# Changing Dynamics of SARS-CoV-2: A Global Challenge
## 2 Structure and Sequence of SARS-CoV-2  
Similar to SARS-CoVs and MERS-CoVs, which also belong to the _Coronaviridae_ family, SARS-CoV-2 is an enveloped, positive single-strand RNA virus [8; 9; 10]. Genome analysis of SARS-CoV-2 has shown that it contains 14 open reading frames (ORFs), which encode 31 proteins [11]. ORF1 and ORF1 ab constitute two-thirds of the known 14 ORFs and encode 16 non-structural proteins (nsp). The remaining one-third of ORFs encodes for eleven accessory proteins and four structural proteins, membrane (M), envelope (E), spike (S) and nucleocapsid (N) [12], as shown in Figure 2a. The eleven accessory proteins include ORF3a, ORF3b, ORF3c, ORF3d, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c and ORF10 [11]. Figure 1: Geographical tracking and mapping of COVID-19 cases globally as of 13 September 2021. (Data Source: Worldometer, Figure redrawn using GeoMaps). The four structural proteins of SARS-CoV-2 and SARS-CoV have amino acid similarity above 90%, excluding the spike glycoprotein, where they diverge. The SARS-CoV-2 spike glycoprotein (1273 Aa) is 18 amino acids longer, compared to the S glycoprotein of SARS-CoV (1255 Aa) [13]. In fact, some of the mutations near the RBD region in the spike glycoprotein are known to make this virus more transmissible; therefore, this protein has been the focus of research to understand the emergence of new variants [14]. Spike glycoprotein is a club-shaped, trimeric class-I viral fusion protein with a length of \(\sim\)20 nm. These spike glycoproteins form huge protrusions from the virus's surface that facilitates virus entry into host cells [13; 15; 16]. It comprises two subunits: subunit S1 mediates receptor recognition, whereas S2 plays a role in membrane fusion [17]. The S1 subunit possesses a receptor-binding domain (RBD), which may be present either at the N-terminal domain (NTD) or C-terminal domain (CTD) or both [18]. The RBD of the virus mediates direct contact with human angiotensin-converting enzyme 2 (hACE2), which is the primary receptor for its entry into the host cell. The mutations in the RBD region of the spike protein are capable of forming closer contact with hACE2, responsible for a higher binding affinity and possibly/probably increased infectivity of VOCs [19]. The S2  
Figure 2: Major amino acid mutations marked on the entire SARS-CoV-2 sequence: (**a**) Wild-type strain, (**b**) Alpha variant, (**c**) Beta variant, (**d**) Gamma variant, (**e**) Delta variant and (**f**) Omicron variant. (M: membrane protein, E: envelope protein, S: Spike protein, N: Nucleocapsid protein, ORF: Open Reading Frame, UTR: Untranslated Region). subunit plays a role in the fusion of the virus membrane with the cell membrane of the host cell. In comparison to SARS-CoV, the spike glycoprotein of SARS-CoV-2 has four additional amino acid residues (PRRA) at the intersection of S1/S2, generating an S1/S2 protease cleavage site (PRRAR) [12; 13] (Figures 3i and 4). It is cleaved by cellular cathepsin L and transmembrane protease serine 2 (TMPRSS2), facilitating the virus entry through the plasma membrane or the endosomal membrane [12; 20]. The spike glycoprotein can acquire two structural states: a closed state (Figure 3(iia)) and an open state (Figure 3(ib-d)) [21]. In a closed state, the RBDs are shielded by the N-terminal domains (NTDs) and the three recognition motifs of this trimeric protein do not protrude from the interface. In contrast, in an open state, the RBD is in the \"up\" conformation where one RBD is exposed upwards, away from the viral membrane, mediating the fusion of viral and host cell membranes (Figure 3(ib)) [21]. This open state is essential for SARS-CoV-2 and host cell membrane fusion, as this facilitates the passage of the virus into the host cells. Some mutations in the spike region promote an enhanced open conformation of the RBD [22]. Apart from the spike mutations, 13 different ORFs of the SARS-CoV-2 were also found to have mutations.