scholarly journals COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning

2020 ◽  
Author(s):  
Edison Ong ◽  
Mei U Wong ◽  
Anthony Huffman ◽  
Yongqun He
Keyword(s):  
Machine Learning ◽  
Vaccine Development ◽  
Reverse Vaccinology ◽  
T Cell Epitopes ◽  
Mhc I ◽  
S Protein ◽  
N Protein ◽  
Mhc Ii ◽  
Human Coronaviruses ◽  
New Strategies

AbstractTo ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that the whole virus, as well as the spike (S) protein, nucleocapsid (N) protein, and membrane protein, have been tested for vaccine development against SARS and MERS. We further used the Vaxign reverse vaccinology tool and the newly developed Vaxign-ML machine learning tool to predict COVID-19 vaccine candidates. The N protein was found to be conserved in the more pathogenic strains (SARS/MERS/COVID-19), but not in the other human coronaviruses that mostly cause mild symptoms. By investigating the entire proteome of SARS-CoV-2, six proteins, including the S protein and five non-structural proteins (nsp3, 3CL-pro, and nsp8-10) were predicted to be adhesins, which are crucial to the viral adhering and host invasion. The S, nsp3, and nsp8 proteins were also predicted by Vaxign-ML to induce high protective antigenicity. Besides the commonly used S protein, the nsp3 protein has not been tested in any coronavirus vaccine studies and was selected for further investigation. The nsp3 was found to be more conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV than among 15 coronaviruses infecting human and other animals. The protein was also predicted to contain promiscuous MHC-I and MHC-II T-cell epitopes, and linear B-cell epitopes localized in specific locations and functional domains of the protein. Our predicted vaccine targets provide new strategies for effective and safe COVID-19 vaccine development.

In silico and in vitro analysis of a multiepitope L1-E7 fusion construct for vaccine development against human papillomaviruses

2021 ◽  
Vol 18 ◽  
Author(s):  
Elnaz Abbasifarid ◽  
Azam Bolhassani ◽  
Shiva Irani ◽  
Fattah Sotoodehnejadnematalahi
Keyword(s):  
Western Blotting ◽  
Vaccine Development ◽  
Fluorescent Microscopy ◽  
Therapeutic Vaccine ◽  
Human Papillomaviruses ◽  
Mhc I ◽  
Fusion Construct ◽  
Mhc Ii ◽  
Hpv Types

Background: Human papillomavirus (HPV) infection is the major risk factor for cervical cancer. Current prophylactic HPV vaccines provide immunity against most genital and carcinogenic HPV types. However, these vaccines failed to produce immune responses against already established HPV infections. Methods: For the design of a therapeutic vaccine candidate, we utilized immunoinformatics tools to design a potential multiepitope fusion construct based on L1 and E7 genes from different high- and low-risk HPV types. After determination of CD4+ and CD8+ T cell epitopes, the allergenicity, toxicity, immunogenicity, conservancy, and population coverage were analyzed for epitope selection. Then, the hemolytic probability of the selected epitopes, and molecular docking between major histocompatibility complex (MHC) and the chosen epitopes were performed by different web servers. Next, a multiepitope peptide construct consisting of 12 epitopes linked by the AAY proteasomal sequence was designed. After that, physicochemical properties, solubility, secondary and tertiary structures of this construct were evaluated by bioinformatics tools. Finally, after amino acid reverse translation of the multiepitope peptide construct, expression of the L1-E7 DNA construct (pEGFP-L1-E7) was investigated in HEK-293T cells using fluorescent microscopy, flow cytometry, and western blotting. Results: Considering various parameters, the immunodominant peptides such as L1(MHC-I)-DLDQFPLGRKFLLQ, L1(MHC-II)-NQLFVTVVDTTRSTN, E7-HPV16(MHC-I)-AEPDRAHYNIVTF, E7-HPV18(MHC-I)-HGPKATVQDIVLHL, E7-HPV31(MHC-I)-KPDTSNYNIVTF, E7-HPV33(MHC-I)-RPDGQAQPATADYYI, E7-HPV45(MHC-I)- RTLQQLFLSFV, E7-HPV16(MHC-II)-TLHEYMLDLQPETTD, E7-HPV18(MHC-II)-LRAFQQLFLNTLSFV, E7-HPV31(MHC-II)-PTLQDYVLDLQPEAT, E7-HPV33(MHC-II)-LKEYVLDLYPEPTDL and E7-HPV45(MHC-II)-LQQLFLSTLSFVCPW were determined to design the vaccine construct. The results indicated efficient expression of the L1-E7 DNA construct (74 ± 2.19%) in vitro. Moreover, the polyepitope peptide generated in the cells was detected as a clear band of ~ 50 kDa in western blotting. Conclusion: Regarding the favorable transfection efficiency of the designed L1-E7 multiepitope construct, in vivo validation study on its therapeutic potential is underway.

scholarly journals Identification of a Promiscuous Conserved CTL Epitope Within the SARS-CoV-2 Spike Protein

2021 ◽  
Author(s):  
Sheng Jiang ◽  
Shuting Wu ◽  
Gan Zhao ◽  
Yue He ◽  
Xinrong Guo ◽  
...  
Keyword(s):  
T Cell ◽  
Cellular Response ◽  
Spike Protein ◽  
Target Antigen ◽  
T Cell Epitopes ◽  
Global Public Health ◽  
Mhc I ◽  
Mhc Ii ◽  
Ctl Epitope ◽  
Infected Cells

Abstract The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. In this study, we predicted several potential T cell epitopes with web-based analytic tools, and narrowed them down from several potential MHC‑I and MHC‑II epitopes by ELIspot and cytolytic assays to a conserved MHC‑I epitope. The epitope is highly conserved in current viral variants and compatible with presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.

scholarly journals Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach

Vaccines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1098
Author(s):  
Blaine Teahan ◽  
Edison Ong ◽  
Zhenhua Yang
Keyword(s):  
Machine Learning ◽  
Mycobacterium Tuberculosis ◽  
Vaccine Development ◽  
Protective Antigen ◽  
Reverse Vaccinology ◽  
In Vivo Studies ◽  
Vaccine Strategy ◽  
Vaccine Potential

Tuberculosis (TB) is the leading cause of death of any single infectious agent, having led to 1.4 million deaths in 2019 alone. Moreover, an estimated one-quarter of the global population is latently infected with Mycobacterium tuberculosis (MTB), presenting a huge pool of potential future disease. Nonetheless, the only currently licensed TB vaccine fails to prevent the activation of latent TB infections (LTBI). These facts together illustrate the desperate need for a more effective TB vaccine strategy that can prevent both primary infection and the activation of LTBI. In this study, we employed a machine learning-based reverse vaccinology approach to predict the likelihood that each protein within the proteome of MTB laboratory reference strain H37Rv would be a protective antigen (PAg). The proteins predicted most likely to be a PAg were assessed for their belonging to a protein family of previously established PAgs, the relevance of their biological processes to MTB virulence and latency, and finally the immunogenic potential that they may provide in terms of the number of promiscuous epitopes within each. This study led to the identification of 16 proteins with the greatest vaccine potential for further in vitro and in vivo studies. It also demonstrates the value of computational methods in vaccine development.

scholarly journals Hepatitis B Virus Covalently Closed Circular DNA Interacting HBx and HBc Proteins Global Conservancy Analysis and Related B or T lymphocyte Epitopes

2021 ◽  
Author(s):  
Umar Saeed ◽  
Zahra Zahid Piracha ◽  
Rizwan Uppal
Keyword(s):  
Hepatitis B Virus ◽  
T Cell ◽  
T Cell Epitopes ◽  
Mhc I ◽  
Circular Dna ◽  
Consensus Sequences ◽  
Global Consensus ◽  
Mhc Ii ◽  
Hbv Genotypes ◽  
B Virus

Abstract Background:The Hepatitis B Virus HBx and HBc proteins associate with covalently closed circular DNA, which is the main reason for intrahepatic viral persistence and major cause due to which HBV cure has not been achieved yet. The aims of present study were to generate HBV genotype-specific consensus sequences of HBx and HBc, align all ten (A to J) consensus sequences to develop global consensus sequences of HBx and HBc, analyze variable and conserved motifs, and to predict highly conserved B and T cell binding epitopes in HBx and HBc proteins, respectively.Methods:237 HBx and 207 HBc sequences, belonging to all HBV genotypes reported globally, were aligned in CLC main workbench to draw global consensus sequences and phylogenetic analysis was performed. The location of possible B cell epitopes were analyzed using immune Epitope Database (IEDB), while possible T cell epitopes were analyzed using ProPred-I and ProPred in-silico prediction tools. Results:The HBx residues 52H to 59P, which are important for augmentation effect in HBV replication and 137C, which is crucial for transactivation of HBx are conserved in all HBV genotypes. The HBc residues 141S to149V, which are crucial for pre-genomic RNA packaging, viral DNA synthesis and virion secretion are highly conserved across all the genotypes of HBV. The HBx related epitopes X-B2 and X-B4, and HBc related C-B6 and C-B7 epitopes could be important candidates for B-cell based vaccine. Among HBx related MHC-I epitopes X-M2, X-M5, X-M8, X-M11, X-M12, X-M20, X-M22, X-M25, X-M27 and X-M32, and MHC-II epitopes the X-T4, X-T6 and X-T8 could be important targets for vaccine development. While among HBc related MHC-I epitopes C-M1, C-M2, C-M4, C-M6-11, C-M13, C-M19, C-M24-26, C-M30, C-M34-36, C-M40 and C-M43-45, and MHC-II epitopes the C-T1-3, C-T9, C-T10, C-T12, C-T14 and C-T16-18 epitopes could be ideal epitopes with high conservancy across all HBV genotypes. Conclusion:The analysis will aid in screening of novel anti-HBV agents and designing of site-specific inhibitors which may show response against all genotypes. Also the predicted B- or T cell epitopes might be effective for designing antibodies against all majorly occurring genotypes of HBV across the world.

scholarly journals Going beyond clinical routine in SARS-CoV-2 antibody testing - A multiplex corona virus antibody test for the evaluation of cross-reactivity to endemic coronavirus antigens

2020 ◽  
Author(s):  
Matthias Becker ◽  
Monika Strengert ◽  
Daniel Junker ◽  
Tobias Kerrinnes ◽  
Philipp D. Kaiser ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Antibody Test ◽  
Cross Reactivity ◽  
Antibody Testing ◽  
N Protein ◽  
Humoral Immune ◽  
In Vitro Diagnostic ◽  
Human Coronaviruses ◽  
Multiplexed Immunoassay

Given the importance of the humoral immune response to SARS-CoV-2 as a global benchmark for immunity, a detailed analysis is needed to (i) monitor seroconversion in the general population, (ii) understand manifestation and progression of the disease, and (iii) predict the outcome of vaccine development. Currently available serological assays utilize single analyte technologies such as ELISA to measure antibodies against SARS-CoV-2 antigens including spike (S) or nucleocapsid (N) protein. To measure individual antibody (IgG and IgA) responses against SARS-CoV-2 and the endemic human coronaviruses (hCoVs) NL63, 229E, OC43, and HKU1, we developed a multiplexed immunoassay (CoVi-plex), for which we included S and N proteins of these coronaviruses in an expanded antigen panel. Compared to commercial in vitro diagnostic (IVD) tests our CoVi-plex achieved the highest sensitivity and specificity when analyzing 310 SARS-CoV-2 infected and 866 uninfected individuals. Simultaneously we see high IgG responses against hCoVs throughout all samples, whereas no consistent cross reactive IgG response patterns can be defined. In summary, our CoVi-plex is highly suited to monitor vaccination studies and will facilitate epidemiologic screenings for the humoral immunity toward pandemic as well as endemic coronaviruses.

scholarly journals Immune response dynamics in COVID-19 patients to SARS-CoV-2 and other human coronaviruses

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254367
Author(s):  
Resmi Ravindran ◽  
Cindy McReynolds ◽  
Jun Yang ◽  
Bruce D. Hammock ◽  
Aamer Ikram ◽  
...  
Keyword(s):  
Serological Test ◽  
High Sensitivity ◽  
Cross Reactivity ◽  
Response Dynamics ◽  
S Protein ◽  
Infected People ◽  
N Protein ◽  
Patient Health ◽  
Antibody Titers ◽  
Human Coronaviruses

COVID-19 serological test must have high sensitivity as well as specificity to rule out cross-reactivity with common coronaviruses (HCoVs). We have developed a quantitative multiplex test, measuring antibodies against spike (S) proteins of SARS-CoV-2, SARS-CoV, MERS-CoV, and common human coronavirus strains (229E, NL63, OC43, HKU1), and nucleocapsid (N) protein of SARS-CoV viruses. Receptor binding domain of S protein of SARS-CoV-2 (S-RBD), and N protein, demonstrated sensitivity (94% and 92.5%, respectively) in COVID-19 patients (n = 53), with 98% specificity in non-COVID-19 respiratory-disease (n = 98), and healthy-controls (n = 129). Anti S-RBD and N antibodies appeared five to ten days post-onset of symptoms, peaking at approximately four weeks. The appearance of IgG and IgM coincided while IgG subtypes, IgG1 and IgG3 appeared soon after the total IgG; IgG2 and IgG4 remained undetectable. Several inflammatory cytokines/chemokines were found to be elevated in many COVID-19 patients (e.g., Eotaxin, Gro-α, CXCL-10 (IP-10), RANTES (CCL5), IL-2Rα, MCP-1, and SCGF-b); CXCL-10 was elevated in all. In contrast to antibody titers, levels of CXCL-10 decreased with the improvement in patient health suggesting it as a candidate for disease resolution. Importantly, anti-N antibodies appear before S-RBD and differentiate between vaccinated and infected people—current vaccines (and several in the pipeline) are S protein-based.

Progress in Studies on Structural and Remedial Aspects of Newly Born Coronavirus, SARS-CoV-2

2020 ◽  
Vol 20 (26) ◽  
pp. 2362-2378
Author(s):  
Satya P. Gupta
Keyword(s):  
Vaccine Development ◽  
Cell Receptor ◽  
Receptor Binding Domain ◽  
S Protein ◽  
Angiotensin Converting Enzyme 2 ◽  
N Protein ◽  
Host Cell Receptor ◽  
The Status ◽  
Novel Coronavirus

The article highlights an up-to-date progress in studies on structural and the remedial aspects of novel coronavirus 2019-nCoV, renamed as SARS-CoV-2, leading to the disease COVID-19, a pandemic. In general, all CoVs including SARS-CoV-2 are spherical positive single-stranded RNA viruses containing spike (S) protein, envelope (E) protein, nucleocapsid (N) protein, and membrane (M) protein, where S protein has a Receptor-binding Domain (RBD) that mediates the binding to host cell receptor, Angiotensin Converting Enzyme 2 (ACE2). The article details the repurposing of some drugs to be tried for COVID-19 and presents the status of vaccine development so far. Besides drugs and vaccines, the role of Convalescent Plasma (CP) therapy to treat COVID-19 is also discussed.

COVIEdb: A database for potential immune epitopes of coronaviruses

2020 ◽  
Author(s):  
Jingcheng Wu ◽  
Wenfan Chen ◽  
Jingjing Zhou ◽  
Wenyi Zhao ◽  
Shuqing Chen ◽  
...  
Keyword(s):  
Immune System ◽  
Large Scale ◽  
Vaccine Development ◽  
Protein Sequences ◽  
T Cell Epitopes ◽  
Human Immune System ◽  
The World ◽  
Human Immune ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract2019 novel coronavirus (2019-nCoV) has caused large-scale pandemic COVID-19 all over the world. It’s essential to find out which parts of the 2019-nCoV sequence are recognized by human immune system for vaccine development. And for the prevention of the potential outbreak of similar coronaviruses in the future, vaccines against immunogenic epitopes shared by different human coronaviruses are essential. Here we predict all the potential B/T-cell epitopes for SARS-CoV, MERS-CoV, 2019-nCoV and RaTG13-CoV based on the protein sequences. We found YFKYWDQTY in ORF1ab protein, VYDPLQPEL and TVYDPLQPEL in spike (S) protein might be pan-coronavirus targets for vaccine development. All the predicted results are stored in a database COVIEdb (http://biopharm.zju.edu.cn/coviedb/).

scholarly journals Immunologic testing for SARS-CoV-2 infection from the antigen perspective

2020 ◽  
pp. JCM.02160-20
Author(s):  
Dandan Li ◽  
Jinming Li
Keyword(s):  
Cross Reactivity ◽  
Diagnostic Methods ◽  
Clinical Samples ◽  
Serological Testing ◽  
S Protein ◽  
N Protein ◽  
Viral Loads ◽  
Improved Performance ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Coronavirus disease 2019 (COVID-19) caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally as a severe pandemic. SARS-CoV-2 infection stimulates antigen-specific antibody responses. Multiple serologic tests have been developed for SARS-CoV-2. However, which antigens are most suitable for serological testing remains poorly understood. Specifically, which antigens have the highest sensitivity and specificity for serological testing and which have the least cross-reactivity with other coronaviruses are currently unknown. Previous studies have shown that the S1 domain of the spike (S) protein has very low cross-reactivity between epidemic coronaviruses and common human coronaviruses, whereas the S2 domain of the S protein, and the nucleocapsid protein (N protein) show low-level cross-reactivity. Therefore, S1 is considered more specific than the native homotrimer of the S protein, and the receptor-binding domain as an antigen to test patient antibodies is more sensitive than the native N protein. In addition, an increasing number of studies have used multi-antigen protein arrays to screen serum from convalescent patients with COVID-19. Antigen combinations demonstrated improved performance as compared to each individual antigen. For rapid antigen detection, the sensitivity of the test is higher in the first week of onset of the disease with high viral loads. Highly sensitive and specific immunological diagnostic methods for antibodies or those that directly detect viral antigens in clinical samples would be beneficial for the rapid and accurate diagnosis of SARS-CoV-2 infection.

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