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Review
. 2021 Jul;86(7):800-817.
doi: 10.1134/S0006297921070026.

COVID-19: Myths and Reality

Affiliations
Review

COVID-19: Myths and Reality

Larisa V Kordyukova et al. Biochemistry (Mosc). 2021 Jul.

Abstract

COVID-19, a new human respiratory disease that has killed nearly 3 million people in a year since the start of the pandemic, is a global public health challenge. Its infectious agent, SARS-CoV-2, differs from other coronaviruses in a number of structural features that make this virus more pathogenic and transmissible. In this review, we discuss some important characteristics of the main SARS-CoV-2 surface antigen, the spike (S) protein, such as (i) ability of the receptor-binding domain (RBD) to switch between the "standing-up" position (open pre-fusion conformation) for receptor binding and the "lying-down" position (closed pre-fusion conformation) for immune system evasion; (ii) advantage of a high binding affinity of the RBD open conformation to the human angiotensin-converting enzyme 2 (ACE2) receptor for efficient cell entry; and (iii) S protein preliminary activation by the intracellular furin-like proteases for facilitation of the virus spreading across different cell types. We describe interactions between the S protein and cellular receptors, co-receptors, and antagonists, as well as a hypothetical mechanism of the homotrimeric spike structure destabilization that triggers the fusion of the viral envelope with the cell membrane at physiological pH and mediates the viral nucleocapsid entry into the cytoplasm. The transition of the S protein pre-fusion conformation to the post-fusion one on the surface of virions after their treatment with some reagents, such as β-propiolactone, is essential, especially in relation to the vaccine production. We also compare the COVID-19 pathogenesis with that of severe outbreaks of "avian" influenza caused by the A/H5 and A/H7 highly pathogenic viruses and discuss the structural similarities between the SARS-CoV-2 S protein and hemagglutinins of those highly pathogenic strains. Finally, we touch on the prospective and currently used COVID-19 antiviral and anti-pathogenetic therapeutics, as well as recently approved conventional and innovative COVID-19 vaccines and their molecular and immunological features.

Keywords: COVID-19; S protein; SARS-CoV-2; hemagglutinin; influenza virus; structure; vaccines.

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Conflict of interest statement

The authors declare no conflict of interest in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

Figures

Fig. 1.
Fig. 1.
Structure of SARS‑CoV‑2 virion and its structural proteins. a) SARS‑CoV‑2 virion with its structural proteins (S, N, M, E) and genomic single stranded (+)RNA (+ssRNA): S, spike protein; E, envelope protein; M, membrane protein; N, nucleocapsid protein. b) SDS-PAGE of purified SARS‑CoV‑2 virions. Lanes: 1) molecular weight markers; 2) major structural proteins (S, its subunits S1 and S2 after proteolytic activation, and N). Adapted with permission from Yao et al. [9]. Copyright Elsevier, 2020.
Fig. 2.
Fig. 2.
S protein structure. a) Virion with S protein spikes; b) homotrimeric spike anchored in the virion membrane; c) 3D-structure of the spike closed conformation (cryo-EM data, PDB ID 6VXX [12]); d) S protein monomer with indicated functional domains and proteolytic activation sites. S1 and S2, S protein subunits; S1/S2, furin cleavage site; SP, signaling peptide; NTD, N-terminal domain; RBD, receptor-binding domain; FP, fusion peptide; IFP, inner fusion peptide emerging after the S2 subunit cleavage at the S2′ site [36]; HR1 and HR2 (heptad repeats 1 and 2), specialized repeats in the amino acid sequence; TM, transmembrane domain; CT, cytoplasmic domain. The image was created using the BioRender.com pattern.
Fig. 3.
Fig. 3.
Modification of SARS‑CoV‑2 S protein (a) and HA/HEF from the influenza A, B, and C viruses (b) with long fatty acids. Covalently bound fatty acid residues are shown for one monomer of the homotrimer spike as black (palmitates, C16:0) and red (stearates, C18:0) zigzag lines. Two fatty acid residues that hypothetically bind stearates are marked with arrows. HAs and S protein are shown approximately to scale (S protein spike height, ~25 nm; [32]; HA spike height, ~13.5 nm [47]).
Fig. 4.
Fig. 4.
Cryo-EM structures of S protein homotrimeric spike on the surface of SARS‑CoV‑2 virions. a) Pre-fusion conformation: 1 and 2 – closed conformation (flail-like shape; all RBDs down); 3 and 4 – open conformation (one RBD up, two RBDs down); shown from the side (1 and 3) and top (2 and 4); b) post-fusion conformation (needle-like); c) tilted spike due to the flexible hinges in the stem (black circles) [41]. The spikes are shown to the scale according to [9, 16, 41]. Adapted with permission from Yao et al. [9]. Copyright Elsevier, 2020.
Fig. 5.
Fig. 5.
Structural variants of lipoplexes: a) multilayer lamellar structure; b) inverted hexagonal structure. Adapted with permission from the review by Ewert et al. [109]. Copyright Taylor & Francis, 2005.

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