Insight into Vaccine Development for Alphacoronaviruses Based on Structural and Immunological Analyses of Spike Proteins
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Abstract
Outbreaks of coronaviruses, especially SARS-CoV-2, pose a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority.
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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 Statement IRB: The experiments were carried out using the protocols approved by the Scientific Ethics Committee of Huazhong Agricultural University (permit number: HZAUSW-2018-009). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Animal immunization: Female BALB/c mice aged 6 weeks were immunized with different proteins at 0 and 3 weeks. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources 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) … 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 Statement IRB: The experiments were carried out using the protocols approved by the Scientific Ethics Committee of Huazhong Agricultural University (permit number: HZAUSW-2018-009). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Animal immunization: Female BALB/c mice aged 6 weeks were immunized with different proteins at 0 and 3 weeks. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources 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 IgGsuggested: (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 IIsuggested: Noneanti-mouse IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources 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. SP2/0suggested: NoneProduction 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). 293Tsuggested: NoneHuh-7suggested: NoneVerosuggested: NoneExperimental Models: Organisms/Strains Sentences Resources Animal immunization: Female BALB/c mice aged 6 weeks were immunized with different proteins at 0 and 3 weeks. BALB/csuggested: RRID:IMSR_ORNL:BALB/cRl)Software and Algorithms Sentences Resources 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). DiscoTopesuggested: (DiscoTope, RRID:SCR_018530)All the predicted residues were then labeled in corresponding structures using PyMOL (Schrödinger). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Additionally, the amino acid sequences of alpha-CoVs RBDs were aligned using ClustalW2 (52). ClustalW2suggested: (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.
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