, besides disrupting the function of the organ involved, also allows the virus to spread further and escape the immune system. By creating double-layered vesicles, coronaviruses block the expression of the Pattern Recognition Receptor, and as a result, the innate immune system does not recognize them and continues to multiply within the vesicle. They disrupt the production of type I interferons as one of the most important anti-viral factors. Coronaviruses disrupt the process of presenting antigens by the immune cells. Investigations into changes in the RBD sequence have indicated that mutation N501 remains stable and enhances the interaction with Y41 through hydrogen bonding, resulting in reinforcing the connection between RBD and the ACE2 receptor. This particular region exhibits a complex role because of its involvement in numerous binding mechanisms. In addition, researchers have observed that mutations in residues N479, T487, L455A, F456A, and Q493A weaken the binding to the ACE2 receptor (34, 37–40). The NSP3a protein is involved in viroporin formation and possibly virus release. This protein causes the upstream expression of fibrinogen subunits FGA, FGB, and FGG in host lung epithelial cells. It also induces apoptosis in cell culture. NSP3a induces serine phosphorylation in interferon alpha receptor subunit 1 (IFNAR1), causing low expression of type 1 interferon receptor and increased ubiquitination in IFNAR1 (41–44).

Researchers believe that a mutation in the S1 protein may cause a malfunction in the function of the virus. Researchers have found that some mutations change the intensity of transmission and contagion of the virus. This can affect the effectiveness of the vaccine and the neutralization of the virus. Although the stem portion of the S2 appendages has experienced fewer mutational changes. However, the breaking of the S appendage into two parts, S1 and S2, is very important in virus attachment and infection.

The study findings suggest that the COVID-19 virus uses ACE2 as a receptor to enter the target cell (45). Besides, the research findings have determined that the S protein of the COVID-19 virus underwent mutations and became glycosylated, resulting in an increased virulence of the virus. However, the study of protein S mutations at a biological level has revealed the existence of a region known as the RBD within the virus’s glycoprotein S. This region enables the virus to attach to its receptor (46). The RBD in protein S comprises five beta strands, specifically β1, β2, β3, β4, and β7, organized in an antiparallel manner and linked by brief spirals and loops in the central protein region (core). The protein’s center contains β4 and β7 strands, as well as short segments of β5 and β6 strands, which attach to α4 and α5 helices and loops. This section contains the RBM and includes amino acid residues that attach to the ACE2 enzyme in the virus. Among these 4 pairs, 3 bonds (Cys336-Cys361, Cys379-Cys432, Cys391-Cys525) in the center help stabilize the structure of β-sheets. While the other (Cys480-Cys488) binds the loops at the distal end of RBM (47).

Protein modeling experiments on glycoprotein S show that the SARS-CoV-2 virus has a sufficient affinity to attach to the ACE2 enzyme in human cells. This enzyme, on the outer surface of the membrane of cells of tissues such as lungs, arteries, heart, kidney, and intestine, is also present. This virus uses this enzyme as a mediator to enter the cell (48). Several research groups have shown this enzyme as the cell surface receptor of SARS-CoV-2 (47, 49–53). Researchers have even observed that HeLa cells expressing ACE2 are susceptible to infection by this virus, while cells lacking ACE2 show no response to this virus (54). Therefore, binding to the ACE2 receptor is an important initial step for SARS-CoV-2 to enter target cells (38, 48). In vitro binding measurements show that the RBD in SARS-CoV-2 binds to ACE2 with an affinity in the nanomolar range. This indicates that the RBD is a key component in the S1 subunit responsible for the binding of SARS-CoV-2 to ACE2 (34, 37). Two repeating regions of heptad peptides 1 and 2, named Membrane-distal Heptad Repeat 1 (HR1) and Membrane-proximal Heptad Repeat 2 (HR2) on S protein, are important for binding to the receptor. After binding of the RBD in the S1 subunit of the S protein to the ACE2 receptor on the target cell, the heptad repeat domains 1 and 2 in the S2 subunit of the S protein interact with each other and form a six-helix bundle. This bundle has a length of 115 Å (angstroms) and a diameter of 25 Å. The three helices in HR1 form a central entangled twist, and the three strands of HR2 join it in an antiparallel shape. This sextuplet complex is not very stable and is likely to form after the initial fusion of the HR1 segment in the receptor membrane (55, 56).

In early January 2020, scientists sequenced the entire genome of the new coronavirus for the first time, which they had isolated from thousands of infected patients worldwide, and they reported the resulting genomic changes. This caused a turning point in the disease control process. Researchers then showed that the rapid spread was because of a slight change in the amino acid or spike proteins on the virus’s surface ( Figure 3 ).

The virus strengthens its ability to attach to its receptor and performs this step faster and with a stronger connection. In this way, by making these changes, it escapes from the patient’s immune system and remains safe; therefore, there is always the possibility that a more effective virus will emerge as a locally or regionally dominant variant. However, the quick transmission doesn’t always indicate a connection to more severe COVID-19 variants or increased mortality rates. This mutation does not always affect the course of the disease, and it can affect the speed of the disease.

The mutated type of COVID-19 occurs because of the replacement of the amino acid phenylalanine (F) with tyrosine (Y). According to the study, the Y453F mutant glycoprotein has a weaker spike binding property to human ACE2 compared to the COVID-19 glycoprotein, which is attributed to the substitution of tyrosine at position 453 with phenylalanine (57). Y453F has occurred in the Netherlands and Denmark in associated with the transmission of disease through mink and humans and in RBD. The existing report shows that Y453F, named mutation B.1.1.298, has infected about 214 humans until November 5, 2020 (58). The N439K mutation increases the affinity of the RBD for ACE2 (59). There are reports in England and later in South Africa of N501Y mutations (60). The N501Y mutation in treated subjects led to alterations in amino acids, resulting in heightened binding affinity to ACE2 (61, 62). The Alpha variant (B.1.1.7) is one of the most dangerous mutations in the UK, the N501Y mutation, and it is very worrying; because it contains one of the six key amino acids that cause the RBD to bind tightly to the ACE2 receptor ( Table 1 ). Modeling analysis suggests that the mutation N501Y has enabled the potential for an aromatic ring connection via an extra hydrogen bond between RBD and ACE2 (63). Therefore, the mutation N501Y has increased the binding affinity of protein S for the ACE2 receptor (64). The Beta variant (B.1.351), an important mutation of concern in the Republic of South Africa, proved that besides N501Y, two mutations K417N and E484K strengthen the binding of RBD in the S region to ACE2 receptor, causing escape from the immune system and increasing speed of virus transmission (65). The Gamma variant (P.1/B.1.1.28) is another worry that was introduced to Japan from Brazil, particularly because of the E484K mutation, which boosts the evasion capability of the immune system, underscoring its significance (66). The Delta variant (B.1.617.2) contains ten mutations, including T19R, del156, del157, R158G, L452R, T478K, D614G, P681R, and D950N, which occurred in the spike protein coding region. Plus Delta variant (B.1.617.2.1), which is the latest mutated variant of corona and the difference is K417N compared to the Delta variant. However, mutations of Alpha (B.1.1.7), Beta (B.1.351); Mutations Gamma (P.1/B.1.1.28), and Delta (B.1.617.2) occur in the RBD and NTD (N-terminal domain) regions. The N501Y mutation found in the RBD is present in all variants except Delta, leading to heightened spike affinity. Together with NTD, the RBD acts as the primary target for neutralization and facilitates an antibody production response to antiserum or vaccine. The N501Y single mutation alone increases affinity between RBD and ACE2 tenfold higher than the ancestral strain (N501- RBD) has increased (67). According to the announcement of the World Health Organization on June 14, 2021, the Lambda variant (B.1.1.1/C.37) was introduced as a significant variant of interest (VOI). Some analysts considered it worrying, and they even predicted that it would probably replace the Delta variant. The spike protein of this mutant strain has point mutations, such as G75V, T76I, del247/253, L452Q, F490S, D614G, and T859N. These point mutations may affect the ability of the mutant strain to transmit and escape the immune system. Lambda and Delta randomly undergo mutations at position L452, and these mutations in this position may have caused the rapid spread of these two virus strains (68, 69). Another variant that the World Health Organization has introduced in the category of worrying cases because of its resistance to the vaccine is the Mu variant (B.1.1.1/C.37), and because it has the same behavior as the beta mutant variant (escape from the immune system), therefore, they are among the cases being monitored, and the likelihood of its widespread occurrence is not far from anticipated. This mutation in P681H is associated with increased transmissibility, while E484K and K417N mutations might aid the virus in evading the immune system. The most recent report is of the C.1.2 variant mutation, which was first identified in South Africa in May 2021 and contains multiple mutations in all four VOCs (Alpha, Beta, Delta, and Gamma) and three VOIs (Kappa, Eta, and Lambda). Additionally, other mutations in NTD (C136F) and RBD (Y449H) have also been discovered. The functional impact of these mutations probably includes reduced antibody effectiveness and evasion of the immune system (70). The latest variant classified by the World Health Organization as a VOC is called the Omicron variant (B.1.1.529), and the first sample was confirmed on November 9, 2021, from South Africa, the first sequence indicating 30 changes in Spike protein that are similar to the Alpha and Delta variants, which are associated with increased infection and the ability to escape infection-inhibiting antibodies (71).

Ribosomal frameshift comprises a biological event that happens along translation that leads to the generation of multiple special proteins by a single mRNA (14). Ribosomal frameshift can be planned by the nucleotide sequence available in mRNA, sometimes influenced by the secondary and tridimensional mRNA complex (149). Typically, -1 ribosomal frameshifting characterizes in viruses (particularly retroviruses, astroviruses, and coronaviruses) bacterial insertion elements, and retrotransposon, and also has been observes in some cellular genes. (150). In other words, -1 ribosomal frameshifting or -1 PRF is a process whereby mRNA cis-acting elements conduct elongating ribosomes to displace the reading frame as much as 1 nucleotide toward 5′. Initially, the Rous sarcoma virus used the -1 ribosomal frame-shifting process for the expression of viral genes (151) followed by some retroviruses (152). By examining a sequence of three nucleotides found on a molecule of messenger RNA, known as codons, the process of protein translation occurs from the 5’ to the 3’ direction of the mRNA strand. This translation process commences with the amino acid methionine, specifically with the initiation codon AUG. Through the process of translation, a per codon becomes an amino acid. The code is designed to be degenerate in nature, allowing for the identification of a particular amino acid through multiple codons. Nevertheless, a relocation of several nucleotides that is not partible upon 3 in the reading format will subsequently next codons to be read variously (153), which impressively alters the ribosomal reading frame.

-1 ribosomal frameshifting can be divided into three distinct sections composed of one slippery site, one connector zone, and an irritating area downstream of the secondary structure of mRNA, usually a mRNA pseudo-knot (13). The initial sequence of the slippery site and its position in association with the input translational reading frame is very important: Must include one of these options N NNW WWZ, Where NNN is tensional of three of the same nucleotides, WWW is either A or U and Z ≠ G. The connector area is less well described. Although it is relatively small, it has a significant impact on determining -1 ribosomal frameshifting. Pausing elongating ribosomes at the stop codon is a crucial step in forming downstream secondary structures, which is essential for inducing efficient -1 ribosomal frameshifting (154). The usually adopted process of -1 ribosomal frameshifting is that the secondary structure of mRNA guides prolonging ribosomes to stop with its A- and P-site attached to aminoacyl- and peptidyl-tRNAs, which on the slippery site are located. The sequence of the slippery site permits for re-coupling of the tRNAs to the -1 framework codons after they “concurrently slippage” by one base toward 5′ in the sequel of the mRNA. The next separation of the downstream secondary structure of mRNA permits the ribosome to carry on the lengthening of the newfangled polypeptide within the new translational reading frame. The downstream irritating components are usually H-type mRNA pseudo-knots. The reason for its name is because they are consists of two superposed with the same axis stem loops whose latter stem comprises base coupling among the sequence in the loop of the first-stem loop, and the supernumerary downstream sequence (155). Because of the presence of a third, inner stem-loop component, the COVID-19 pseudo-knot becomes exceedingly complicated (156–158). Mutations effective in this structure reduced the amount of -1 ribosomal frameshifting and had harmful impacts on virus dissemination, therefore, proposing that may aim for treatment use of small molecules (159, 160). Besides, researchers have recorded the attendance of a hairpin that was promptly deployed 5’ of the slippery site to adjust -1 ribosomal frameshifting by reducing its action (161) ( Figure 8 ).

The presence of divalent cation is of significant importance in the regulation of essential cellular processes. Researchers have established that an excessive accumulation of these cations contributes to aging and to neurodegenerative diseases and cancer (162–165). Divalent cation-dependent metalloproteins and metalloenzymes play a central role in regular physiological processes and pathological conditions (166–170). The importance of these proteins is clear in their role in vital cellular functions, for instance, signal transduction (171), cell division (172), excretion (173), transcription of genes (174), immune response regulation (175, 176), and cell adhesion (177, 178). This is why eukaryotic cells possess multiple receptors and ligands that facilitate these divalent cations sorting, transportation, and delivery (179–191). In the realm of host-pathogen interactions, divalent cations assume prominent roles (192–194). It is crucial to regulate the levels of these cations in order to maintain homeostasis, as they have the potential to affect microbial infection (195, 196). The COVID-19 virus relies on Mg²⁺ for the function of its NSP 13, NSP 14, and NSP 16 proteins. Furthermore, within the array of viruses associated with the -1 ribosomal frameshifting event, HIV stands out as a significant example. Emphasizing the crucial role of Mg²⁺, specific enzymes in the HIV virus rely heavily on its presence and interaction for efficient functioning.

The role of RT (reverse transcriptase) in HIV (human immunodeficiency virus) is crucial for the process of converting viral RNA into viral DNA. RT consists of two subunits, p66 and p51, which are activated by viral proteases originating from the Gag-Pol polyprotein. Furthermore, the activity of RT necessitates the presence of divalent cations, specifically Mg²⁺ and Mn²⁺ (Manganese) (197). The functions of both enzymes of RNAase H and DNA polymerase rely on the presence of both subunits (p66 and p51), resulting in the production of ds-DNA (198, 199). RNAase H (subunit p51) possesses specific sites for the attachment of divalent cations, such as Mn²⁺ and Mg²⁺ (200–202).

Metal ions like Mg²⁺, Na⁺ (sodium), and K⁺ (potassium) are of significant importance in various biological processes as they interact with nucleic acids, particularly RNA (203). The specific properties of Mg²⁺ make it particularly well-suited for neutralizing the negative charge density associated with the RNA phosphate backbone for two reasons (204). Firstly, it is the most abundant multivalent cation found within cells (205). Secondly, it possesses the highest charge density among all biologically available ions due to its relatively small ionic radius of 0.6 Å. The binding of Mg²⁺ ions to RNA can occur in two different general modes: (1) a “diffuse binding” mode which involves nonspecific long-range electrostatic interactions with Mg²⁺ hexahydrate, and (2) a “site binding” mode which involves specific coordination of anionic ligands to partially dehydrated Mg²⁺ (206). Both modes are crucial for the structural stabilization of RNA (204, 207). For years, it has been well recognized that the ribosome’s configuration and function are significantly impacted by the presence of metal ions, especially Mg²⁺. For instance, the combination of the small and large ribosomal subunits in vitro to create intact ribosomes is heavily reliant on the concentration of Mg²⁺ ions (208–210). Moreover, Mg²⁺ deficiency in Escherichia coli cells leads to a depletion of ribosomes (211), thus indicating the vital role of Mg²⁺ in assembling and structurally stabilizing ribosomes. In line with this, if various polyamines are used to replace Mg²⁺ in purified preparations of E. coli large ribosomal subunits, it leads to irreversible unfolding and loss of peptidyl transferase activity (212). Mg²⁺ also influences other ribosomal activities, such as poly-U-directed phenylalanine polymerization (213), the binding of polynucleotides to ribosomes (214), and the attachment of ribosomes to endoplasmic reticulum membranes (215). However, it is challenging to ascertain the extent to which these effects are direct or indirect consequences of structural disturbances to the ribosome (204). Although other divalent cations may exhibit sufficient similarity to Mg²⁺ to allow for coordination in its place, the divergent characteristics of these cations can have an impact on the biomolecule to which they are bound. For instance, kinases, which typically rely on Mg²⁺, can form associations with other trace metal ions but experience a decrease in efficacy (216). Divalent metal cations are essential for DNA polymerases, with Mg²⁺ being the most commonly employed in this capacity. While coordination with alternate metal cofactors such as Mn²⁺ and Co²⁺ (Cobalt) can enhance enzymatic activity, it can also have a detrimental effect on fidelity and potentially lead to carcinogenicity (217–219). Ribosomes in eukaryotic cells have the responsibility of conducting protein synthesis and exist as large molecular complexes. Within the process of translation, the smaller 40S subunit and larger 60S subunit come together. The presence of Mg²⁺ is of utmost importance as they partake in the critical task of stabilizing the structure of the ribosome through their binding to the phosphate backbones of rRNA. Additionally, Mg²⁺ can enhance the binding of tRNA to the ribosome during the decoding of mRNA, resulting in facilitating precise protein synthesis. They also contribute to the proper folding of rRNA and effectively maintain the active site of the ribosome required for the formation of peptide bonds. Moreover, Mg²⁺ play a significant role in coordinating ribosomal proteins with rRNA, which in turn assists in the assembly of ribosomal subunits. Additionally, they have a crucial function in the regulation of ribosome biogenesis and the maintenance of pre-ribosomal particle stability throughout maturation ( Figure 9 ).

In modern molecular biology, researchers have observed numerous instances where they initially identified fundamental biological regulatory mechanisms in viruses. This is not because of any uniqueness of viruses, but because their compact genomes enhance the signal-to-noise ratios, thus facilitating the process of scientific discovery. Viruses, as intracellular parasites, follow the same rules and regulations that apply to their host cells. Consequently, although researchers initially considered −1 PRF to be specific to viruses, it is now evident that cellular mRNAs also employ this mechanism. The exploration of PRF continues to shed light on our comprehension of the normal maintenance of the reading frame by ribosomes. Generally, −1 PRF involves a heptameric slippery site, a short spacer, and a complex tertiary mRNA structure known as an H‐type pseudoknot. This phenomenon can occur at three distinct stages of translation at the frameshift signal. The pseudoknot can induce a two-nucleotide translocation event either when the ribosome enters or exits the slippery site. Alternatively, the accommodation of the aminoacyl tRNA (aa‐tRNA) into the slippery site results in the downstream mRNA being pulled into the ribosome by a distance of 9Å, which creates a tension between the slippery site and pseudoknot. This tension is subsequently alleviated by decoupling tRNAs from the mRNA, causing the mRNA to slip backward by one base. As mentioned, viruses in the Coronaviridae and Retroviridae families undergo genetic mutations of type -1 ribosomal frameshifting. On the other hand, NSP 13, NSP14 and NSP 16 proteins in COVID-19 virus need Mg²⁺ for their function. The best source of Mg²⁺ for these proteins is the ribosome because the stability of the ribosome is dependent on the Mg²⁺, any interference in the gradient of the Mg²⁺ concentration will disrupt the function of the ribosome and, as a result, stop the translation process. In other words, NSP13, NSP14, and NSP16 proteins, by consuming Mg²⁺ present in the ribosome, stop the function of the ribosome and convert it from polysome to monosome, which results in the stop of translation. This stopping of translation plays a role in the initial formation of the -1 ribosomal frameshifting phenomenon. Since the ribosome needs to obtain Mg2+ from various sources to continue the translation process, if it encounters the start codon, NSP14, which has the role of proofreading, pulls back a codon, causing the -1 ribosomal frameshifting phenomenon to occur.

AK: Writing – original draft, Writing – review & editing. AN: Writing – review & editing, Data curation. JH: Writing – review & editing, Data curation. MT: Writing – review & editing. FN: Writing – review & editing. SAH: Writing – review & editing