Biology of the SARS-CoV-2 Coronavirus

Abstract

New coronavirus infection causing COVID-19, which was first reported in late 2019 in China, initiated severe social and economic crisis that affected the whole world. High frequency of the errors in replication of RNA viruses, zoonotic nature of transmission, and high transmissibility allowed betacoronaviruses to cause the third pandemic in the world since the beginning of 2003: SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. The latest pandemic united scientific community and served as a powerful impetus in the study of biology of coronaviruses: new routes of virus penetration into the human cells were identified, features of the replication cycle were studied, and new functions of coronavirus proteins were elucidated. It should be recognized that the pandemic was accompanied by the need to obtain and publish results within a short time, which led to the emergence of an array of conflicting data and low reproducibility of research results. We systematized and analyzed scientific literature, filtered the results according to reliability of the methods of analysis used, and prepared a review describing molecular mechanisms of functioning of the SARS-CoV-2 coronavirus. This review considers organization of the genome of the SARS-CoV-2 virus, mechanisms of its gene expression and entry of the virus into the cell, provides information on key mutations that characterize different variants of the virus, and their contribution to pathogenesis of the disease.

Keywords: COVID-19; S protein; SARS-CoV-2; VOC; mutation.

Fig. 1.

Coronavirus structure: N, S, M, E, HE structural proteins and genomic RNA are indicated.

Fig. 2.

Schematic representation of coronavirus genome organization using SARS-CoV-2 as an example. Presence of the 5′-cap and a 3′-polyA tail at the ends of the genomic RNA allows immediate translation of nonstructural proteins from the ORF1a and ORF1b highlighted in gray. Reading frames are separated from each other by the reading frameshift site (slippery sequence). Translation results in two polyprotein chains, pp1a and pp1ab. Nonstructural proteins are formed as a result of proteolytic processing of pp1a and pp1ab by PLpro and 3-chymotrypsin-like proteases Mpro. Genes of structural and accessory proteins are transcribed into a set of subgenomic mRNAs. Genomic RNA and all subgenomic mRNAs contain the same leader sequence at their 5′-ends. Genes of structural and accessory proteins as well as their transcripts are highlighted in blue and orange, respectively.

Fig. 3.

Life cycle of coronaviruses. Surface of the virus is coated with the S protein, which interacts with the receptor and activates fusion of the virus with the cell membrane after being cleaved by the cell surface protease (1). Genomic RNA, getting inside the cell, is immediately recognized by the ribosome, and translation of polyproteins and their processing to individual non-structural proteins occurs (2). Formation of the double-membrane vesicles (DMV) occurs in the membranes of endoplasmic reticulum with the replication–transcription complex (RTC) assembling in DMV (3). Genomic sense RNA is first converted into the antisense form to form genomic and subgenomic RNAs (4), and then into the sense form of the genomic RNA and subgenomic mRNAs (5). Subgenomic mRNAs are translated in endoplasmic reticulum into structural and accessory proteins (6). Genomic RNA interacts with N protein, forming a nucleocapsid (7), which combines with the structural proteins to form a virion (8). The mature virion (9) is released from the cell by exocytosis (10).

Fig. 4.

Frameshift during SARS-CoV-2 pp1ab synthesis. Not far from the regulatory sequence (slippery sequence) is a stop codon, followed by a stable RNA structure (pseudoknot) (1). When the ribosome approaches the pseudoknot, the rate of translation slows down, making it possible for the ribosome to jump back 1 nucleotide. This leads to the change in codon composition, which is associated with disappearance of the stop codon (2). The released third nucleotide of the triplet becomes the first in the new triplet. The corresponding tRNA approaches it, and protein translation continues (3).

Fig. 5.

Replication and transcription of subgenomic RNAs take place within the double-membrane vesicle (DMV). The polymerase complex consists of nonstructural proteins nsp7, nsp8, nsp9, nsp10, nsp12, nsp13, nsp14, and nsp16 (indicated by numbers). RNA produced inside the DMV exits through the membrane pores. Subgenomic RNAs are translated into non-structural and accessory proteins; N protein meets with genomic RNA and forms a nucleocapsid.

Fig. 6.

Replication and “discontinuous” transcription. Genomic RNA of the virus serves as a template for the synthesis of new copies of genomic RNA (left) and for transcription in subgenomic mRNAs according to the “discontinuous” principle (right). Copies of genomic RNAs are used for synthesis of non-structural proteins, replication, transcription into subgenomic RNAs, and packaging into a virion. Subgenomic mRNAs are translated into structural and accessory proteins.

Fig. 7.

Domain organization of S protein and its participation in the fusion of a viral particle with a cell. 3D (a) and primary (b) structure of the SARS-CoV-2 S protein. The following domains are recognized within the S1 and S2 subunits: NTD, N-terminal domain; RBD, receptor-binding domain; FP fusion peptide; HR1 and HR2 domains; transmembrane and cytoplasmic domains. c) Scheme of interaction between a cell and a coronavirus particle. S protein located on the surface of the viral membrane finds the corresponding receptor on the cell membrane. After their interaction with each other, cellular protease cleaves the S protein at the S1/S2 and S2′ sites. This results in the release of the activated S2 subunit with the FP fusion peptide protruding towards the cell. The peptide is integrated into the cell membrane, the HR1 and HR2 domains interact with each other, “pulling” both membranes close to each other.

Table 2

Mutations in the S protein of SARS-CoV-2 VOCs [41, 42] affecting immune response and affinity to ACE2 receptor Note. Gray background indicates presence of mutation that changes response to neutralizing antibodies or binding affinity to ACE2; colorless background indicates absence of mutations. ¹ WHO designation. ² Pango designation. ³ The column contains references to literary sources, which describe effect of the mutations on the ability of the virus to avoid neutralizing antibodies or changing its affinity to ACE2 (increase ↑ or decrease ↓).