scholarly journals Profiling the Immune Vulnerability Landscape of the 2019 Novel Coronavirus

2020 ◽  
Author(s):  
James Zhu ◽  
Jiwoong Kim ◽  
Xue Xiao ◽  
Yunguan Wang ◽  
Danni Luo ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Peptide Vaccine ◽  
Immune Clearance ◽  
Clearance Mechanism ◽  
Therapeutic Development ◽  
Antiviral Antibody ◽  
Research Outcome ◽  
The Moment ◽  
Novel Coronavirus ◽  
Antibody Epitopes

The outbreak of the 2019 Novel Coronavirus (2019-nCoV) has rapidly spread from Wuhan, China to multiple countries, causing staggering number of infections and deaths. A systematic profiling of the immune vulnerability landscape of 2019-nCoV is lacking, which can bring critical insights into the immune clearance mechanism, peptide vaccine development, and antiviral antibody development. In this study, we predicted the potential of all the 2019-nCoV viral proteins to induce class I and II MHC presentation and form linear antibody epitopes. We showed that the enrichment for T cell and B cell epitopes is not uniform on the viral genome, with several focused regions that generate abundant epitopes and may be more targetable. We showed that genetic variations in 2019-nCoV, though fewer for the moment, already follow the pattern of mutations in related coronaviruses, and could alter the immune vulnerability landscape of this virus, which should be considered in the development of therapies. We create an online database to broadly share our research outcome. Overall, we present an immunological resource for 2019-nCoV that could significantly promote both therapeutic development and mechanistic research.

scholarly journals Non-Synonymous Mutation Analysis in SARS-CoV-2 Variants Isolated from Humans and Prediction of Conserved Linear Antibody Epitopes for Use in Country-wise Epitope-Based Vaccine Development

2020 ◽  
Author(s):  
Pankaj Kumar ◽  
Kunal Sharma ◽  
Naima Noor Khan ◽  
Hamza Bin Sana ◽  
Mohammad Ali Khan
Keyword(s):  
Large Scale ◽  
Vaccine Development ◽  
Time Window ◽  
High Rate ◽  
Synonymous Mutation ◽  
Large Outbreak ◽  
Therapeutic Development ◽  
Sporadic Cases ◽  
Potential Vaccine ◽  
Antibody Epitopes

COVID-19 pandemic has caused a large-scale havoc in almost every country across the globe, putting major challenges for the healthcare system in many parts of the world. Several of the laboratories are running in the race with undying efforts for developing potential vaccine, drugs or therapeutics to treat or prevent the infection. However, with the limited time window and high rate of infection, the task is very big for humanity to find a cure. With hundreds of genomic data of SARS-CoV-2 virus isolates from humans are being submitted almost every day, it is coming into knowledge that virus is mutating, slower in countries with sporadic cases, but higher in countries experiencing large outbreak. These types of mutations in virus may bring challenges in vaccine or therapeutic development for use in each and every country, as each hotspot region may have their own pattern of mutations in virus with ongoing outbreak. In our current study, we retrieved non-synonymous mutation data of around 12,225 SARS-CoV-2 virus samples isolated from humans globally, and discovered all mutations that are collectively happening in antibody epitope regions of the virus country-wise. We found a few numbers of epitope regions in SARS-CoV-2 that are highly conserved collectively in all variants and may be used for epitope-based vaccine development for whole world. We also found epitope regions that are conserved collectively in SARS-CoV-2 variants country-wise and can be used for customized epitope-based vaccine development in each different country.

scholarly journals Epitope-based peptide vaccine design and target site characterization against novel coronavirus disease caused by SARS-CoV-2

2020 ◽  
Author(s):  
Lin Li ◽  
Ting Sun ◽  
Yufei He ◽  
Wendong Li ◽  
Yubo Fan ◽  
...  
Keyword(s):  
T Cell ◽  
Mhc Class Ii ◽  
Vaccine Development ◽  
Peptide Vaccine ◽  
Human Leukocyte ◽  
Surface Glycoprotein ◽  
T Cell Epitopes ◽  
Leukocyte Antigen ◽  
The Stability ◽  
Novel Coronavirus

AbstractThe outbreak of the 2019 novel coronavirus (SARS-CoV-2) has infected thousands of people with a large number of deaths across 26 countries. The sudden appearance of the virus leads to the limited existing therapies for SARS-CoV-2. Therefore, vaccines and antiviral medicines are in desperate need. This study took immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein (S) of SARS-CoV-2, followed by estimating their antigenicity and interactions with the human leukocyte antigen (HLA) alleles. We identified four B cell epitopes, two MHC class-I and nine MHC class-II binding T-cell epitopes, which showed highly antigenic features. Allergenicity, toxicity and physiochemical properties analysis confirmed the specificity and selectivity of epitopes. The stability and safety of epitopes were confirmed by digestion analysis. No mutations were observed in all the selected B- and T-cell epitopes across all isolates from different locations worldwide. Epitopes were thus identified and some of them can be potential candidates for vaccine development.

scholarly journals Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development

2020 ◽  
Author(s):  
Arunachalam Ramaiah ◽  
Vaithilingaraja Arumugaswami
Keyword(s):  
Binding Affinity ◽  
Vaccine Development ◽  
Asia Pacific ◽  
Potential Candidate ◽  
T Cell Epitopes ◽  
Live Animal ◽  
Synonymous Mutations ◽  
Wide Range ◽  
Novel Coronavirus ◽  
N Proteins

ABSTRACTNovel Coronavirus (nCoV) outbreak in the city of Wuhan, China during December 2019, has now spread to various countries across the globe triggering a heightened containment effort. This human pathogen is a member of betacoronavirus genus carrying 30 kilobase of single positive-sense RNA genome. Understanding the evolution, zoonotic transmission, and source of this novel virus would help accelerating containment and prevention efforts. The present study reported detailed analysis of 2019-nCoV genome evolution and potential candidate peptides for vaccine development. This nCoV genotype might have been evolved from a bat-CoV by accumulating non-synonymous mutations, indels, and recombination events. Structural proteins Spike (S), and Membrane (M) had extensive mutational changes, whereas Envelope (E) and Nucleocapsid (N) proteins were very conserved suggesting differential selection pressures exerted on 2019-nCoV during evolution. Interestingly, 2019-nCoV Spike protein contains a 39 nucleotide sequence insertion relative to SARS-like bat-SL-CoVZC45/2017. Furthermore, we identified eight high binding affinity (HBA) CD4 T-cell epitopes in the S, E, M and N proteins, which can be commonly recognized by HLA-DR alleles of Asia and Asia-Pacific Region population. These immunodominant epitopes can be incorporated in universal subunit CoV vaccine. Diverse HLA types and variations in the epitope binding affinity may contribute to the wide range of immunopathological outcomes of circulating virus in humans. Our findings emphasize the requirement for continuous surveillance of CoV strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic CoV strains.

scholarly journals In silico identification of vaccine targets for 2019-nCoV

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 145 ◽  
Author(s):  
Chloe Hyun-Jung Lee ◽  
Hashem Koohy
Keyword(s):  
T Cell ◽  
In Silico ◽  
Vaccine Development ◽  
De Novo ◽  
Cell Receptor ◽  
Binding Potential ◽  
Hla Alleles ◽  
Immunogenic Peptides ◽  
Novel Coronavirus ◽  
Positional Weight

Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.

scholarly journals Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Pranam Chatterjee ◽  
Manvitha Ponnapati ◽  
Christian Kramme ◽  
Alexandru M. Plesa ◽  
George M. Church ◽  
...  
Keyword(s):  
Computational Design ◽  
The Novel ◽  
Receptor Binding Domain ◽  
Experimental Characterization ◽  
Viral Production ◽  
Health Crisis ◽  
Intracellular Degradation ◽  
Protein Receptor ◽  
Therapeutic Development ◽  
Novel Coronavirus

AbstractThe COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has elicited a global health crisis of catastrophic proportions. With only a few vaccines approved for early or limited use, there is a critical need for effective antiviral strategies. In this study, we report a unique antiviral platform, through computational design of ACE2-derived peptides which both target the viral spike protein receptor binding domain (RBD) and recruit E3 ubiquitin ligases for subsequent intracellular degradation of SARS-CoV-2 in the proteasome. Our engineered peptide fusions demonstrate robust RBD degradation capabilities in human cells and are capable of inhibiting infection-competent viral production, thus prompting their further experimental characterization and therapeutic development.

scholarly journals SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far

Pathogens ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 231 ◽  
Author(s):  
Firas A. Rabi ◽  
Mazhar S. Al Zoubi ◽  
Ghena A. Kasasbeh ◽  
Dunia M. Salameh ◽  
Amjad D. Al-Nasser
Keyword(s):  
Vaccine Development ◽  
Current Knowledge ◽  
Treatment Options ◽  
The Novel ◽  
Clinical Criteria ◽  
Health Authorities ◽  
Close Relationship ◽  
Public Health Authorities ◽  
Molecular Information ◽  
Novel Coronavirus

In December 2019, a cluster of fatal pneumonia cases presented in Wuhan, China. They were caused by a previously unknown coronavirus. All patients had been associated with the Wuhan Wholefood market, where seafood and live animals are sold. The virus spread rapidly and public health authorities in China initiated a containment effort. However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. Based on clinical criteria and available serological and molecular information, the new disease was called coronavirus disease of 2019 (COVID-19), and the novel coronavirus was called SARS Coronavirus-2 (SARS-CoV-2), emphasizing its close relationship to the 2002 SARS virus (SARS-CoV). The scientific community raced to uncover the origin of the virus, understand the pathogenesis of the disease, develop treatment options, define the risk factors, and work on vaccine development. Here we present a summary of current knowledge regarding the novel coronavirus and the disease it causes.

scholarly journals Nanobiosensors for the Detection of Novel Coronavirus 2019-nCoV and Other Pandemic/Epidemic Respiratory Viruses: A Review

Sensors ◽  
2020 ◽  
Vol 20 (22) ◽  
pp. 6591
Author(s):  
Badriyah Alhalaili ◽  
Ileana Nicoleta Popescu ◽  
Olfa Kamoun ◽  
Feras Alzubi ◽  
Sami Alawadhia ◽  
...  
Keyword(s):  
Public Health ◽  
Vaccine Development ◽  
Respiratory Viruses ◽  
Public Health Emergency ◽  
Detection Methods ◽  
Origin And Evolution ◽  
The World ◽  
Human Coronaviruses ◽  
Novel Coronavirus ◽  
Made In

The coronavirus disease 2019 (COVID-19) pandemic is considered a public health emergency of international concern. The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused this pandemic has spread rapidly to over 200 countries, and has drastically affected public health and the economies of states at unprecedented levels. In this context, efforts around the world are focusing on solving this problem in several directions of research, by: (i) exploring the origin and evolution of the phylogeny of the SARS-CoV-2 viral genome; (ii) developing nanobiosensors that could be highly effective in detecting the new coronavirus; (iii) finding effective treatments for COVID-19; and (iv) working on vaccine development. In this paper, an overview of the progress made in the development of nanobiosensors for the detection of human coronaviruses (SARS-CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV) is presented, along with specific techniques for modifying the surface of nanobiosensors. The newest detection methods of the influenza virus responsible for acute respiratory syndrome were compared with conventional methods, highlighting the newest trends in diagnostics, applications, and challenges of SARS-CoV-2 (COVID-19 causative virus) nanobiosensors.

scholarly journals Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach

2020 ◽  
Author(s):  
Aftab Alam ◽  
Arbaaz Khan ◽  
Nikhat Imam ◽  
Mohd Faizan Siddiqui ◽  
Mohd Waseem ◽  
...  
Keyword(s):  
T Cell ◽  
Vaccine Development ◽  
Peptide Vaccine ◽  
Specific Treatment ◽  
T Cell Response ◽  
Surface Glycoprotein ◽  
Antigenic Peptides ◽  
Population Coverage ◽  
Geographical Regions ◽  
Cluster Of Differentiation

Abstract The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.

scholarly journals COVID-19: Coronavirus Vaccine Development Updates

2020 ◽  
Vol 11 ◽  
Author(s):  
Jing Zhao ◽  
Shan Zhao ◽  
Junxian Ou ◽  
Jing Zhang ◽  
Wendong Lan ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Viral Vector ◽  
Peptide Vaccine ◽  
Adenovirus Vector ◽  
Human Adenovirus ◽  
Research Progress ◽  
Nucleic Acid Vaccines ◽  
Inactivated Vaccines ◽  
The Common ◽  
Common Genus

Coronavirus Disease 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a newly emerged coronavirus, and has been pandemic since March 2020 and led to many fatalities. Vaccines represent the most efficient means to control and stop the pandemic of COVID-19. However, currently there is no effective COVID-19 vaccine approved to use worldwide except for two human adenovirus vector vaccines, three inactivated vaccines, and one peptide vaccine for early or limited use in China and Russia. Safe and effective vaccines against COVID-19 are in urgent need. Researchers around the world are developing 213 COVID-19 candidate vaccines, among which 44 are in human trials. In this review, we summarize and analyze vaccine progress against SARS-CoV, Middle-East respiratory syndrome Coronavirus (MERS-CoV), and SARS-CoV-2, including inactivated vaccines, live attenuated vaccines, subunit vaccines, virus like particles, nucleic acid vaccines, and viral vector vaccines. As SARS-CoV-2, SARS-CoV, and MERS-CoV share the common genus, Betacoronavirus, this review of the major research progress will provide a reference and new insights into the COVID-19 vaccine design and development.

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