Adaptation‐Proof SARS‐CoV‐2 Vaccine Design
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) surface spike glycoprotein—a major antibody target—is critical for virus entry via engagement of human angiotensin‐converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS‐CoV‐2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, candidate stable immunogens are designed that mimic surface features of selected conserved regions of spike protein through “epitope grafting,” in which the target epitope topology is presented on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope‐scaffolds showed stark agreement with computational models and target epitopes. The sera from mice immunized with engineered designs display epitope‐scaffolds and spike binding activity. The utility of the designed epitope‐scaffolds in diagnostic applications is also demonstrated. Taken all together, this study provides an important methodology for targeting the conserved, non‐RBD structural motifs of spike protein for SARS‐CoV‐2 epitope vaccine design and demonstrates the potential utility of “epitope grafting” in rational vaccine design.
Article activity feed
-
-
SciScore for 10.1101/2022.05.17.492310: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources We added horseradish peroxidase (HRP)-conjugated goat anti-human IgG (1:5000, SouthernBiotech #2016-05) to detect the binding in COVID-19 patients’ serum samples, HRP-conjugated goat anti-mouse IgG (1:5000, Sigma-Aldrich, #AP124P) to detect the binding in mouse serum samples, HRP-conjugated goat anti-rabbit IgG (1:5000, ThermoFisher Scientific, #31460) to detect the binding in commercial anti-spike antibodies, for 1 h at 37 °C. anti-human IgGsuggested: Noneanti-mouse IgGsuggested: (Millipore Cat# AP124P, RRID:AB_90456)anti-rabbit IgGsuggested: (Thermo Fisher Scientific Cat# 31460, RRID:AB_228341)anti-sp…SciScore for 10.1101/2022.05.17.492310: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources We added horseradish peroxidase (HRP)-conjugated goat anti-human IgG (1:5000, SouthernBiotech #2016-05) to detect the binding in COVID-19 patients’ serum samples, HRP-conjugated goat anti-mouse IgG (1:5000, Sigma-Aldrich, #AP124P) to detect the binding in mouse serum samples, HRP-conjugated goat anti-rabbit IgG (1:5000, ThermoFisher Scientific, #31460) to detect the binding in commercial anti-spike antibodies, for 1 h at 37 °C. anti-human IgGsuggested: Noneanti-mouse IgGsuggested: (Millipore Cat# AP124P, RRID:AB_90456)anti-rabbit IgGsuggested: (Thermo Fisher Scientific Cat# 31460, RRID:AB_228341)anti-spikesuggested: NoneExperimental Models: Cell Lines Sentences Resources The antibody–virus mixture was then added to monolayers of Vero E6 cells (CRL-1586, ATCC, USA) in 96-well microtiter plates and incubated further for 72 h at 5% CO2 at 36 ± 2 °C. Vero E6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Mice (strain FVB) were immunized by standard methods using purified epitope-scaffolds admixed with sigma adjuvant (RIBI adjuvant) at a 1:1 ratio as described by the manufacturer. FVBsuggested: RRID:IMSR_TAC:fvb)Recombinant DNA Sentences Resources Protein expression and purification: We obtained the genes encoding the designed proteins in pET28a vectors from GenScript (Genscript.com). pET28asuggested: RRID:Addgene_139598)Software and Algorithms Sentences Resources We optimized the chimeric structures using Chiron and Gaia. Gaiasuggested: (GAIA, RRID:SCR_009182)We solved the crystal structure by the molecular replacement method using the apolipoprotein E amino-terminal domain structure (1BZ4) as a search model in the PHENIX software. PHENIXsuggested: (Phenix, RRID:SCR_014224)Several iterations of model building in COOT program and refinement in the PHENIX program were done to complete the structure. COOTsuggested: (Coot, RRID:SCR_014222)Pymol software was used for all the structural analysis and figures. Pymolsuggested: (PyMOL, RRID:SCR_000305)We subsequently used the program DAMMIN, part of ATSAS suite, for ab initio low resolution shape determination. ATSASsuggested: (ATSAS, RRID:SCR_015648)Subsequently, energy minimization of the dimer was done using the YASARA server. YASARAsuggested: (YASARA, RRID:SCR_017591)Statistics and reproducibility: We performed all statistical analyses by unpaired two-tailed Student’s t-test using GraphPad Prism 8 v8.2.1 software and Microsoft Excel v16.49. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)We used GraphPad Prism 8 version 8.2.1 and Adobe Illustrator to draw and assemble the figures. Adobe Illustratorsuggested: (Adobe Illustrator, RRID:SCR_010279)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A limitation of our study is that only linear epitopes were included in the design. Conformational epitopes could be included in further optimization and future designs for improved response. Here, we conceptually demonstrated the applicability of these epitope-scaffolds in detecting epitope-specific antibodies from serological samples. ED2-based ELISA was used to detect IgG antibodies in serum samples from RT-PCR confirmed COVID-19 patients and pre-pandemic samples. Most COVID-19 patients showed strong reactivity against ED2. All pre-pandemic serum samples remained unreactive. Some samples in the COVID-19 group showed low OD readouts similar to healthy samples, suggesting a lack of or a weak seroconversion64,68,69. Next steps may involve testing cross reactivity with patient samples of other coronaviruses. When available, studies may also include the COVID-19 positive samples with known times from symptom onset for better analysis of seroconversion. Nonetheless, our results confirm the usefulness of these epitope-scaffolds for ELISA. We also show the extension of the conventional detection assays to a user-friendly, magnetic nanoparticle-based ELISA approach suitable for a rapid detection of epitope specific antibodies by coupling epitope-scaffolds to magnetic beads. Examples are shown to highlight the utility of epitope-scaffolds; assay optimization may be required before adopting it to specific needs. The magnetic nanoparticle-based ELISA assays are simple to perform and v...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
