Coronavirus Spike Protein and Tropism Changes

Abstract

Coronaviruses (CoVs) have a remarkable potential to change tropism. This is particularly illustrated over the last 15 years by the emergence of two zoonotic CoVs, the severe acute respiratory syndrome (SARS)- and Middle East respiratory syndrome (MERS)-CoV. Due to their inherent genetic variability, it is inevitable that new cross-species transmission events of these enveloped, positive-stranded RNA viruses will occur. Research into these medical and veterinary important pathogens-sparked by the SARS and MERS outbreaks-revealed important principles of inter- and intraspecies tropism changes. The primary determinant of CoV tropism is the viral spike (S) entry protein. Trimers of the S glycoproteins on the virion surface accommodate binding to a cell surface receptor and fusion of the viral and cellular membrane. Recently, high-resolution structures of two CoV S proteins have been elucidated by single-particle cryo-electron microscopy. Using this new structural insight, we review the changes in the S protein that relate to changes in virus tropism. Different concepts underlie these tropism changes at the cellular, tissue, and host species level, including the promiscuity or adaptability of S proteins to orthologous receptors, alterations in the proteolytic cleavage activation as well as changes in the S protein metastability. A thorough understanding of the key role of the S protein in CoV entry is critical to further our understanding of virus cross-species transmission and pathogenesis and for development of intervention strategies.

Keywords: Coronavirus spike; Cross-species transmission; Cryo-EM structure; Membrane fusion; Receptor interaction; Tropism.

Fig. 1

Spike protein features and structure of the mouse hepatitis coronavirus spike glycoprotein trimer. (A) Schematic linear representation of the coronavirus S protein with relevant domains/sites indicated: signal peptide (SP), two proteolytic cleavage sites (S₁/S₂ and S₂′), two proposed fusion peptides (FP1 and FP2), two heptad repeat regions (HR1 and HR2), transmembrane domain (TD), and cytoplasmic tail (CT). (B) Front and top view of the trimeric mouse hepatitis coronavirus (strain A59) spike glycoprotein ectodomain obtained by cryo-electron microscopy analysis (Walls et al., 2016; PDB: 3JCL). Three S₁ protomers (surface presentation) are colored in red, blue, and green. The S₂ trimer (cartoon presentation) is colored in light orange. (C) Schematic representation of MHV spike protein sequence (drawn to scale), the S₁ domains A, B, C, and D are colored in blue, green, yellow, and orange, respectively, and the linker region connecting domains A and B in gray, the S₂ region is colored in red, and the TM region is indicated as a black box. Red-shaded region indicates spike region that was not resolved in the cryo-EM structure. (Lower panel) Two views on the structure of the mouse hepatitis virus spike glycoprotein protomer (cartoon representation); domains are colored as depicted earlier. (D) Comparison of the S₂ HR1 region in its pre- and postfusion conformation. (Lower left) Structure of the MHV S₂ protomer (cartoon presentation) with four helices of the HR1 region (and consecutive linker region) and the downstream central helix colored in blue, green, yellow, orange, and red, respectively. (Upper right) The structure of a single SARS-CoV S HR1 helix of the postfusion six-helix bundle structure (PDB: 1WYY) is colored according to the homologous HR1 region in the MHV S₂ prefusion structure shown in the lower left panel. Structures are aligned based on the N-terminal segment of the central helix (in red). Figures were generated with PyMOL.

Fig. 2

Overview of currently known receptors and their binding domains within S₁. Schematic representation of coronavirus spike proteins drawn to scale. Yellow boxes indicate signal peptides. Blue boxes indicate the N-terminal regions in alpha- and betacoronavirus spike proteins, which were mapped based on sequence homology between viruses within the same genus. Green boxes indicate known receptor-binding domains in the C-terminal region of S₁. Known receptors are indicated in the boxes: APN, aminopeptidase N; ACE2, angiotensin-converting enzyme 2; CEACAM, carcinoembryonic antigen-related cell adhesion molecule 1; Sia, sialic acid; O-ac Sia, O-acetylated sialic acid; DPP4, dipeptidyl peptidase-4. Gray boxes indicate transmembrane domains. Spikes proteins are shown of PEDV strain CV777 (GB: AAK38656.1), TGEV strain Purdue P115 (GB: ABG89325.1), PRCoV strain ISU-1 (GB: ABG89317.1), Feline CoV strain UU23 (GB: ADC35472.1), Feline CoV strain UU21 (GB: ADL71466.1), Human CoV NL63 (GB: YP_003767.1), 229E-related bat CoV with one N domains (GB: ALK28775.1), 229E-related bat CoV with two N domains (GB: ALK28765.1), Human CoV 229E strain inf-1 (GB: NP_073551.1), MHV strain A59 (GB: ACO72893), BCoV strain KWD1 (GB: AAX38489), HCoV-OC43 strain Paris (GB: AAT84362), HCoV-HKU1 (GB: AAT98580), SARS-CoV strain Urbani (GB: AAP13441), MERS-CoV strain EMC/2012 (GB: YP_009047204), HKU4 (GB: AGP04928), HKU5 (GB: AGP04943), IBV strain Beaudette (GB: ADP06471), and PDCoV strain USA/Ohio137/2014 (GB: AIB07807). PSI-BLAST analysis using the NTR of the HCoV-NL63 S protein (residues 16–196) as a query detected two homologous regions in the first 425 residues of the 229E-related bat coronavirus spike protein (GB: ALK28765.1)—designated N1 (residues 32–213) and N2 (residues 246–422) with 32% and 35% amino acid sequence identity, respectively, suggesting a duplication of the NTR. Spike proteins are drawn to scale and aligned at the position of the conserved fusion peptide (FP1).