SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

Corbett, Kizzmekia S.; Edwards, Darin K.; Leist, Sarah R.; Abiona, Olubukola M.; Boyoglu-Barnum, Seyhan; Gillespie, Rebecca A.; Himansu, Sunny; Schäfer, Alexandra; Ziwawo, Cynthia T.; DiPiazza, Anthony; Dinnon, Kenneth H.; Elbashir, Sayda M.; Shaw, Christine A.; Woods, Angela; Fritch, Ethan J.; Martinez, David R.; Bock, Kevin W.; Minai, Mahnaz; Nagata, Bianca M.; Hutchinson, Geoffrey B.; Wu, Kai; Henry, Carole; Bahl, Kapil; Garcia-Dominguez, Dario; Zhi, Liu; Renzi, Isabella; Kong, Wing Pui; Schmidt, Stephen D.; Wang, Lingshu; Zhang, Yi; Phung, Emily; Chang, Lauren; Loomis, Rebecca J.; Altaras, Nedim Emil; Narayanan, Elisabeth; Metkar, Mihir; Presnyak, Vladimir; Liu, Cuiping; Louder, Mark K.; Shi, Wei; Leung, Kwanyee; Yang, Eun Sung; West, Ande; Gully, Kendra L.; Stevens, Laura J.; Wang, Nianshuang; Wrapp, Daniel; Doria‐Rose, Nicole A.; Stewart-Jones, Guillaume; Bennett, Hamilton; Alvarado, Gabriela; Nason, Martha; Ruckwardt, Tracy J.; McLellan, Jason S.; Denison, Mark R.; Chappell, James D.; Moore, Ian N.; Morabito, Kaitlyn M.; Mascola, John R.; Baric, Ralph S.; Carfı́, Andrea; Graham, Barney S.

doi:10.1038/s41586-020-2622-0

Cited by 1,301 publications

(1,319 citation statements)

References 44 publications

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“…While it fortunately appears that SARS-CoV-2 and many of the vaccine candidates in clinical trials can readily stimulate immune responses, (see e.g. (Corbett et al, 2020; Feng et al, 2020; Mulligan et al, 2020; Suthar et al, 2020; Wu, S. et al, 2020)), stringent assessment of antigens and careful selection of delivery vehicles are still necessary before it comes to mass vaccination. Careful selection of antigens is critical for avoiding unfavorable immune reactions and disease enhancement, as in the past experienced with RSV, measles and dengue vaccines (for reviews see (Lee et al, 2020; Ruckwardt et al, 2019)).…”

Section: Discussionmentioning

confidence: 99%

“…A soluble trimeric RBD, as applied in the BNT162b1 mRNA vaccine, showed promising immunogenicity in clinical trials, including stimulation of antibodies and T cell responses (Mulligan et al, 2020; Sahin et al, 2020). In addition to trimerization, membrane anchoring seems to further improve immunogenicity, as transmembrane anchored full-length S prefusion-stabilized protein was reported to elicit higher VNA levels than corresponding secreted constructs (Corbett et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

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Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19

Hennrich

Banda

Oberhuber

et al. 2020

Preprint

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The large SARS-CoV-2 spike (S) protein is the main target of current COVID-19 vaccine candidates but can induce non-neutralizing antibodies, which may cause vaccination-induced complications or enhancement of COVID-19 disease. Besides, encoding of a functional S in replication-competent virus vector vaccines may result in the emergence of viruses with altered or expanded tropism. Here, we have developed a safe single round rhabdovirus replicon vaccine platform for enhanced presentation of the S receptor-binding domain (RBD). Structure-guided design was employed to build a chimeric minispike comprising the globular RBD linked to a transmembrane stem-anchor sequence derived from rabies virus (RABV) glycoprotein (G). Vesicular stomatitis virus (VSV) and RABV replicons encoding the minispike not only allowed expression of the antigen at the cell surface but also incorporation into the envelope of secreted non-infectious particles, thus combining classic vector-driven antigen expression and particulate virus-like particle (VLP) presentation. A single dose of a prototype replicon vaccine, VSVΔG-minispike-eGFP (G), stimulated high titers of SARS-CoV-2 neutralizing antibodies in mice, equivalent to those found in COVID-19 patients. Boost immunization with the identical replicon further enhanced neutralizing activity. These results demonstrate that rhabdovirus minispike replicons represent effective and safe alternatives to vaccination approaches using replication-competent viruses and/or the entire S antigen.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19

Hennrich

Banda

Oberhuber

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Introduction of two consecutive proline (PP) substitutions in the S2 subunit in the hinge loop between the CH and heptad repeat 1 (HR1) stabilized the S proteins of SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) 9,10 and recently also the SARS-CoV-2 S protein in which also the furin cleavage site present at the boundary of the S1/S2 subunits was mutated 11,12 . Several vaccine approaches using different designs of the S protein (e.g., with or without stabilizing substitutions, using a wild-type (wt) signal peptide (SP) or Tissue Plasminogen Activator (tPA) SP 13 , have been described, which induce neutralizing antibodies (NAbs) and protection in animal challenge models against SARS-CoV 14 , MERS-CoV 13 , and SARS-CoV-2 infections [15][16][17][18] . It is assumed that an effective vaccine against coronavirus infections should induce NAbs and a Th1-skewed immune response.…”

Section: Introductionmentioning

confidence: 99%

Ad26 vector-based COVID-19 vaccine encoding a prefusion-stabilized SARS-CoV-2 Spike immunogen induces potent humoral and cellular immune responses

et al. 2020

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Development of effective preventative interventions against SARS-CoV-2, the etiologic agent of COVID-19 is urgently needed. The viral surface spike (S) protein of SARS-CoV-2 is a key target for prophylactic measures as it is critical for the viral replication cycle and the primary target of neutralizing antibodies. We evaluated design elements previously shown for other coronavirus S protein-based vaccines to be successful, e.g., prefusion-stabilizing substitutions and heterologous signal peptides, for selection of a S-based SARS-CoV-2 vaccine candidate. In vitro characterization demonstrated that the introduction of stabilizing substitutions (i.e., furin cleavage site mutations and two consecutive prolines in the hinge region of S2) increased the ratio of neutralizing versus non-neutralizing antibody binding, suggestive for a prefusion conformation of the S protein. Furthermore, the wild-type signal peptide was best suited for the correct cleavage needed for a natively folded protein. These observations translated into superior immunogenicity in mice where the Ad26 vector encoding for a membrane-bound stabilized S protein with a wild-type signal peptide elicited potent neutralizing humoral immunity and cellular immunity that was polarized towards Th1 IFN-γ. This optimized Ad26 vector-based vaccine for SARS-CoV-2, termed Ad26.COV2.S, is currently being evaluated in a phase I clinical trial (ClinicalTrials.gov Identifier: NCT04436276).

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“…However, for polyclonal sera, the cryo-EM approach identifies the predominant epitopes targeted. In the absence of any enrichment strategy, these are unlikely to be neutralizing epitopes, since neutralizing antibodies typically make up a small fraction of the total antibody response (45). The present methodology is similar in overall principle, to recently developed saturation mutagenesis approaches (13,35,36) to identify neutralization epitopes.…”

Section: Discussionmentioning

confidence: 93%

A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing

Datta

Chowdhury

Manjunath

et al. 2020

Preprint

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13Identification of specific epitopes targeted by neutralizing antibodies is essential to advance 14 epitope-based vaccine design strategies. We report a methodology for rapid epitope mapping 15 of neutralizing antibodies against HIV-1 Env at single residue resolution, using viral 16 neutralization assays and deep sequencing. We extended our methodology to map multiple 17 specificities of epitopes targeted in polyclonal sera, elicited in immunized animals as well as 18 in HIV-We recently described a methodology to decipher epitopes of monoclonal antibody panels 35 using yeast surface display, Cys labeling and deep sequencing 1, 2 . Here we built on this to map 36 epitopes of neutralizing monoclonal antibodies and polyclonal sera against the HIV-1 virus. 37 The design of an effective vaccine against HIV-1 has met with limited success so far, because 38 of the inability of immunogens to elicit broadly neutralizing antibodies (bNAbs) targeted to the 39 trimeric envelope (Env) glycoprotein, the sole viral antigen on the surface of the virus. Most 40 bNAbs isolated from infected individuals are directed to one of the major sites of vulnerability 41 on Env: V1/V2 loop apex, V3 loop, CD4-binding site, centre of the gp120 silent face, gp120-42 gp41 subunit interface, gp41 fusion peptide and membrane proximal external region (MPER) 43 of gp41. 44 We developed a facile methodology for mapping neutralizing HIV-1 epitopes at single residue 45 resolution. To this end, a library of single-site Cys mutations were engineered at selected 46 solvent-exposed sites in the Env glycoprotein on the surface of the virus. Cys mutants were 47 covalently labeled using a Cys reactive reagent (Maleimide-PEG2-Biotin) that masks epitope 48 residues, followed by infection of the labeled mutant viruses in mammalian cells in the 49 presence of bNAbs. Subsequently, deep sequencing of the env gene from bNAb-resistant 50 viruses was used to delineate epitopes ( Figure 1). We focused our epitope mapping efforts to 51 the Env ectodomain of the clade B, CCR5-tropic primary HIV-1 isolate JRFL, which has been 52 extensively characterized both biochemically and structurally, and is used as a model primary 53 virus. 54A total of 81 solvent-exposed residues (Table S1) were selected from the X-ray crystal structure 55 of the pre-fusion HIV-1 Env ectodomain using a combined criterion of >30% solvent 56 accessibility and sidechain-sidechain centroid distance >8 Å ( Figure S1). This led to the 57 identification of a set of solvent-exposed residues which collectively exhibit uniform surface 58 coverage of the Env trimer ( Figure S2). These Env residues were mutated to Cys in the pLAI-59 JRFL molecular clone, pooled in equimolar quantities to create a plasmid DNA library, and 60 transfected in HEK293T cells to produce the Exposed Cys Library, a library of single-site Cys 61 mutant viruses. Wt Env lacks free Cys residues. In single-cycle and multi-cycle infectivity 62 assays, the Exposed Cys Library retained significant viral infectivity ( Figure S3) and ...

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SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

Cited by 1,301 publications

References 44 publications

Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19

Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19

Ad26 vector-based COVID-19 vaccine encoding a prefusion-stabilized SARS-CoV-2 Spike immunogen induces potent humoral and cellular immune responses

A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing

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