1
|
Soltan MA, Abdulsahib WK, Amer M, Refaat AM, Bagalagel AA, Diri RM, Albogami S, Fayad E, Eid RA, Sharaf SMA, Elhady SS, Darwish KM, Eldeen MA. Mining of Marburg Virus Proteome for Designing an Epitope-Based Vaccine. Front Immunol 2022; 13:907481. [PMID: 35911751 PMCID: PMC9334820 DOI: 10.3389/fimmu.2022.907481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/16/2022] [Indexed: 12/11/2022] Open
Abstract
Marburg virus (MARV) is one of the most harmful zoonotic viruses with deadly effects on both humans and nonhuman primates. Because of its severe outbreaks with a high rate of fatality, the world health organization put it as a risk group 4 pathogen and focused on the urgent need for the development of effective solutions against that virus. However, up to date, there is no effective vaccine against MARV in the market. In the current study, the complete proteome of MARV (seven proteins) was analyzed for the antigenicity score and the virulence or physiological role of each protein where we nominated envelope glycoprotein (Gp), Transcriptional activator (VP30), and membrane-associated protein (VP24) as the candidates for epitope prediction. Following that, a vaccine construct was designed based on CTL, HTL, and BCL epitopes of the selected protein candidates and to finalize the vaccine construct, several amino acid linkers, β-defensin adjuvant, and PADRE peptides were incorporated. The generated potential vaccine was assessed computationally for several properties such as antigenicity, allergenicity, stability, and other structural features where the outcomes of these assessments nominated this potential vaccine to be validated for its binding affinity with two molecular targets TLR-8 and TLR-4. The binding score and the stability of the vaccine-receptor complex, which was deeply studied through molecular docking-coupled dynamics simulation, supported the selection of our designed vaccine as a putative solution for MARV that should be validated through future wet-lab experiments. Here, we describe the computational approach for designing and analysis of this potential vaccine.
Collapse
Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
| | - Waleed K. Abdulsahib
- Department of pharmacology and Toxicology, College of Pharmacy, Al- Farahidi University, Baghdad, Iraq
| | - Mahmoud Amer
- Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed M. Refaat
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Alaa A. Bagalagel
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem M. Diri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | | | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology and Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
| |
Collapse
|
2
|
Tiper I, Kourout M, Lanning B, Fisher C, Konduru K, Purkayastha A, Kaplan G, Duncan R. Tracking ebolavirus genomic drift with a resequencing microarray. PLoS One 2022; 17:e0263732. [PMID: 35143574 PMCID: PMC8830711 DOI: 10.1371/journal.pone.0263732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.
Collapse
Affiliation(s)
- Irina Tiper
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Moussa Kourout
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Bryan Lanning
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Carolyn Fisher
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Krishnamurthy Konduru
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | | | - Gerardo Kaplan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Robert Duncan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
- * E-mail:
| |
Collapse
|
3
|
Yao W, Yang Z, Lou X, Mao H, Yan H, Zhang Y. Simultaneous Detection of Ebola Virus and Pathogens Associated With Hemorrhagic Fever by an Oligonucleotide Microarray. Front Microbiol 2021; 12:713372. [PMID: 34394063 PMCID: PMC8363200 DOI: 10.3389/fmicb.2021.713372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Ebola virus infection causes severe hemorrhagic fever, and its mortality rates varied from 25 to 90% in the previous outbreaks. The highly infectious and lethal nature of this virus highlights the need for reliable and sensitive diagnostic methods to distinguish it from other diseases present with similar clinical symptoms. Based on multiplex polymerase chain reaction (PCR) and oligonucleotide microarray technology, a cost-effective, multipathogen and high-throughput method was developed for simultaneous detection of Ebola virus and other pathogens associated with hemorrhagic fever, including Marburg virus, Lassa fever virus, Junin virus, Machupo virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever virus, malaria parasite, hantavirus, severe fever with thrombocytopenia syndrome virus, dengue virus, yellow fever virus, Chikungunya virus, influenza A virus, and influenza B virus. This assay had an excellent specificity for target pathogens, without overlap signal between the probes. The limit of detection was approximately 103 pathogen copies/μl. A total of 60 positive nucleic acid samples for different pathogens were detected, a concordance of 100% was observed between microarray assay and real-time PCR analysis. Consequently, the described oligonucleotide microarray may be specific and sensitive assay for diagnosis and surveillance of infections caused by Ebola virus and other species of hemorrhagic fever pathogens.
Collapse
Affiliation(s)
- Wenwu Yao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhangnv Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiuyu Lou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Haiyan Mao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Hao Yan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| |
Collapse
|
4
|
Abstract
Ebolaviruses have gained much attention recently due to the outbreak from 2014 through 2016. The related marburgviruses also have been responsible for large outbreaks with high case fatality rates. The purpose of this article is to provide the clinical laboratory scientist with a review of the most current developments in marburgvirus research. The PubMed database was reviewed using the keywords "Marburg virus," "Ravn virus," and "marburgviruses," with publication dates from January 1, 2015 through June 20, 2017. The search yielded 345 articles. In total, 52 articles met the inclusion criteria and were reviewed. Advances have been made in the areas of ecology and host reservoir studies, seroprevalence studies, pathology and pathogenesis studies, laboratory assay development, and treatment and vaccine development. Marburgviruses are highly lethal viruses that pose a significant threat to the human population. Although numerous advances have been made, there are still large gaps in knowledge, and it is imperative that scientists gain more information to fully understand virus/host interactions. An approved vaccine and treatment remain elusive.
Collapse
|