Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins

  1. Yuejun Shi
  2. Jiale Shi
  3. Limeng Sun
  4. Yubei Tan
  5. Gang Wang
  6. Fenglin Guo
  7. Guangli Hu
  8. Yanan Fu
  9. Zhen F. Fu
  10. Shaobo Xiao
  11. Guiqing Peng

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Abstract

Coronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. However, no commercial vaccines against the coronaviruses that can infect humans are available. The spike (S) homotrimers bind to their receptors through the receptor-binding domain (RBD), which is believed to be a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs were observed to adopt two different conformational states (lying or standing). Then, structural and immunological analyses were used to explore differences in the immune response with RBDs among these coronaviruses. Our results showed that more RBD-specific antibodies were induced by the S trimer with the RBD in the “standing” state (SARS-CoV and SARS-CoV-2) than the S trimer with the RBD in the “lying” state (HCoV-229E), and the affinity between the RBD-specific antibodies and S trimer was also higher in the SARS-CoV and SARS-CoV-2. In addition, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was much lower and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus . Our findings will provide important implications for future development of coronavirus vaccines.

Importance

Outbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. Here, we tested the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that Beta-CoVs RBDs are in a standing state, and their S proteins can induce more neutralizing antibodies targeting RBD. However, HCoV-229E RBD is in a lying state, and its S protein induces a low level of neutralizing antibody targeting RBD. Our results indicate that Alpha-coronavirus is more conducive to escape host immune recognition, and also provide novel ideas for the development of vaccines targeting S protein.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.09.141580: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: The experiments were carried out using the protocols approved by the Scientific Ethics Committee of Huazhong Agricultural University (permit number: HZAUSW-2018-009).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableAnimal immunization: Female BALB/c mice aged 6 weeks were immunized with different proteins at 0 and 3 weeks.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Then, horseradish peroxidase (HRP)-conjugated goat anti-mouse/rabbit IgG (1:10,000 diluted in PBST with 1% BSA (w/v), Boster) was used as the secondary antibody, and 3,3’,5,5’-tetramethylbenzidine (TMB) (Beyotime) was used as the substrate for detection.
    anti-mouse/rabbit IgG
    suggested: (Biorbyt Cat# orb27530, RRID:AB_10954533)
    Then, the mouse anti-Strep-tag II antibody (SAB, 1:3,000 diluted in PBST with 1% BSA (w/v)) and HRP-conjugated goat anti-mouse IgG (1:5,000 diluted in PBST with 1% BSA (w/v), Boster) was used for detection.
    anti-Strep-tag II
    suggested: None
    anti-mouse IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Three days after the last injection, spleen cells were collected and fused with SP2/0 cells with PEG1450 (Sigma-Aldrich, P7181) to generate hybridoma cells.
    SP2/0
    suggested: None
    Production and entry assay of pseudoviruses: Pseudo-typed viruses were produced as previously described (50), 293T (ATCC, CRL-3216), Huh-7 and Vero (ATCC, CCL-81) cells were maintained in high glucose DMEM (Gibco, USA) supplemented with 10% FBS (FBS; Natocor, Argentina), penicillin (100 IU/ml) and streptomycin (100 μg/ml).
    293T
    suggested: None
    Huh-7
    suggested: None
    Vero
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Animal immunization: Female BALB/c mice aged 6 weeks were immunized with different proteins at 0 and 3 weeks.
    BALB/c
    suggested: RRID:IMSR_ORNL:BALB/cRl)
    Software and Algorithms
    SentencesResources
    Briefly, structure-based B-cell epitope prediction was performed by DiscoTope 2.0 with a positive cutoff greater than −3.7 (corresponding to a specificity greater than or equal to 0.75 and a sensitivity less than 0.47) using the following protein structures: the HCoV-229E S-trimer and RBD (PDB IDs: 6U7H and 6ATK, respectively), the SARS-CoV S-trimer and RBD (PDB IDs: 5X5B and 2AJF, respectively), the SARS-CoV-2 S-trimer and RBD (PDB IDs: 6VYB and 6M0J, respectively), the PEDV RBD (PDB ID: 6U7K), the FIPV RBD (PDB ID: 6JX7), the PRCoV RBD (PDB ID: 4F5C), and the transmissible gastroenteritis virus (TGEV) RBD (PDB ID: 4F2M).
    DiscoTope
    suggested: (DiscoTope, RRID:SCR_018530)
    All the predicted residues were then labeled in corresponding structures using PyMOL (Schrödinger).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Additionally, the amino acid sequences of alpha-CoVs RBDs were aligned using ClustalW2 (52).
    ClustalW2
    suggested: (ClustalW2, RRID:SCR_002909)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 38. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.06.09.141580 on bioRxiv