An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), various vaccines are being developed, with most vaccine candidates focusing on the viral spike protein. Here, we developed a previously unknown subunit vaccine comprising the receptor binding domain (RBD) of the spike protein fused with the tetanus toxoid epitope P2 (RBD-P2) and tested its efficacy in rodents and nonhuman primates (NHPs). We also investigated whether the SARS-CoV-2 nucleocapsid protein (N) could increase vaccine efficacy. Immunization with N and RBD-P2 (RBDP2/N) + alum increased T cell responses in mice and neutralizing antibody levels in rats compared with those obtained using RBD-P2 + alum. Furthermore, in NHPs, RBD-P2/N + alum induced slightly faster SARS-CoV-2 clearance than that induced by RBD-P2 + alum, albeit without statistical significance. Our study supports further development of RBD-P2 as a vaccine candidate against SARS-CoV-2. Also, it provides insights regarding the use of N in protein-based vaccines against SARS-CoV-2.

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Synthesis and immunological evaluation of synthetic peptide based anti-SARS-CoV-2 vaccine candidates

Chemical Communications ◽

10.1039/d0cc08265a ◽

2021 ◽

Author(s):

Qingyu Zhao ◽

Yanan Gao ◽

Min Xiao ◽

Xuefei Huang ◽

Xuanjun Wu

Keyword(s):

Synthetic Peptide ◽

Spike Protein ◽

Effective Vaccine ◽

The Novel ◽

Vaccine Candidates ◽

Peptide Epitopes ◽

Novel Coronavirus ◽

Immunological Evaluation

For prevention of the coronavirus disease 2019 caused by the novel coronavirus SARS-CoV-2, an effective vaccine is critical. Herein, several potential peptide epitopes from the spike protein of SARS-CoV-2 have...

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Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach

10.1101/2020.07.01.150805 ◽

2020 ◽

Author(s):

Rohit Pritam Das ◽

Manaswini Jagadeb ◽

Surya Narayan Rath

Keyword(s):

Global Health ◽

Viral Infection ◽

B Cell ◽

Molecular Interaction ◽

Vaccine Candidate ◽

Virus Disease ◽

Spike Protein ◽

Vaccine Candidates ◽

Mhc Molecules ◽

Peptide Candidate

Novel corona virus disease 2019 (COVID-19) is emerging as a pandemic situation and declared as a global health emergency by WHO. Due to lack of specific medicine and vaccine, viral infection has gained a frightening rate and created a devastating state across the globe. Here authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. We have predicted a 9-mer peptide as representative of both B-cell and T-cell epitopic region along with suitable properties such as antigenic and non-allergenic. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The present study may helpful to step forward in the development of vaccine candidates against COVID-19.

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Protective Immunity against SARS Subunit Vaccine Candidates Based on Spike Protein: Lessons for Coronavirus Vaccine Development

Journal of Immunology Research ◽

10.1155/2020/7201752 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Atin Khalaj-Hedayati

Keyword(s):

Neutralizing Antibodies ◽

Protective Immunity ◽

Subunit Vaccine ◽

Vaccine Development ◽

Spike Protein ◽

Effective Vaccine ◽

Universal Vaccine ◽

Health Security ◽

Vaccine Candidates ◽

Novel Coronavirus

The recent outbreak of the novel coronavirus disease, COVID-19, has highlighted the threat that highly pathogenic coronaviruses have on global health security and the imminent need to design an effective vaccine for prevention purposes. Although several attempts have been made to develop vaccines against human coronavirus infections since the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2003, there is no available licensed vaccine yet. A better understanding of previous coronavirus vaccine studies may help to design a vaccine for the newly emerged virus, SARS-CoV-2, that may also cover other pathogenic coronaviruses as a potentially universal vaccine. In general, coronavirus spike protein is the major antigen for the vaccine design as it can induce neutralizing antibodies and protective immunity. By considering the high genetic similarity between SARS-CoV and SARS-CoV-2, here, protective immunity against SARS-CoV spike subunit vaccine candidates in animal models has been reviewed to gain advances that can facilitate coronavirus vaccine development in the near future.

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A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

10.1101/2020.04.27.064774 ◽

2020 ◽

Cited By ~ 5

Author(s):

Bethany Dearlove ◽

Eric Lewitus ◽

Hongjun Bai ◽

Yifan Li ◽

Daniel B. Reeves ◽

...

Keyword(s):

Vaccine Candidate ◽

Sequence Diversity ◽

Spike Protein ◽

Effective Vaccine ◽

Virus Spread ◽

Vaccine Candidates ◽

Human Host

AbstractThe magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine should be efficacious against current global strains.One Sentence SummaryThe limited diversification of SARS-CoV-2 reflects drift and bottleneck events rather than adaptation to humans as the virus spread.

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Limiting the priming dose of a SARS CoV-2 vaccine improves virus-specific immunity

10.1101/2021.03.31.437931 ◽

2021 ◽

Author(s):

Sarah Sanchez ◽

Nicole Palacio ◽

Tanushree Dangi ◽

Thomas Ciucci ◽

Pablo Penaloza-MacMaster

Keyword(s):

Immune Responses ◽

Low Dose ◽

Standard Dose ◽

Spike Protein ◽

Priming Dose ◽

Vaccine Candidates ◽

Global Pandemic ◽

Rational Vaccine Design ◽

Vaccine Availability

Since late 2019, SARS-CoV-2 has caused a global pandemic that has infected 128 million people worldwide. Although several vaccine candidates have received emergency use authorization (EUA), there are still a limited number of vaccine doses available. To increase the number of vaccinated individuals, there are ongoing discussions about administering partial vaccine doses, but there is still a paucity of data on how vaccine fractionation affects vaccine-elicited immunity. We performed studies in mice to understand how the priming dose of a SARS CoV-2 vaccine affects long-term immunity to SARS CoV-2. We first primed C57BL/6 mice with an adenovirus-based vaccine encoding SARS CoV-2 spike protein (Ad5-SARS-2 spike), similar to that used in the CanSino and Sputnik V vaccines. This prime was administered either at a low dose (LD) of 106 PFU or at a standard dose (SD) of 109 PFU, followed by a SD boost in all mice four weeks later. As expected, the LD prime induced lower immune responses relative to the SD prime. However, the LD prime elicited immune responses that were qualitatively superior, and upon boosting, mice that were initially primed with a LD exhibited significantly more potent immune responses. Overall, these data demonstrate that limiting the priming dose of a SARS CoV-2 vaccine may confer unexpected benefits. These findings may be useful for improving vaccine availability and for rational vaccine design.

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Recombinant subunits of SARS-CoV-2 spike protein as vaccine candidates to elicit neutralizing antibodies

10.21203/rs.3.rs-414366/v1 ◽

2021 ◽

Author(s):

Faezeh Noorabad ghahroodi ◽

Saeed Khalili ◽

Mohammad Javad Rasaee

Keyword(s):

Recombinant Proteins ◽

In Silico ◽

Neutralizing Antibodies ◽

Spike Protein ◽

Serum Samples ◽

Strong Immune Response ◽

Live Virus ◽

Vaccine Candidates ◽

Antibody Titers

Abstract The spike protein has been reported as one of the most critical targets for vaccine design strategies against the SARS-COV-2 infection. Hence, we have designed, produced, and evaluated the potential use of recombinant proteins derived from spike protein as vaccine candidates capable of neutralizing SARS-COV-2 virus. In silico tools were used to design spike-based subunit recombinant proteins (P1, P2, and P3). These proteins were checked for their ability to be identified by the anti-SARS-COV-2 antibodies by exposing them to Covid-19 serum samples. The proteins were then injected into mice and rabbits and the antibody titers were measured for 170 days. The virus neutralization test (VNT) was performed to analyze the obtained antibodies for their neutralization efficiency. The antibodies that existed in the serum of COVID-19 patients have identified the designed proteins. The anti-spike antibody titer was increased in the animals injected with recombinant proteins. The VNT results revealed that the produced antibodies could neutralize the cultured live virus. The long-lasting antibody titers (130 and 170 days for rabbit and mouse groups) indicated the elicitation of a strong immune response by the recombinant proteins. Subunit vaccines could also be considered as robust tools for effective vaccination against COVID-19. Using a combination of in silico, in vitro, and in vivo experiments, it was shown that the injection of spike-based recombinant proteins could stimulate long-lasting and neutralizing antibody responses. Further evaluation of the recombinant proteins examined in our studies in higher primates and human would elucidate their true potentials.

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A thermostable, closed, SARS-CoV-2 spike protein trimer

10.1101/2020.06.15.152835 ◽

2020 ◽

Cited By ~ 3

Author(s):

Xiaoli Xiong ◽

Kun Qu ◽

Katarzyna A. Ciazynska ◽

Myra Hosmillo ◽

Andrew P. Carter ◽

...

Keyword(s):

Immune System ◽

Receptor Binding ◽

Conformational Flexibility ◽

Cell Entry ◽

Spike Protein ◽

Receptor Binding Site ◽

S Protein ◽

Vaccine Candidates ◽

Diagnostic Assays ◽

Potential Applications

AbstractThe spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.

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A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2008281117 ◽

2020 ◽

Vol 117 (38) ◽

pp. 23652-23662 ◽

Cited By ~ 25

Author(s):

Bethany Dearlove ◽

Eric Lewitus ◽

Hongjun Bai ◽

Yifan Li ◽

Daniel B. Reeves ◽

...

Keyword(s):

Viral Entry ◽

Neutralizing Antibodies ◽

Vaccine Candidate ◽

Spike Protein ◽

Reference Sequence ◽

Viral Population ◽

Effective Vaccine ◽

Nucleotide Substitutions ◽

Bioinformatics Analyses ◽

Vaccine Candidates

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.

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Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

Science ◽

10.1126/science.abe1502 ◽

2020 ◽

Vol 370 (6520) ◽

pp. 1089-1094 ◽

Cited By ~ 5

Author(s):

Sandhya Bangaru ◽

Gabriel Ozorowski ◽

Hannah L. Turner ◽

Aleksandar Antanasijevic ◽

Deli Huang ◽

...

Keyword(s):

Immune Responses ◽

Neutralizing Antibodies ◽

Subunit Vaccine ◽

Structural Integrity ◽

Vaccine Candidate ◽

Full Length ◽

Spike Protein ◽

Primary Target ◽

Site Specific ◽

Vaccine Candidates

Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo–election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.

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