Structures and distributions of SARS-CoV-2 spike proteins on intact virions

Ke, Zunlong; Otón, Joaquı́n; Qu, Kun; Cortese, Mirko; Žíla, Vojtěch; McKeane, Lesley; Nakane, Takanori; Zivanov, Jasenko; Neufeldt, Christopher J.; Cerikan, Berati; Lu, John M.; Peukes, Julia; Xiong, Xiaoli; Kräusslich, Hans Georg; Scheres, S.H.W.; Bartenschlager, Ralf; Briggs, John

doi:10.1038/s41586-020-2665-2

Cited by 1,072 publications

(1,354 citation statements)

References 60 publications

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“…While our results here demonstrate that CR3022 Fab could form a stable complex with SARS-CoV S protein in a prefusion conformation, a recent study reported that prefusion SARS-CoV-2 S protein fell apart upon binding to CR3022 Fab as indicated by cryo-EM [29]. It should be noted that the three-up conformation is much more rarely observed than the other RBD conformations (all-down, one-up, and two-up) in SARS-CoV by cryo-EM [26][27][28], or SARS-CoV-2 by cryo-EM [30][31][32] and cryo-electron tomography [33,34], and could relate to differences in the stability of S trimers in SARS-CoV versus SARS CoV-2 when CR3022 is bound. Further studies will be required to investigate whether such a difference between SARS-CoV-2 and SARS-CoV is related to stability differences in the recombinant spike proteins, or to different dynamics of the RBD on the virus or infected cells.…”

Section: Cr3022-bound Sars-cov S Protein Exhibits a Rare Three-up Conmentioning

confidence: 95%

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Yuan

Bangaru

et al. 2020

Preprint

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Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that can cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential for cross-neutralizing epitopes on SARS-like viruses.

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Section: Cr3022-bound Sars-cov S Protein Exhibits a Rare Three-up Conmentioning

confidence: 95%

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Yuan

Bangaru

et al. 2020

Preprint

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“…The receptor binding domain (RBD) has been identified as the critical component to initiate virus attachment to ACE2, a cellular receptor for viral infection 33 . Interestingly, the RBD is present in both up and down configurations in the pre-fusion form of S protein, and the up position has been speculated as the prerequisite for interaction with ACE2 6,31 . The furin cleavage at the S1/S2 boundary of SARS-CoV-2 S occurs during viral biosynthesis 34 .…”

Section: Resultsmentioning

confidence: 99%

“…This feature is believed to have emerged during viral transmission from zoonotic host to human 25–27 , and is key to SARS-CoV-2 high transmissibility in humans 28,29 . Although robust SARS-CoV-2 infection of human lungs requires a multibasic cleavage site 30 , interestingly, both cleaved and uncleaved versions of S protein co-exist on virions purified from viral culture on Vero cells 31,32 . Thus, it remains unclear how the cleavage provides an advantage for viral transmission.…”

Section: Introductionmentioning

confidence: 99%

Immunogenicity of novel mRNA COVID-19 vaccine MRT5500 in mice and non-human primates

Kalnin

Plitnik²,

Kishko

et al. 2020

Preprint

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An effective vaccine to address the global pandemic of coronavirus disease 2019 (COVID-19) is an urgent public health priority. Novel synthetic mRNA and vector-based vaccine technologies offer an expeditious development path alternative to traditional vaccine approaches. Here we describe the efforts to utilize an mRNA platform for rational design and evaluations of mRNA vaccine candidates based on Spike (S) glycoprotein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus causing COVID-19. Several mRNA constructs expressing various structural conformations of S-protein, including wild type (WT), a pre-fusion stabilized mutant (2P), a furin cleavage-site mutant (GSAS) and a double mutant form (2P/GSAS), were tested in a preclinical animal model for their capacity to elicit neutralizing antibodies (nAbs). The lead 2P/GSAS candidate was further assessed in dose-ranging studies in mice and Cynomolgus macaques. The selected 2P/GSAS vaccine formulation, now designated MRT5500, elicited potent nAbs as measured in two types of neutralization assays. In addition, MRT5500 elicited TH1-biased responses in both mouse and non-human primate species, a result that helps to address a hypothetical concern regarding potential vaccine-associated enhanced respiratory diseases associated with TH2-biased responses. These data position MRT5500 as a viable vaccine candidate for clinical development against COVID-19.

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“…Additionally, we designed a second nanoparticle construct in which we deleted the C-terminal 70 residues of the ectodomain and expressed this truncated spike (residues 1-1143) on ferritin (SΔC-Fer). These C-terminal residues are unresolved in the cryo-EM structures of the spike trimer (3,7) and it has been suggested that they have extensive conformational flexibility based on electron microscopy of soluble trimers and viral particles (39)(40)(41). Additionally, this region of the spike contains an immunodominant linear epitope, as determined via analysis of convalescent sera from COVID-19 patients (42,43).…”

Section: Introductionmentioning

confidence: 99%

A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice

Chen

Zhang

Sanyal

et al. 2020

Preprint

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Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.

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Structures and distributions of SARS-CoV-2 spike proteins on intact virions

Cited by 1,072 publications

References 60 publications

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody

Immunogenicity of novel mRNA COVID-19 vaccine MRT5500 in mice and non-human primates

A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice

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