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. 2021 Oct 13;95(21):e0135721.
doi: 10.1128/JVI.01357-21. Epub 2021 Aug 18.

Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage

Affiliations

Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage

Nikita Shiliaev et al. J Virol. .

Abstract

One of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virulence factors is the ability to interact with high affinity to the ACE2 receptor, which mediates viral entry into cells. The results of our study demonstrate that within a few passages in cell culture, both the natural isolate of SARS-CoV-2 and the recombinant cDNA-derived variant acquire an additional ability to bind to heparan sulfate (HS). This promotes a primary attachment of viral particles to cells before their further interactions with the ACE2. Interaction with HS is acquired through multiple mechanisms. These include (i) accumulation of point mutations in the N-terminal domain (NTD) of the S protein, which increases the positive charge of the surface of this domain, (ii) insertions into the NTD of heterologous peptides containing positively charged amino acids, and (iii) mutation of the first amino acid downstream of the furin cleavage site. This last mutation affects S protein processing, transforms the unprocessed furin cleavage site into the heparin-binding peptide, and makes viruses less capable of syncytium formation. These viral adaptations result in higher affinity of viral particles to heparin, dramatic increase in plaque sizes, more efficient viral spread, higher infectious titers, and 2 orders of magnitude higher infectivity. The detected adaptations also suggest an active role of NTD in virus attachment and entry. As in the case of other RNA-positive (RNA+) viruses, evolution to HS binding may result in virus attenuation in vivo. IMPORTANCE The spike protein of SARS-CoV-2 is a major determinant of viral pathogenesis. It mediates binding to the ACE2 receptor and, later, fusion of viral envelope and cellular membranes. The results of our study demonstrate that SARS-CoV-2 rapidly evolves during propagation in cultured cells. Its spike protein acquires mutations in the NTD and in the P1' position of the furin cleavage site (FCS). The amino acid substitutions or insertions of short peptides in NTD are closely located on the protein surface and increase its positive charge. They strongly increase affinity of the virus to heparan sulfate, make it dramatically more infectious for the cultured cells, and decrease the genome equivalent to PFU (GE/PFU) ratio by orders of magnitude. The S686G mutation also transforms the FCS into the heparin-binding peptide. Thus, the evolved SARS-CoV-2 variants efficiently use glycosaminoglycans on the cell surface for primary attachment before the high-affinity interaction of the spikes with the ACE2 receptor.

Keywords: ACE2; SARS-CoV-2; coronavirus; furin cleavage; heparin binding; recombinant virus; spike NTD; spike protein; viral evolution.

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Figures

FIG 1
FIG 1
The original sample of WA1/2020 is heterogeneous. (A) The original WA1/2020 (P4) isolate received was titrated in parallel on Vero E6 and Vero/ACE2 cells (see Materials and Methods for details). Cells were fixed and stained at 68 hpi. (B) Expression of ACE2 in different cell lines and cell clones. “Total” indicates that cells were not cloned after blasticidin selection.
FIG 2
FIG 2
WA1/2020 isolate evolves to the large plaque phenotype and higher infectivity. (A) Plaques formed by WA1/2020 virus on Vero E6 and Vero/ACE2 cells. Plaques were stained by crystal violet at 68 hpi. (B) Concentrations of GE and PFU and GE/PFU ratios in the samples of WA1/2020 at P5 (passage 1 following receipt) and P9 (passage 5 following receipt). Significance of differences was determined by the unpaired t test with Welch’s correction (****, P < 0.0001; n= 3). (C) Schematic presentation of the SARS-CoV-2 spike protein, position of the identified insertion, and its nt and aa sequences. (D) Evolution of WA1/2020 pool during virus replication in Vero E6 cells for 5 passages.
FIG 3
FIG 3
The cDNA-derived CoV-2/GFP rapidly adapts during passaging in Vero cells to higher infectivity and large plaque phenotype. (A) Schematic presentation of the coding strategy of the recombinant CoV-2/GFP genome. (B) Vero/ACE2 cells were infected with CoV-2/GFP at an MOI of 10 PFU/cell and fixed at 8 hpi with paraformaldehyde (PFA) and stained with phalloidin, labeled with Alexa Fluor 546. Images were acquired on a Zeiss LSM 800 confocal microscope in Airyscan mode with a 63×/1.4 numerical-aperture (NA) PlanApochromat oil objective. (C) Plaques formed on Vero/ACE2 by CoV-2/GFP P0 (harvested after electroporation) and by the same virus after 5 passages on Vero/ACE2 cells. Staining was performed at the same time postinfection. (D) Concentrations of GE and PFU and GE/PFU ratios in the samples of CoV-2/GFP harvested at P0, P1, and P5 on Vero E6 cells. P5/2 indicates a sample harvested at passage 5 on Vero/ACE2 cells. Significance of differences was determined by the unpaired t test with Welch’s correction (****, P < 0.0001; n= 3).
FIG 4
FIG 4
CoV-2/GFP acquires an S686G mutation in P1′ of FCS. (A) Schematic presentation of the SARS-CoV-2 S protein, position of the mutation, and nt and aa sequences of the gene fragment in the parental and Vero cells-adapted variant. (B) Evolution of CoV-2/GFP pool during virus replication in Vero E6 cells for 5 passages. (C) Western blot analysis of S protein in the particles released from cells infected with WA1/2020 and CoV-2/GFP harvested at different passages on Vero E6 cells (see Materials and Methods for details).
FIG 5
FIG 5
Mutations in the S protein-coding sequence confirm the large plaque phenotype and higher infectivities of the recombinant viruses to Vero cells. (A) Plaques formed by the early-passage (P1) isolate of CoV-2/UAB and the recombinant CoV-2/GFP-based variants, containing either the insertion in the NTD or S686G mutation or both modifications. In all cases, P1 viruses were assessed in the standard plaque assay, and plaques were stained at day 3 postinfection. (B) Concentrations of GE and PFU and GE/PFU ratios in the samples of CoV-2/GFP encoding the S protein with the indicated modifications. (C) Vero/ACE2 cells were infected with the indicated viruses at an MOI of 0.01 PFU/cell. After 1 h of infection, cells were washed 3 times with PBS and further incubated in the corresponding complete media. At the indicated time points, media were replaced, and viral titers were determined by plaque assay on Vero/ACE2 cells. For panels B and C, significance of differences was determined by the unpaired t test with Welch’s correction (**, P < 0.01; ***, P < 0.001; ****, P < 0.0001; n= 3). (D) Western blot analysis of S protein in the particles released from Vero cells infected with CoV-2/GFP, CoV-2/GFP/ins, CoV-2/GFP/G, and CoV-2/GFP/ins/G (see Materials and Methods for details).
FIG 6
FIG 6
After passaging on Vero cells, SARS-CoV-2 acquires higher affinity to heparin Sepharose. Samples of the indicated viruses were prepared in the serum-free media, diluted to 0.1 M NaCl, and loaded to a column of heparin Sepharose. After washing with 0.66× PBS, which contains 0.1 M NaCl, viruses were eluted with PBS containing increasing concentrations of NaCl. Viral titers in each fraction, including FT, were determined by plaque assay on Vero/ACE2 cells. Titers were normalized to those in the fraction with the highest viral concentration. The experiments were repeated twice with reproducible results. The data from one of the experiments are presented.
FIG 7
FIG 7
Recombinant viruses with the indicated mutations in the S protein exhibit high affinity to heparin Sepharose. Viral samples were prepared in serum-free media and analyzed as described in the legend to Fig. 6. Viral titers in each fraction, including FT, were determined by plaque assay on Vero/ACE2 cells. Titers were normalized to those in the fraction with the highest concentration of infectious virus. The experiments were repeated twice with reproducible results. Data from one of the representative experiments are presented.
FIG 8
FIG 8
Heparin efficiently inhibits infectivity of high-passage-number but not low-passage-number viruses. The indicated viruses were incubated with heparin at the indicated concentrations for 1 h and then used for infection of Vero/ACE2 cells (see Materials and Methods for details). The data were normalized to those generated on the samples incubated without heparin. The experiment was repeated 3 times; means and SDs are indicated. Significances of differences between CoV-2/UAB P2 and other variants at each concentration of heparin were determined by one-way analysis of variance (ANOVA) with Dunnett’s test. For all concentrations, the differences were highly significant with P < 0.0001.
FIG 9
FIG 9
The S686G mutation has negative effect on the ability of SARS-CoV-2 virus to form syncytia. Vero/ACE2 cells in 6-well Costar plates were infected with the indicated variants at an MOI of 2 PFU/cell and incubated in serum-free media for 16 h at 37°C. Then they were fixed by 4% PFA, and images were acquired on EVOS microscope. Syncytia are indicated by black arrows.
FIG 10
FIG 10
Mutations acquired by the NTD during virus passaging in Vero cells increase the positive charge of the protein surface. Electrostatic surface rendering is presented. Blue and red indicate electronegative and electropositive surfaces, respectively. Positions of the indicated aa substitutions and peptide insertion GLTSKRN between amino acid residues 214 and 215 are shown by black circles and asterisks. Images were generated with BIOVIA Discovery Studio Visualizer.
FIG 11
FIG 11
Three-dimensional model of the trimeric SARS-CoV-2 spike ectodomain is shown. The individual spike subunits are shown in green, yellow, and blue. Locations of the single mutations, the insertion in the NTD, and uncleaved FCS are highlighted with red spheres.

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