Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design

Wang, Dongliang; Mai, Jinhui; Zhou, Wenfeng; Yu, Wanting; Zhan, Yang; Wang, Naidong; Epstein, Neal D.; Yang, Yi

doi:10.3390/vaccines8030355

Cited by 59 publications

(63 citation statements)

References 58 publications

(66 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 9 , 10 To protect against SARS-CoV-2 infection, it is important to form neutralising antibodies targeting S1 RBD, S1 N-terminal domain, or the S2 region; these antibodies block binding of the RBD to the ACE2 receptor and prevent S2-mediated membrane fusion or entry into the host cell, thus inhibiting viral infection. 11 , 12 …”

Section: Introductionmentioning

confidence: 99%

Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia

et al. 2020

View full text Add to dashboard Cite

Background We developed a heterologous COVID-19 vaccine consisting of two components, a recombinant adenovirus type 26 (rAd26) vector and a recombinant adenovirus type 5 (rAd5) vector, both carrying the gene for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (rAd26-S and rAd5-S). We aimed to assess the safety and immunogenicity of two formulations (frozen and lyophilised) of this vaccine. Methods We did two open, non-randomised phase 1/2 studies at two hospitals in Russia. We enrolled healthy adult volunteers (men and women) aged 18–60 years to both studies. In phase 1 of each study, we administered intramuscularly on day 0 either one dose of rAd26-S or one dose of rAd5-S and assessed the safety of the two components for 28 days. In phase 2 of the study, which began no earlier than 5 days after phase 1 vaccination, we administered intramuscularly a prime-boost vaccination, with rAd26-S given on day 0 and rAd5-S on day 21. Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). Secondary outcome measures were antigen-specific cellular immunity (T-cell responses and interferon-γ concentration) and change in neutralising antibodies (detected with a SARS-CoV-2 neutralisation assay). These trials are registered with ClinicalTrials.gov , NCT04436471 and NCT04437875 . Findings Between June 18 and Aug 3, 2020, we enrolled 76 participants to the two studies (38 in each study). In each study, nine volunteers received rAd26-S in phase 1, nine received rAd5-S in phase 1, and 20 received rAd26-S and rAd5-S in phase 2. Both vaccine formulations were safe and well tolerated. The most common adverse events were pain at injection site (44 [58%]), hyperthermia (38 [50%]), headache (32 [42%]), asthenia (21 [28%]), and muscle and joint pain (18 [24%]). Most adverse events were mild and no serious adverse events were detected. All participants produced antibodies to SARS-CoV-2 glycoprotein. At day 42, receptor binding domain-specific IgG titres were 14 703 with the frozen formulation and 11 143 with the lyophilised formulation, and neutralising antibodies were 49·25 with the frozen formulation and 45·95 with the lyophilised formulation, with a seroconversion rate of 100%. Cell-mediated responses were detected in all participants at day 28, with median cell proliferation of 2·5% CD4 + and 1·3% CD8 + with the frozen formulation, and a median cell proliferation of 1·3% CD4 + and 1·1% CD8 + with the lyophilised formulation. Interpretation The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong...

show abstract

Section: Introductionmentioning

confidence: 99%

Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Since the RBD contains important antigenic epitopes, frequent mutations in RBD, especially those that change the amino acid properties, may weaken the binding affinity of any antibody raised against the prototype strain [20,21] . This may lead to decreased vaccine efficacy and should be further studied.…”

Section: Discussionmentioning

confidence: 99%

“…The S protein expresses antigenic sites on its protein surface, likely with both T-cell and B-cell epitopes. The main antibody binding sites substantially overlap with RBD, and an antibody binding to these sites is likely to block viral entry into cells [19][20][21] .…”

Section: Introductionmentioning

confidence: 99%

V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity

Zhou

Dai

et al. 2020

Preprint

128

121

View full text Add to dashboard Cite

250 words 25 Importance: 150 words 26 Abstract 28 A novel coronavirus SARS-CoV-2 is associated with the current global pandemic of Coronavirus 29Disease 2019 . Spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the 30 critical determinant of viral tropism and infectivity. To investigate whether the mutations in the RBD 31 have altered the receptor binding affinity and caused these strains more infectious, we performed 32 molecular dynamics simulations of the binding affinity between the mutant SARS-CoV-2 RBDs to 33 date and the human ACE2 receptor. Among 1609 genomes of global SARS-CoV-2 strains, 32 34 non-synonymous RBD mutants were identified and clustered into 9 mutant types under high positive 35 selection pressure. Three mutant types (V367F, W436R, and D364Y) emerging in Wuhan, Shenzhen, 36 Hong Kong, and France, displayed higher human ACE2 affinity, and probably higher infectivity. This 37 is due to the enhanced structural stabilization of the RBD beta-sheet scaffold. High frequencies of 38 RBD mutations were identified: V367F from five France and one Hong Kong mutants, 13 V483A and 39 7 G476S mutants from the U.S.A. This suggested they originated as novel sub-lineages. The 40 enhancement of the binding affinity of the mutant type (V367F) was further validated by the 41 receptor-ligand binding ELISA assay. The molecular dynamics simulations also indicated that it 42 would be difficult for bat SARS-like CoV to infect humans. However, the pangolin CoV is potentially 43 infectious to humans. The analysis of critical RBD mutations provides further insights into the 44 evolutionary history of SARS-CoV-2 under high selection pressure. An enhancement of the 45 SARS-CoV-2 binding affinity to human ACE2 receptor reveals higher infectivity of the mutant 46 strains. 47 48 Importance 49 A novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of 50 SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain 51 (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the 52 mutations in the RBD of the circulating SARS-CoV-2 strains have altered the receptor binding 53affinity and caused these strains more infectious, should be paid more attentions to. Here, 32 54 non-synonymous RBD mutants were identified and clustered into 9 mutant types under high positive 55 . CC-BY-NC-ND 4.0 International license (which was not certified by peer review) is the author/funder. It is made available under a selection pressure, suggesting they originated as novel sub-lineages. Three mutant types displayed 56 higher human ACE2 affinity, and probably higher infectivity, one of which (V367F) was validated 57 by wet bench. The RBD mutation analysis provides insights into SARS-CoV-2 evolution. The 58 emergence of RBD mutations with increased human ACE2 affinity reveals higher risk of severe 59 morbidity and mortality during a sustained COVID-19 pandemic, particularly if no effective 60 precautions are implemented. 61 62

show abstract

“…Spike of SARS-CoV-2 adopts an architecture similar to that of the SARS-CoV ( Figure 1A), with S1 constituted by four sub-domains: NTD (N-terminal domain), receptor binding domain (RBD), and two CTDs (C-terminal domains). The S2-protein domain, instead, covers a second proteolytic site (S2′) upstream of the fusion peptide (FP), an internal fusion peptide (IFP), that is similar in SARS-CoV and SARS-CoV-2, and two heptad-repeat domains preceding the transmembrane domain (TM) (Wang D. et al, 2020).…”

Section: Structural Proteins Homologies and Differences Between Humamentioning

confidence: 99%

Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic

et al. 2020

View full text Add to dashboard Cite

At the end of December 2019, an epidemic form of respiratory tract infection now named COVID-19 emerged in Wuhan, China. It is caused by a newly identified viral pathogen, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which can cause severe pneumonia and acute respiratory distress syndrome. On January 30, 2020, due to the rapid spread of infection, COVID-19 was declared as a global health emergency by the World Health Organization. Coronaviruses are enveloped RNA viruses belonging to the family of Coronaviridae, which are able to infect birds, humans and other mammals. The majority of human coronavirus infections are mild although already in 2003 and in 2012, the epidemics of SARS-CoV and Middle East Respiratory Syndrome coronavirus (MERS-CoV), respectively, were characterized by a high mortality rate. In this regard, many efforts have been made to develop therapeutic strategies against human CoV infections but, unfortunately, drug candidates have shown efficacy only into in vitro studies, limiting their use against COVID-19 infection. Actually, no treatment has been approved in humans against SARS-CoV-2, and therefore there is an urgent need of a suitable vaccine to tackle this health issue. However, the puzzled scenario of biological features of the virus and its interaction with human immune response, represent a challenge for vaccine development. As expected, in hundreds of research laboratories there is a running out of breath to explore different strategies to obtain a safe and quickly spreadable vaccine; and among others, the peptide-based approach represents a turning point as peptides have demonstrated unique features of selectivity and specificity toward specific targets. Peptide-based vaccines imply the identification of different epitopes both on human cells and virus capsid and the design of peptide/peptidomimetics able to counteract the primary host-pathogen interaction, in order to induce a specific host immune response. SARS-CoV-2 immunogenic regions are mainly distributed, as well as for other coronaviruses, across structural areas such as spike, envelope, membrane or nucleocapsid proteins. Herein, we aim to highlight the molecular basis of the infection and recent peptide-based vaccines strategies to fight the COVID-19 pandemic including their delivery systems.

show abstract

Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design

Cited by 59 publications

References 58 publications

Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia

Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia

V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity

Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic

Contact Info

Product

Resources

About