1
|
Vaknin A, Grossman A, Durham ND, Lupovitz I, Goren S, Golani G, Roichman Y, Munro JB, Sorkin R. Ebola Virus Glycoprotein Strongly Binds to Membranes in the Absence of Receptor Engagement. ACS Infect Dis 2024; 10:1590-1601. [PMID: 38684073 PMCID: PMC11091876 DOI: 10.1021/acsinfecdis.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Ebola virus (EBOV) is an enveloped virus that must fuse with the host cell membrane in order to release its genome and initiate infection. This process requires the action of the EBOV envelope glycoprotein (GP), encoded by the virus, which resides in the viral envelope and consists of a receptor binding subunit, GP1, and a membrane fusion subunit, GP2. Despite extensive research, a mechanistic understanding of the viral fusion process is incomplete. To investigate GP-membrane association, a key step in the fusion process, we used two approaches: high-throughput measurements of single-particle diffusion and single-molecule measurements with optical tweezers. Using these methods, we show that the presence of the endosomal Niemann-Pick C1 (NPC1) receptor is not required for primed GP-membrane binding. In addition, we demonstrate this binding is very strong, likely attributed to the interaction between the GP fusion loop and the membrane's hydrophobic core. Our results also align with previously reported findings, emphasizing the significance of acidic pH in the protein-membrane interaction. Beyond Ebola virus research, our approach provides a powerful toolkit for studying other protein-membrane interactions, opening new avenues for a better understanding of protein-mediated membrane fusion events.
Collapse
Affiliation(s)
- Alisa Vaknin
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Alon Grossman
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Natasha D. Durham
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Inbal Lupovitz
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shahar Goren
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gonen Golani
- Department
of Physics and Haifa Research Center for Theoretical Physics and Astrophysics, University of Haifa, Haifa 3498838, Israel
| | - Yael Roichman
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Raymond
and Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
| | - James B. Munro
- Department
of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department
of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Raya Sorkin
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
2
|
Takano KA, Wong AAL, Brown R, Situ K, Chua BA, Abu AE, Pham TT, Reyes GC, Ramachandran S, Kamata M, Li MMH, Wu TT, Rao DS, Arumugaswami V, Dorshkind K, Cole S, Morizono K. Envelope protein-specific B cell receptors direct lentiviral vector tropism in vivo. Mol Ther 2024; 32:1311-1327. [PMID: 38449314 PMCID: PMC11081870 DOI: 10.1016/j.ymthe.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/11/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
While studying transgene expression after systemic administration of lentiviral vectors, we found that splenic B cells are robustly transduced, regardless of the types of pseudotyped envelope proteins. However, the administration of two different pseudotypes resulted in transduction of two distinct B cell populations, suggesting that each pseudotype uses unique and specific receptors for its attachment and entry into splenic B cells. Single-cell RNA sequencing analysis of the transduced cells demonstrated that different pseudotypes transduce distinct B cell subpopulations characterized by specific B cell receptor (BCR) genotypes. Functional analysis of the BCRs of the transduced cells demonstrated that BCRs specific to the pseudotyping envelope proteins mediate viral entry, enabling the vectors to selectively transduce the B cell populations that are capable of producing antibodies specific to their envelope proteins. Lentiviral vector entry via the BCR activated the transduced B cells and induced proliferation and differentiation into mature effectors, such as memory B and plasma cells. BCR-mediated viral entry into clonally specific B cell subpopulations raises new concepts for understanding the biodistribution of transgene expression after systemic administration of lentiviral vectors and offers new opportunities for BCR-targeted gene delivery by pseudotyped lentiviral vectors.
Collapse
Affiliation(s)
- Kari-Ann Takano
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anita A L Wong
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rebecca Brown
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kathy Situ
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bernadette Anne Chua
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angel Elma Abu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Truc T Pham
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Glania Carel Reyes
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sangeetha Ramachandran
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Masakazu Kamata
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Melody M H Li
- UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ting-Ting Wu
- UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center (JCCC), University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dinesh S Rao
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center (JCCC), University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Vaithilingaraja Arumugaswami
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kenneth Dorshkind
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steve Cole
- Departments of Psychiatry & Biobehavioral Sciences and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kouki Morizono
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
3
|
Srikrishna D. Pentagon Found Daily, Metagenomic Detection of Novel Bioaerosol Threats to Be Cost-Prohibitive: Can Virtualization and AI Make It Cost-Effective? Health Secur 2024; 22:108-129. [PMID: 38625036 DOI: 10.1089/hs.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
In 2022, the Pentagon Force Protection Agency found threat agnostic detection of novel bioaerosol threats to be "not feasible for daily operations" due to the cost of reagents used for metagenomics, cost of sequencing instruments, and cost of labor for subject matter experts to analyze bioinformatics. Similar operational difficulties might extend to many of the 280,000 buildings (totaling 2.3 billion square feet) at 5,000 secure US Department of Defense military sites, 250 Navy ships, as well as many civilian buildings. These economic barriers can still be addressed in a threat agnostic manner by dynamically pooling samples from dry filter units, called spike-triggered virtualization, whereby pooling and sequencing depth are automatically modulated based on novel biothreats in the sequencing output. By running at a high average pooling factor, the daily and annual cost per dry filter unit can be reduced by 10 to 100 times depending on the chosen trigger thresholds. Artificial intelligence can further enhance the sensitivity of spike-triggered virtualization. The risk of infection during the 12- to 24-hour window between a bioaerosol incident and its detection remains, but in some cases it can be reduced by 80% or more with high-speed indoor air cleaning exceeding 12 air changes per hour, which is similar to the rate of air cleaning in passenger airplanes in flight. That level of air changes per hour or higher is likely to be cost-prohibitive using central heating ventilation and air conditioning systems, but it can be achieved economically by using portable air filtration in rooms with typical ceiling heights (less than 10 feet) for a cost of approximately $0.50 to $1 per square foot for do-it-yourself units and $2 to $5 per square foot for high-efficiency particulate air filters.
Collapse
|
4
|
Yu M, Zhang Y, Zhang L, Wang S, Liu Y, Xu Z, Liu P, Chen Y, Guo R, Meng L, Zhang T, Fan W, Qi X, Gao L, Zhang Y, Cui H, Gao Y. N123I mutation in the ALV-J receptor-binding domain region enhances viral replication ability by increasing the binding affinity with chNHE1. PLoS Pathog 2024; 20:e1011928. [PMID: 38324558 PMCID: PMC10878525 DOI: 10.1371/journal.ppat.1011928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 02/20/2024] [Accepted: 12/28/2023] [Indexed: 02/09/2024] Open
Abstract
The subgroup J avian leukosis virus (ALV-J), a retrovirus, uses its gp85 protein to bind to the receptor, the chicken sodium hydrogen exchanger isoform 1 (chNHE1), facilitating viral invasion. ALV-J is the main epidemic subgroup and shows noteworthy mutations within the receptor-binding domain (RBD) region of gp85, especially in ALV-J layer strains in China. However, the implications of these mutations on viral replication and transmission remain elusive. In this study, the ALV-J layer strain JL08CH3-1 exhibited a more robust replication ability than the prototype strain HPRS103, which is related to variations in the gp85 protein. Notably, the gp85 of JL08CH3-1 demonstrated a heightened binding capacity to chNHE1 compared to HPRS103-gp85 binding. Furthermore, we showed that the specific N123I mutation within gp85 contributed to the enhanced binding capacity of the gp85 protein to chNHE1. Structural analysis indicated that the N123I mutation primarily enhanced the stability of gp85, expanded the interaction interface, and increased the number of hydrogen bonds at the interaction interface to increase the binding capacity between gp85 and chNHE1. We found that the N123I mutation not only improved the viral replication ability of ALV-J but also promoted viral shedding in vivo. These comprehensive data underscore the notion that the N123I mutation increases receptor binding and intensifies viral replication.
Collapse
Affiliation(s)
- Mengmeng Yu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yao Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Suyan Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongzhen Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhuangzhuang Xu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Peng Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuntong Chen
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ru Guo
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lingzhai Meng
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tao Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenrui Fan
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaole Qi
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yanping Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongyu Cui
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yulong Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
- National Poultry Laboratory Animal Resource Center, Harbin, China
| |
Collapse
|
5
|
Normandin E, Triana S, Raju SS, Lan TC, Lagerborg K, Rudy M, Adams GC, DeRuff KC, Logue J, Liu D, Strebinger D, Rao A, Messer KS, Sacks M, Adams RD, Janosko K, Kotliar D, Shah R, Crozier I, Rinn JL, Melé M, Honko AN, Zhang F, Babadi M, Luban J, Bennett RS, Shalek AK, Barkas N, Lin AE, Hensley LE, Sabeti PC, Siddle KJ. Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses. CELL GENOMICS 2023; 3:100440. [PMID: 38169842 PMCID: PMC10759212 DOI: 10.1016/j.xgen.2023.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/27/2023] [Accepted: 10/15/2023] [Indexed: 01/05/2024]
Abstract
Ebola virus (EBOV) causes Ebola virus disease (EVD), marked by severe hemorrhagic fever; however, the mechanisms underlying the disease remain unclear. To assess the molecular basis of EVD across time, we performed RNA sequencing on 17 tissues from a natural history study of 21 rhesus monkeys, developing new methods to characterize host-pathogen dynamics. We identified alterations in host gene expression with previously unknown tissue-specific changes, including downregulation of genes related to tissue connectivity. EBOV was widely disseminated throughout the body; using a new, broadly applicable deconvolution method, we found that viral load correlated with increased monocyte presence. Patterns of viral variation between tissues differentiated primary infections from compartmentalized infections, and several variants impacted viral fitness in a EBOV/Kikwit minigenome system, suggesting that functionally significant variants can emerge during early infection. This comprehensive portrait of host-pathogen dynamics in EVD illuminates new features of pathogenesis and establishes resources to study other emerging pathogens.
Collapse
Affiliation(s)
- Erica Normandin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sergio Triana
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Siddharth S. Raju
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tammy C.T. Lan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Kim Lagerborg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gordon C. Adams
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Liu
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Daniel Strebinger
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arya Rao
- Columbia University, New York, NY, USA
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | | | - Molly Sacks
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ricky D. Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Krisztina Janosko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Dylan Kotliar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rickey Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John L. Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain
| | - Anna N. Honko
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Feng Zhang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mehrtash Babadi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeremy Luban
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Richard S. Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Alex K. Shalek
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nikolaos Barkas
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aaron E. Lin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Lisa E. Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Pardis C. Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| |
Collapse
|
6
|
Odongo L, Habtegebrael BH, Kiessling V, White JM, Tamm LK. A novel in vitro system of supported planar endosomal membranes (SPEMs) reveals an enhancing role for cathepsin B in the final stage of Ebola virus fusion and entry. Microbiol Spectr 2023; 11:e0190823. [PMID: 37728342 PMCID: PMC10581071 DOI: 10.1128/spectrum.01908-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 09/21/2023] Open
Abstract
Ebola virus (EBOV) causes a hemorrhagic fever with fatality rates up to 90%. The EBOV entry process is complex and incompletely understood. Following attachment to host cells, EBOV is trafficked to late endosomes/lysosomes where its glycoprotein (GP) is processed to a 19-kDa form, which binds to the EBOV intracellular receptor Niemann-Pick type C1. We previously showed that the cathepsin protease inhibitor, E-64d, blocks infection by pseudovirus particles bearing 19-kDa GP, suggesting that further cathepsin action is needed to trigger fusion. This, however, has not been demonstrated directly. Since 19-kDa Ebola GP fusion occurs in late endosomes, we devised a system in which enriched late endosomes are used to prepare supported planar endosomal membranes (SPEMs), and fusion of fluorescent (pseudo)virus particles is monitored by total internal reflection fluorescence microscopy. We validated the system by demonstrating the pH dependencies of influenza virus hemagglutinin (HA)-mediated and Lassa virus (LASV) GP-mediated fusion. Using SPEMs, we showed that fusion mediated by 19-kDa Ebola GP is dependent on low pH, enhanced by Ca2+, and augmented by the addition of cathepsins. Subsequently, we found that E-64d inhibits full fusion, but not lipid mixing, mediated by 19-kDa GP, which we corroborated with the reversible cathepsin inhibitor VBY-825. Hence, we provide both gain- and loss-of-function evidence that further cathepsin action enhances the fusion activity of 19-kDa Ebola GP. In addition to providing new insights into how Ebola GP mediates fusion, the approach we developed employing SPEMs can now be broadly used for studies of virus and toxin entry through endosomes. IMPORTANCE Ebola virus is the causative agent of Ebola virus disease, which is severe and frequently lethal. EBOV gains entry into cells via late endosomes/lysosomes. The events immediately preceding fusion of the viral and endosomal membranes are incompletely understood. In this study, we report a novel in vitro system for studying virus fusion with endosomal membranes. We validated the system by demonstrating the low pH dependencies of influenza and Lassa virus fusion. Moreover, we show that further cathepsin B action enhances the fusion activity of the primed Ebola virus glycoprotein. Finally, this model endosomal membrane system should be useful in studying the mechanisms of bilayer breaching by other enveloped viruses, by non-enveloped viruses, and by acid-activated bacterial toxins.
Collapse
Affiliation(s)
- Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Betelihem H. Habtegebrael
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Volker Kiessling
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Judith M. White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
7
|
Kumar R, Srivastava Y, Muthuramalingam P, Singh SK, Verma G, Tiwari S, Tandel N, Beura SK, Panigrahi AR, Maji S, Sharma P, Rai PK, Prajapati DK, Shin H, Tyagi RK. Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses 2023; 15:856. [PMID: 37112836 PMCID: PMC10142771 DOI: 10.3390/v15040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.
Collapse
Affiliation(s)
- Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Yogesh Srivastava
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Sunil Kumar Singh
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Geetika Verma
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Savitri Tiwari
- Division of Life Sciences, Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Gautam Buddha Nagar, Greater Noida 201310, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG Highway, Gujarat 382481, India
| | - Samir Kumar Beura
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | | | - Somnath Maji
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prakriti Sharma
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, IIET, Invertis University, Bareilly 243001, India
| | | | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Rajeev K. Tyagi
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| |
Collapse
|
8
|
Dong X, Tree J, Banadyga L, He S, Zhu W, Tipton T, Gouriet J, Qiu X, Elmore MJ, Hall Y, Carroll M, Hiscox JA. Linked Mutations in the Ebola Virus Polymerase Are Associated with Organ Specific Phenotypes. Microbiol Spectr 2023; 11:e0415422. [PMID: 36946725 PMCID: PMC10101120 DOI: 10.1128/spectrum.04154-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
Ebola virus (EBOV) causes a severe infection called Ebola virus disease (EVD). The pathogenesis of EBOV infection is complex, and outcome has been associated with a variety of immunological and cellular factors. Disease can result from several mechanisms, including direct organ and endothelial cell damage as a result of viral replication. During the2013 to 2016 Western Africa EBOV outbreak, several mutants emerged, with changes in the genes of nucleoprotein (NP), glycoprotein (GP), and the large (L) protein. Reverse genetic analysis has been used to investigate whether these mutations played any role in pathogenesis with mixed results depending on the experimental system used. Previous studies investigated the impact of three single nonsynonymous mutations (GP-A82V, NP-R111C, and L-D759G) on the fatality rate of mouse and ferret models and suggested that the L-D759G mutation decreased the virulence of EBOV. In this study, the effect of these three mutations was further evaluated by deep sequencing to determine viral population genetics and the host response in longitudinal samples of blood, liver, kidney, spleen, and lung tissues taken from the previous ferret model. The data indicated that the mutations were maintained in the different tissues, but the frequency of minor genomic mutations were different. In addition, compared to wild-type virus, the recombinant mutants had different within host effects, where the D759G (and accompanying Q986H) substitution in the L protein resulted in an upregulation of the immune response in the kidney, liver, spleen, and lungs. Together these studies provide insights into the biology of EBOV mutants both between and within hosts. IMPORTANCE Ebola virus infection can have dramatic effects on the human body which manifest in Ebola virus disease. The outcome of infection is either survival or death and in the former group with the potential of longer-term health consequences and persistent infection. Disease severity is undoubtedly associated with the host response, often with overt inflammatory responses correlated with poorer outcomes. The scale of the2013 to 2016 Western African Ebola virus outbreak revealed new aspects of viral biology. This included the emergence of mutants with potentially altered virulence. Biobanked tissue from ferret models of EBOV infected with different mutants that emerged in the Western Africa outbreak was used to investigate the effect of EBOV genomic variation in different tissues. Overall, the work provided insights into the population genetics of EBOV and showed that different organs in an animal model can respond differently to variants of EBOV.
Collapse
Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julia Tree
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Wenjun Zhu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Tom Tipton
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Jade Gouriet
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Yper Hall
- UK-Health Security Agency, Salisbury, United Kingdom
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| |
Collapse
|
9
|
Escudero-Pérez B, Lalande A, Mathieu C, Lawrence P. Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans. Viruses 2023; 15:v15030599. [PMID: 36992308 PMCID: PMC10060007 DOI: 10.3390/v15030599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.
Collapse
Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Alexandre Lalande
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
- Correspondence:
| |
Collapse
|
10
|
Odongo L, Zadrozny KK, Diehl WE, Luban J, White JM, Ganser-Pornillos BK, Tamm LK, Pornillos O. Purification and structure of luminal domain C of human Niemann-Pick C1 protein. Acta Crystallogr F Struct Biol Commun 2023; 79:45-50. [PMID: 36748341 PMCID: PMC9903137 DOI: 10.1107/s2053230x23000705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Niemann-Pick C1 protein (NPC1) is a membrane protein that primarily resides in late endosomes and lysosomes, and plays an important role in cholesterol homeostasis in the cell. The second luminal domain of NPC1 (NPC1-C) serves as the intracellular receptor for Ebola and Marburg viruses. Here, the recombinant production of nonglycosylated and glycosylated NPC1-C and a new crystal form of the nonglycosylated protein are reported. The crystals belonged to space group P21 and diffracted to 2.3 Å resolution. The structure is similar to other reported structures of NPC1-C, with differences observed in the protruding loops when compared with NPC1-C in complex with Ebola virus glycoprotein or NPC2.
Collapse
Affiliation(s)
- Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Kaneil K. Zadrozny
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Judith M. White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Barbie K. Ganser-Pornillos
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA,Correspondence e-mail:
| | - Owen Pornillos
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
11
|
Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023; 11:vaccines11020308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure. Theoretical derivation for the origin of a quasispecies is owed to the error-prone replication by polymerase and mutants of RNA replicators. Here, we briefly addressed the theoretical and mathematical origin of quasispecies and their dynamics. The impact of quasispecies for major salient human pathogens is reviewed. In the current global scenario, rapid changes in geographical landscapes favor the origin and selection of mutants. It comes as no surprise that a cauldron of mutants poses a significant risk to public health, capable of causing pandemics. Mutation rates in RNA viruses are magnitudes higher than in DNA organisms, explaining their enhanced virulence and evolvability. RNA viruses cause the most devastating pandemics; for example, members of the Orthomyxoviridae family caused the great influenza pandemic (1918 flu or Spanish flu), the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreak, and the human immunodeficiency viruses (HIV), lentiviruses of the Retroviridae family, caused worldwide devastation. Rapidly evolving RNA virus populations are a daunting challenge for the designing of effective control measures like vaccines. Developing awareness of the evolutionary dispositions of RNA viral mutant spectra and what influences their adaptation and virulence will help curtail outbreaks of past and future pathogens.
Collapse
|
12
|
Pseudotyped Viruses for Marburgvirus and Ebolavirus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:105-132. [PMID: 36920694 DOI: 10.1007/978-981-99-0113-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Marburg virus (MARV) and Ebola virus (EBOV) of the Filoviridae family are the most lethal viruses in terms of mortality rate. However, the development of antiviral treatment is hampered by the requirement for biosafety level-4 (BSL-4) containment. The establishment of BSL-2 pseudotyped viruses can provide important tools for the study of filoviruses. This chapter summarizes general information on the filoviruses and then focuses on the construction of replication-deficient pseudotyped MARV and EBOV (e.g., lentivirus system and vesicular stomatitis virus system). It also details the potential applications of the pseudotyped viruses, including neutralization antibody detection, the study of infection mechanisms, the evaluation of antibody-dependent enhancement, virus entry inhibitor screening, and glycoprotein mutation analysis.
Collapse
|
13
|
Khan MZI, Nazli A, Al-furas H, Asad MI, Ajmal I, Khan D, Shah J, Farooq MA, Jiang W. An overview of viral mutagenesis and the impact on pathogenesis of SARS-CoV-2 variants. Front Immunol 2022; 13:1034444. [PMID: 36518757 PMCID: PMC9742215 DOI: 10.3389/fimmu.2022.1034444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are submicroscopic, obligate intracellular parasites that carry either DNA or RNA as their genome, protected by a capsid. Viruses are genetic entities that propagate by using the metabolic and biosynthetic machinery of their hosts and many of them cause sickness in the host. The ability of viruses to adapt to different hosts and settings mainly relies on their ability to create de novo variety in a short interval of time. The size and chemical composition of the viral genome have been recognized as important factors affecting the rate of mutations. Coronavirus disease 2019 (Covid-19) is a novel viral disease that has quickly become one of the world's leading causes of mortality, making it one of the most serious public health problems in recent decades. The discovery of new medications to cope with Covid-19 is a difficult and time-consuming procedure, as new mutations represent a serious threat to the efficacy of recently developed vaccines. The current article discusses viral mutations and their impact on the pathogenicity of newly developed variants with a special emphasis on Covid-19. The biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its mutations, pathogenesis, and treatment strategies are discussed in detail along with the statistical data.
Collapse
Affiliation(s)
| | - Adila Nazli
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hawaa Al-furas
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, China
| | - Muhammad Imran Asad
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iqra Ajmal
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Dildar Khan
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jaffer Shah
- Department of Health, New York, NY, United States,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
| | - Muhammad Asad Farooq
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
| | - Wenzheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
| |
Collapse
|
14
|
Djiomba Njankou SD, Nyabadza F. Modelling the potential influence of human migration and two strains on Ebola virus disease dynamics. Infect Dis Model 2022; 7:645-659. [PMID: 36313151 PMCID: PMC9583178 DOI: 10.1016/j.idm.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/08/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022] Open
Abstract
Migration of infected animals and humans, and mutation are considered as the source of the introduction of new pathogens and strains into a country. In this paper, we formulate a mathematical model of Ebola virus disease dynamics, that describes the introduction of a new strain of ebolavirus, through either mutation or immigration (which can be continuous or impulsive) of infectives. The mathematical analysis of the model shows that when the immigration of infectives is continuous, the new strain invades a country if its invasion reproduction number is greater than one. When the immigration is impulsive, a newly introduced strain is controllable when its reproduction number is less than the ratio of mortality to the population inflow and only locally stable equilibria exist. This ratio is one if the population size is constant. In case of mutation of the resident strain of ebolavirus, the coexistence of the resident and mutated strains is possible at least if their respective reproduction numbers are greater than one. Results indicate that the competition for the susceptible population is the immediate consequence of the coexistence of two different strains of ebolavirus in a country and this competition is favourable to the most infectious strain. Results also indicate that impulsive immigration of infectives when compared with continuous immigration of infectives gives time for the implementation of control measures. Our model results suggest controlled movements of people between countries that have had Ebola outbreaks despite the fact that closing boundaries is impossible.
Collapse
Affiliation(s)
- Sylvie Diane Djiomba Njankou
- Department of Mathematics, University of Buea, PO Box 63, Buea, South West Region, Cameroon,Corresponding author.
| | - Farai Nyabadza
- Mathematics and Applied Mathematics Department, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| |
Collapse
|
15
|
Sevilla JP. The value of vaccines. Curr Opin Immunol 2022; 78:102243. [PMID: 36156412 DOI: 10.1016/j.coi.2022.102243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/24/2022] [Accepted: 08/11/2022] [Indexed: 01/28/2023]
Abstract
Optimizing vaccine spending depends on recognizing the full value of vaccination (VoV). Existing taxonomies of such value are not comprehensive because they are not guided by general theories. I rely on two such theories: subjective-value theory claims that what has value is determined by what people actually or ideally want in life. A welfarist theory of government states that a fundamental objective of government is to promote social value (or social welfare). These jointly imply that any aspect of life that individuals actually or ideally value and that could be negatively affected by vaccine-preventable diseases (and therefore positively affected by preventive vaccines) is an element of VoV. I build a more comprehensive-value taxonomy than currently exists based on this implication.
Collapse
Affiliation(s)
- J P Sevilla
- Data for Decisions, LLC, Harvard T. H. Chan School of Public Health, USA.
| |
Collapse
|
16
|
Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID‐19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS‐CoV‐2 delta variant performing different computational analysis. Results From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS‐CoV‐2 delta variant.
Collapse
Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology University of Rajshahi Rajshahi Bangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical Engineering Noakhali Science and Technology University Noakhali Bangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular Biology Noakhali Science and Technology University Noakhali Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy BGC Trust University Bangladesh Chittagong Bangladesh
- Department of Pharmacy Faculty of Allied Health Sciences, Daffodil International University Dhaka Bangladesh
| |
Collapse
|
17
|
Tai JH, Sun HY, Tseng YC, Li G, Chang SY, Yeh SH, Chen PJ, Chaw SM, Wang HY. Contrasting patterns in the early stage of SARS-CoV-2 evolution between humans and minks. Mol Biol Evol 2022; 39:6658056. [PMID: 35934827 PMCID: PMC9384665 DOI: 10.1093/molbev/msac156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor binding domain and receptor binding motif. An excess of high frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies the virus may not be pre-adapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.
Collapse
Affiliation(s)
- Jui Hung Tai
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Hsiao Yu Sun
- Taipei Municipal Zhongshan Girls High School, Taipei 10490, Taiwan
| | - Yi Cheng Tseng
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Guanghao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sui Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Shiou Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Pei Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan.,Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Medical Research, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Shu Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hurng Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| |
Collapse
|
18
|
Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
Collapse
Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| |
Collapse
|
19
|
Zhang M, Wang X, Hu L, Zhang Y, Zheng H, Wu H, Wang J, Luo L, Xiao H, Qiao C, Li X, Huang W, Wang Y, Feng J, Chen G. TIM-1 Augments Cellular Entry of Ebola Virus Species and Mutants, Which Is Blocked by Recombinant TIM-1 Protein. Microbiol Spectr 2022; 10:e0221221. [PMID: 35384693 PMCID: PMC9241846 DOI: 10.1128/spectrum.02212-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/07/2022] [Indexed: 01/12/2023] Open
Abstract
Ebola virus, a member of the Filoviridae family, utilizes the attachment factors on host cells to support its entry and cause severe tissue damage. TIM-1 has been identified as a predominant attachment factor via interaction with phosphatidylserine (PS) localized on the viral envelope and glycoprotein (GP). In this study, we give the first demonstration that TIM-1 enhances the cellular entry of three species of Ebola virus, as well as those harboring GP mutations (A82V, T544I, and A82V T544I). Furthermore, two TIM-1 variants (i.e., TIM-1-359aa and TIM-1-364aa) had comparable effects on promoting Zaire Ebola virus (EBOV) attachment, internalization, and infection. Importantly, recombinant TIM-1 ectodomain (ECD) protein could decrease the infectivity of Ebola virus and display synergistic inhibitory effects with ADI-15946, a monoclonal antibody with broad neutralizing activity to Ebola virus. Of note, EBOV strains harboring GP mutations (K510E and D552N), which were refractory to antibody treatment, were still sensitive to TIM-1 protein-mediated impairment of infectivity, indicating that TIM-1 protein may represent an alternative therapeutic regimen when antibody evasion occurs. IMPORTANCE The viral genome has acquired numerous mutations with the potential to increase transmission during the 2013-to-2016 outbreak of Ebola virus. EBOV strains harboring GP mutations (A82V, T544I, and A82V T544I), which have been identified to increase viral infectivity in humans, have attracted our attention. Herein, we give the first report that polymorphic TIM-1 enhances the infectivity of three species of Ebola virus, as well as those harboring GP mutations (A82V, T544I, and A82V T544I). We show that recombinant TIM-1 ECD protein could decrease the infectivity of Ebola virus with or without a point mutation and displays synergistic inhibitory effects with ADI-15946. Furthermore, TIM-1 protein potently blocked cell entry of antibody-evading Ebola virus species. These findings highlight the role of TIM-1 in Ebola virus infection and indicate that TIM-1 protein represents a potential therapeutic avenue for Ebola virus and its mutated species.
Collapse
Affiliation(s)
- Min Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Xinwei Wang
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Linhan Hu
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Yuting Zhang
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Hang Zheng
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Haiyan Wu
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Jing Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Longlong Luo
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - He Xiao
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Chunxia Qiao
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Xinying Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Jiannan Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| | - Guojiang Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Beijing, China
| |
Collapse
|
20
|
Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of Coronaviruses, Filoviruses, Henipaviruses and Rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
Collapse
|
21
|
Abstract
6 years ago, I published a Cell Host and Microbe paper that described randomization of virus genetic populations during mosquito infection. From within the evolutionary chaos, however, there is an order that can reveal a virus' past. Using these insights, I forged a career harnessing virus evolution to understand epidemiological patterns.
Collapse
|
22
|
Liu Y, Sun B, Wang J, Sun H, Lu Z, Chen L, Lan M, Xu J, Pan J, Shi J, Sun Y, Zhang X, Wang J, Jiang D, Yang K. In silico analyses and experimental validation of the MHC class-I restricted epitopes of Ebolavirus GP. Int Immunol 2022; 34:313-325. [PMID: 35192720 DOI: 10.1093/intimm/dxac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Ebolavirus (EBOV) causes an extremely high mortality and prevalence disease called Ebola virus disease (EVD). There is only one glycoprotein (GP) on the virus particle surface, which mediates entry into the host cell. MHC class-I restricted CD8 + T cell responses are important antiviral immune responses. Therefore, it is of great importance to understand EBOV GP-specific MHC class-I restricted epitopes within immunogenicity. In this study, computational approaches were employed to predict the dominant MHC class-I molecule epitopes of EBOV GP for mouse H2 and major alleles of HLA class-I supertypes. Our results yielded 42 dominant epitopes in H2 haplotypes and 301 dominant epitopes in HLA class-I haplotypes. After validation by ELISpot assay, in-depth analyses to ascertain their nature of conservation, immunogenicity, and docking with the corresponding MHC class-I molecules were undertaken. Our study predicted MHC class-I restricted epitopes that may aid the advancement of anti-EBOV immune responses. And the integrated strategy of epitope prediction, validation, and comparative analyses were postulated, promising for epitope-based immunotherapy development and application to viral epidemics.
Collapse
Affiliation(s)
- Yang Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Shaanxi Provincial Center for Disease Control and Prevention, Xi'an, Shaanxi, P.R. China
| | - Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiawei Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Hao Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Tangshan Sannvhe Airport, Tangshan, Hebei, P.R. China
| | - Zhenhua Lu
- Department of Epidemiology, Public Health School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Longyu Chen
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Mingfu Lan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiahao Xu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingyu Pan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingqi Shi
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Yuanjie Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Xiyang Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jing Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| |
Collapse
|
23
|
Yamaoka S, Ebihara H. Pathogenicity and Virulence of Ebolaviruses with Species- and Variant-specificity. Virulence 2021; 12:885-901. [PMID: 33734027 PMCID: PMC7993122 DOI: 10.1080/21505594.2021.1898169] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 01/05/2023] Open
Abstract
Ebola virus (EBOV), belonging to the species Zaire ebolavirus in the genus Ebolavirus, causes a severe febrile illness in humans with case fatality rates (CFRs) up to 90%. While there have been six virus species classified, which each have a single type virus in the genus Ebolavirus, CFRs of ebolavirus infections vary among viruses belonging to each distinct species. In this review, we aim to define the ebolavirus species-specific virulence on the basis of currently available laboratory and experimental findings. In addition, this review will also cover the variant-specific virulence of EBOV by referring to the unique biological and pathogenic characteristics of EBOV variant Makona, a new EBOV variant isolated from the 2013-2016 EBOV disease outbreak in West Africa. A better definition of species-specific and variant-specific virulence of ebolaviruses will facilitate our comprehensive knowledge on genus Ebolavirus biology, leading to the development of therapeutics against well-focused pathogenic mechanisms of each Ebola disease.
Collapse
Affiliation(s)
- Satoko Yamaoka
- Department of Molecular Medicine, Mayo Clinic, Rochester, USA
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, USA
| |
Collapse
|
24
|
Tang X, Ying R, Yao X, Li G, Wu C, Tang Y, Li Z, Kuang B, Wu F, Chi C, Du X, Qin Y, Gao S, Hu S, Ma J, Liu T, Pang X, Wang J, Zhao G, Tan W, Zhang Y, Lu X, Lu J. Evolutionary analysis and lineage designation of SARS-CoV-2 genomes. Sci Bull (Beijing) 2021; 66:2297-2311. [PMID: 33585048 PMCID: PMC7864783 DOI: 10.1016/j.scib.2021.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022]
Abstract
The pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has caused immense global disruption. With the rapid accumulation of SARS-CoV-2 genome sequences, however, thousands of genomic variants of SARS-CoV-2 are now publicly available. To improve the tracing of the viral genomes' evolution during the development of the pandemic, we analyzed single nucleotide variants (SNVs) in 121,618 high-quality SARS-CoV-2 genomes. We divided these viral genomes into two major lineages (L and S) based on variants at sites 8782 and 28144, and further divided the L lineage into two major sublineages (L1 and L2) using SNVs at sites 3037, 14408, and 23403. Subsequently, we categorized them into 130 sublineages (37 in S, 35 in L1, and 58 in L2) based on marker SNVs at 201 additional genomic sites. This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages. We also provide a companion website (www.covid19evolution.net) that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification. Finally, we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2's evolution. These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2's genome evolution.
Collapse
Affiliation(s)
- Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruochen Ying
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xinmin Yao
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Guanghao Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yiyuli Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhida Li
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Bishan Kuang
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Feng Wu
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Changsheng Chi
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Xiaoman Du
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Yi Qin
- Yuxi Rongjian Information Technology Co., Ltd., Yuxi 653100, China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources (SKLMR), The Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources (SKLMR), The Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juncai Ma
- The Microresource and Big Data Center, The Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xinghuo Pang
- Beijing Center for Disease Prevention and Control (CDC) & Research Center for Preventive Medicine of Beijing, Beijing 100013, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
25
|
Tsu BV, Fay EJ, Nguyen KT, Corley MR, Hosuru B, Dominguez VA, Daugherty MD. Running With Scissors: Evolutionary Conflicts Between Viral Proteases and the Host Immune System. Front Immunol 2021; 12:769543. [PMID: 34790204 PMCID: PMC8591160 DOI: 10.3389/fimmu.2021.769543] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/08/2021] [Indexed: 12/28/2022] Open
Abstract
Many pathogens encode proteases that serve to antagonize the host immune system. In particular, viruses with a positive-sense single-stranded RNA genome [(+)ssRNA], including picornaviruses, flaviviruses, and coronaviruses, encode proteases that are not only required for processing viral polyproteins into functional units but also manipulate crucial host cellular processes through their proteolytic activity. Because these proteases must cleave numerous polyprotein sites as well as diverse host targets, evolution of these viral proteases is expected to be highly constrained. However, despite this strong evolutionary constraint, mounting evidence suggests that viral proteases such as picornavirus 3C, flavivirus NS3, and coronavirus 3CL, are engaged in molecular ‘arms races’ with their targeted host factors, resulting in host- and virus-specific determinants of protease cleavage. In cases where protease-mediated cleavage results in host immune inactivation, recurrent host gene evolution can result in avoidance of cleavage by viral proteases. In other cases, such as recently described examples in NLRP1 and CARD8, hosts have evolved ‘tripwire’ sequences that mimic protease cleavage sites and activate an immune response upon cleavage. In both cases, host evolution may be responsible for driving viral protease evolution, helping explain why viral proteases and polyprotein sites are divergent among related viruses despite such strong evolutionary constraint. Importantly, these evolutionary conflicts result in diverse protease-host interactions even within closely related host and viral species, thereby contributing to host range, zoonotic potential, and pathogenicity of viral infection. Such examples highlight the importance of examining viral protease-host interactions through an evolutionary lens.
Collapse
Affiliation(s)
- Brian V Tsu
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Elizabeth J Fay
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Katelyn T Nguyen
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Miles R Corley
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Bindhu Hosuru
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Viviana A Dominguez
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Matthew D Daugherty
- Division of Biological Sciences, University of California, San Diego, CA, United States
| |
Collapse
|
26
|
Xi H, Jiang H, Juhas M, Zhang Y. Multiplex Biosensing for Simultaneous Detection of Mutations in SARS-CoV-2. ACS OMEGA 2021; 6:25846-25859. [PMID: 34632242 PMCID: PMC8491437 DOI: 10.1021/acsomega.1c04024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/10/2021] [Indexed: 05/02/2023]
Abstract
COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become the world's largest public health emergency of the past few decades. Thousands of mutations were identified in the SARS-CoV-2 genome. Some mutants are more infectious and may replace the original strains. Recently, B.1.1.7(Alpha), B1.351(Beta), and B.1.617.2(Delta) strains, which appear to have increased transmissibility, were detected. These strains accounting for the high proportion of newly diagnosed cases spread rapidly over the world. Particularly, the Delta variant has been reported to account for a vast majority of the infections in several countries over the last few weeks. The application of biosensors in the detection of SARS-CoV-2 is important for the control of the COVID-19 pandemic. Due to high demand for SARS-CoV-2 genotyping, it is urgent to develop reliable and efficient systems based on integrated multiple biosensor technology for rapid detection of multiple SARS-CoV-2 mutations simultaneously. This is important not only for the detection and analysis of the current but also for future mutations. Novel biosensors combined with other technologies can be used for the reliable and effective detection of SARS-CoV-2 mutants.
Collapse
Affiliation(s)
- Hui Xi
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Hanlin Jiang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Mario Juhas
- Medical
and Molecular Microbiology Unit, Department of Medicine, Faculty of
Science and Medicine, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Yang Zhang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| |
Collapse
|
27
|
On-Demand Patient-Specific Phenotype-to-Genotype Ebola Virus Characterization. Viruses 2021; 13:v13102010. [PMID: 34696439 PMCID: PMC8537714 DOI: 10.3390/v13102010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
Biosafety, biosecurity, logistical, political, and technical considerations can delay or prevent the wide dissemination of source material containing viable virus from the geographic origin of an outbreak to laboratories involved in developing medical countermeasures (MCMs). However, once virus genome sequence information is available from clinical samples, reverse-genetics systems can be used to generate virus stocks de novo to initiate MCM development. In this study, we developed a reverse-genetics system for natural isolates of Ebola virus (EBOV) variants Makona, Tumba, and Ituri, which have been challenging to obtain. These systems were generated starting solely with in silico genome sequence information and have been used successfully to produce recombinant stocks of each of the viruses for use in MCM testing. The antiviral activity of MCMs targeting viral entry varied depending on the recombinant virus isolate used. Collectively, selecting and synthetically engineering emerging EBOV variants and demonstrating their efficacy against available MCMs will be crucial for answering pressing public health and biosecurity concerns during Ebola disease (EBOD) outbreaks.
Collapse
|
28
|
Vasudevan K, Thirumal Kumar D, Udhaya Kumar S, Saleem A, Nagasundaram N, Siva R, Tayubi IA, George Priya Doss C, Zayed H. A computational overview on phylogenetic characterization, pathogenic mutations, and drug targets for Ebola virus disease. Curr Opin Pharmacol 2021; 61:28-35. [PMID: 34563987 DOI: 10.1016/j.coph.2021.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/18/2022]
Abstract
The World Health Organization declared Ebola virus disease (EVD) as the major outbreak in the 20th century. EVD was first identified in 1976 in South Sudan and the Democratic Republic of the Congo. EVD was transmitted from infected fruit bats to humans via contact with infected animal body fluids. The Ebola virus (EBOV) has a genome size of ∼18,959 bp. It encodes seven distinct proteins: nucleoprotein (NP), glycoprotein (GP), viral proteins VP24, VP30, VP35, matrix protein VP40, and polymerase L is considered a prime target for potential antiviral strategies. The current US FDA-approved anti-EVD vaccine, ERVERBO, and the other equally effective anti-EBOV combinations of three fully human monoclonal antibodies such as REGN-EB3, primarily target the envelope glycoprotein. This work elaborates on the EBOV's phylogenetic structure and the crucial mutations associated with viral pathogenicity.
Collapse
Affiliation(s)
- Karthick Vasudevan
- School of Applied Sciences, Reva University, Bengaluru, Karnataka, India.
| | - D Thirumal Kumar
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, India.
| | - S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Aisha Saleem
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - N Nagasundaram
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - R Siva
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar.
| |
Collapse
|
29
|
Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks. Nature 2021; 597:539-543. [PMID: 34526718 DOI: 10.1038/s41586-021-03901-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak-between 14 February and 19 June 2021-near the epicentre of the previous epidemic1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization.
Collapse
|
30
|
|
31
|
A Naturally Occurring Polymorphism in the Base of Sudan Virus Glycoprotein Decreases Glycoprotein Stability in a Species-Dependent Manner. J Virol 2021; 95:e0107321. [PMID: 34232742 DOI: 10.1128/jvi.01073-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sudan virus (SUDV) is one of five filoviruses that compose the genus Ebolavirus that has been responsible for episodic outbreaks in Central Africa. While the SUDV glycoprotein (GP) structure has been solved, GP residues that affect SUDV entry have not been extensively examined; many of the entry characteristics of SUDV GP are inferred from studies with the Zaire Ebola virus (EBOV) GP. Here, we investigate the effect on virus entry of a naturally occurring polymorphism in SUDV GP. Two of the earliest SUDV isolates contain glutamine at residue 95 (Q95) within the base region of GP1, whereas more recent SUDV isolates and GPs from all other ebolaviruses carry lysine at this position (K95). A K95Q change dramatically decreased titers of pseudovirions bearing SUDV GP, whereas the K95Q substitution in EBOV GP had no effect on titer. We evaluated virus entry to identify SUDV GP Q95-specific entry defects. The presence of Q95 in either EBOV or SUDV GP resulted in enhanced sensitivity of GP to proteolytic processing, yet this could not account for the SUDV-specific decrease in GP Q95 infectivity. We found that SUDV GP Q95 pseudovirions were more sensitive to imipramine, a GP-destabilizing antiviral. In contrast, SUDV GP K95 was more stable, requiring elevated temperatures to inhibit virus infection. Thus, the residue present at GP 95 has a critical role in stabilizing the SUDV glycoprotein, whereas this polymorphism has no effect on EBOV GP stability. These results provide novel insights into filovirus species-specific GP structure that affects virus infectivity. IMPORTANCE Filovirus outbreaks are associated with significant morbidity and mortality. Understanding the structural constraints of filoviral GPs that control virus entry into cells is critical for rational development of novel antivirals to block infection. Here, we identify a naturally occurring glutamine (Q) to lysine (K) polymorphism at residue 95 as a critical determinant of Sudan virus GP stability but not Zaire Ebola virus GP stability. We propose that glutamine at residue 95 in Sudan virus GP mediates decreased virus entry, thereby reducing infectivity. Our findings highlight a unique structural characteristic of Sudan virus GP that affects GP-mediated functionality. Further, it provides a cautionary note for the development of future broad-spectrum filovirus antivirals.
Collapse
|
32
|
The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response. Viruses 2021; 13:v13081605. [PMID: 34452470 PMCID: PMC8402630 DOI: 10.3390/v13081605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE-detected in the Yoruba population of Nigeria-conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the "emerging" nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz's critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.
Collapse
|
33
|
Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
Collapse
|
34
|
Kang L, He G, Sharp AK, Wang X, Brown AM, Michalak P, Weger-Lucarelli J. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell 2021; 184:4392-4400.e4. [PMID: 34289344 PMCID: PMC8260498 DOI: 10.1016/j.cell.2021.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/07/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic underscores the need to better understand animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned more than 182,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes for selective sweep signatures and found a distinct footprint of positive selection located around a non-synonymous change (A1114G; T372A) within the spike protein receptor-binding domain (RBD), predicted to remove glycosylation and increase binding to human ACE2 (hACE2), the cellular receptor. This change is present in all human SARS-CoV-2 sequences but not in closely related viruses from bats and pangolins. As predicted, T372A RBD bound hACE2 with higher affinity in experimental binding assays. We engineered the reversion mutant (A372T) and found that A372 (wild-type [WT]-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect that was 20 times greater than the well-known D614G mutation. Our findings suggest that this mutation likely contributed to SARS-CoV-2 emergence from animal reservoirs or enabled sustained human-to-human transmission.
Collapse
Affiliation(s)
- Lin Kang
- Edward Via College of Osteopathic Medicine, Monroe, LA 71203, USA; Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
| | - Guijuan He
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Amanda K Sharp
- Program in Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiaofeng Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Anne M Brown
- Program in Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA; Research and Informatics, University Libraries, Virginia Tech, Blacksburg, VA 24061, USA; Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Monroe, LA 71203, USA; Center for One Health Research, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA 24060, USA; Institute of Evolution, Haifa University, Haifa 3498838, Israel.
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA.
| |
Collapse
|
35
|
Brinkmann A, Ulm SL, Uddin S, Förster S, Seifert D, Oehme R, Corty M, Schaade L, Michel J, Nitsche A. AmpliCoV: Rapid Whole-Genome Sequencing Using Multiplex PCR Amplification and Real-Time Oxford Nanopore MinION Sequencing Enables Rapid Variant Identification of SARS-CoV-2. Front Microbiol 2021; 12:651151. [PMID: 34276587 PMCID: PMC8281033 DOI: 10.3389/fmicb.2021.651151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/01/2021] [Indexed: 11/22/2022] Open
Abstract
Since the emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in December 2019, the scientific community has been sharing data on epidemiology, diagnostic methods, and whole-genomic sequences almost in real time. The latter have already facilitated phylogenetic analyses, transmission chain tracking, protein modeling, the identification of possible therapeutic targets, timely risk assessment, and identification of novel variants. We have established and evaluated an amplification-based approach for whole-genome sequencing of SARS-CoV-2. It can be used on the miniature-sized and field-deployable sequencing device Oxford Nanopore MinION, with sequencing library preparation time of 10 min. We show that the generation of 50,000 total reads per sample is sufficient for a near complete coverage (>90%) of the SARS-CoV-2 genome directly from patient samples even if virus concentration is low (Ct 35, corresponding to approximately 5 genome copies per reaction). For patient samples with high viral load (Ct 18–24), generation of 50,000 reads in 1–2 h was shown to be sufficient for a genome coverage of >90%. Comparison to Illumina data reveals an accuracy that suffices to identify virus mutants. AmpliCoV can be applied whenever sequence information on SARS-CoV-2 is required rapidly, for instance for the identification of circulating virus mutants.
Collapse
Affiliation(s)
- Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie-Luisa Ulm
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Steven Uddin
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Sophie Förster
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Dominique Seifert
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Rainer Oehme
- Landesgesundheitsamt Baden-Württemberg, Stuttgart, Germany
| | - Merle Corty
- LADR Laboratory Group Dr. Kramer & Colleagues, Geesthacht, Germany
| | - Lars Schaade
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
36
|
Tea F, Ospina Stella A, Aggarwal A, Ross Darley D, Pilli D, Vitale D, Merheb V, Lee FXZ, Cunningham P, Walker GJ, Fichter C, Brown DA, Rawlinson WD, Isaacs SR, Mathivanan V, Hoffmann M, Pöhlman S, Mazigi O, Christ D, Dwyer DE, Rockett RJ, Sintchenko V, Hoad VC, Irving DO, Dore GJ, Gosbell IB, Kelleher AD, Matthews GV, Brilot F, Turville SG. SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants. PLoS Med 2021; 18:e1003656. [PMID: 34228725 PMCID: PMC8291755 DOI: 10.1371/journal.pmed.1003656] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/20/2021] [Accepted: 05/12/2021] [Indexed: 01/12/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antibody neutralization response and its evasion by emerging viral variants and variant of concern (VOC) are unknown, but critical to understand reinfection risk and breakthrough infection following vaccination. Antibody immunoreactivity against SARS-CoV-2 antigens and Spike variants, inhibition of Spike-driven virus-cell fusion, and infectious SARS-CoV-2 neutralization were characterized in 807 serial samples from 233 reverse transcription polymerase chain reaction (RT-PCR)-confirmed Coronavirus Disease 2019 (COVID-19) individuals with detailed demographics and followed up to 7 months. A broad and sustained polyantigenic immunoreactivity against SARS-CoV-2 Spike, Membrane, and Nucleocapsid proteins, along with high viral neutralization, was associated with COVID-19 severity. A subgroup of "high responders" maintained high neutralizing responses over time, representing ideal convalescent plasma donors. Antibodies generated against SARS-CoV-2 during the first COVID-19 wave had reduced immunoreactivity and neutralization potency to emerging Spike variants and VOC. Accurate monitoring of SARS-CoV-2 antibody responses would be essential for selection of optimal responders and vaccine monitoring and design.
Collapse
Affiliation(s)
- Fiona Tea
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Alberto Ospina Stella
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - David Ross Darley
- St Vincent’s Hospital, Sydney, New South Wales, Australia
- School of Medicine, St Vincent’s Clinical School, The University of New South Wales, Sydney, New South Wales, Australia
| | - Deepti Pilli
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Daniele Vitale
- Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Vera Merheb
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Fiona X. Z. Lee
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Philip Cunningham
- St Vincent’s Applied Medical Research, Sydney, New South Wales, Australia
| | | | - Christina Fichter
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - David A. Brown
- Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Sydney, Australia
| | - William D. Rawlinson
- New South Wales Health Pathology, Sydney, Australia
- School of Medical Sciences, Biotechnology and Biomolecular Sciences and School of Women’s and Children’s Health, The University of New South Wales Sydney, New South Wales, Australia
- Serology and Virology Division (SAViD), NSW HP SEALS, Randwick, Australia
| | | | - Vennila Mathivanan
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlman
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Ohan Mazigi
- School of Medicine, St Vincent’s Clinical School, The University of New South Wales, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Daniel Christ
- School of Medicine, St Vincent’s Clinical School, The University of New South Wales, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- New South Wales Health Pathology, Sydney, Australia
- Centre for Infectious Diseases & Microbiology, Public Health, New South Wales Health Pathology, Institute of Clinical Pathology & Medical Research (ICPMR), Westmead, Sydney, New South Wales, Australia
- Marie Bashir Institute for Biosecurity, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases & Microbiology, Public Health, New South Wales Health Pathology, Institute of Clinical Pathology & Medical Research (ICPMR), Westmead, Sydney, New South Wales, Australia
- Marie Bashir Institute for Biosecurity, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- New South Wales Health Pathology, Sydney, Australia
- Centre for Infectious Diseases & Microbiology, Public Health, New South Wales Health Pathology, Institute of Clinical Pathology & Medical Research (ICPMR), Westmead, Sydney, New South Wales, Australia
- Marie Bashir Institute for Biosecurity, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - David O. Irving
- Australian Red Cross Lifeblood, Melbourne, Victoria, Australia
- Faculty of Health, University of Technology, Sydney, New South Wales, Australia
| | - Gregory J. Dore
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
- St Vincent’s Hospital, Sydney, New South Wales, Australia
| | - Iain B. Gosbell
- Australian Red Cross Lifeblood, Melbourne, Victoria, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Anthony D. Kelleher
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Gail V. Matthews
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
- St Vincent’s Hospital, Sydney, New South Wales, Australia
| | - Fabienne Brilot
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, New South Wales, Australia
- Marie Bashir Institute for Biosecurity, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Stuart G. Turville
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
37
|
Influence of Different Glycoproteins and of the Virion Core on SERINC5 Antiviral Activity. Viruses 2021; 13:v13071279. [PMID: 34209034 PMCID: PMC8310182 DOI: 10.3390/v13071279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Host plasma membrane protein SERINC5 is incorporated into budding retrovirus particles where it blocks subsequent entry into susceptible target cells. Three structurally unrelated proteins encoded by diverse retroviruses, human immunodeficiency virus type 1 (HIV-1) Nef, equine infectious anemia virus (EIAV) S2, and ecotropic murine leukemia virus (MLV) GlycoGag, disrupt SERINC5 antiviral activity by redirecting SERINC5 from the site of virion assembly on the plasma membrane to an internal RAB7+ endosomal compartment. Pseudotyping retroviruses with particular glycoproteins, e.g., vesicular stomatitis virus glycoprotein (VSV G), renders the infectivity of particles resistant to inhibition by virion-associated SERINC5. To better understand viral determinants for SERINC5-sensitivity, the effect of SERINC5 was assessed using HIV-1, MLV, and Mason-Pfizer monkey virus (M-PMV) virion cores, pseudotyped with glycoproteins from Arenavirus, Coronavirus, Filovirus, Rhabdovirus, Paramyxovirus, and Orthomyxovirus genera. SERINC5 restricted virions pseudotyped with glycoproteins from several retroviruses, an orthomyxovirus, a rhabdovirus, a paramyxovirus, and an arenavirus. Infectivity of particles pseudotyped with HIV-1, amphotropic-MLV (A-MLV), or influenza A virus (IAV) glycoproteins, was decreased by SERINC5, whether the core was provided by HIV-1, MLV, or M-PMV. In contrast, particles pseudotyped with glycoproteins from M-PMV, parainfluenza virus 5 (PIV5), or rabies virus (RABV) were sensitive to SERINC5, but only with particular retroviral cores. Resistance to SERINC5 did not correlate with reduced SERINC5 incorporation into particles, route of viral entry, or absolute infectivity of the pseudotyped virions. These findings indicate that some non-retroviruses may be sensitive to SERINC5 and that, in addition to the viral glycoprotein, the retroviral core influences sensitivity to SERINC5.
Collapse
|
38
|
Mengist HM, Kombe Kombe AJ, Mekonnen D, Abebaw A, Getachew M, Jin T. Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity. Semin Immunol 2021; 55:101533. [PMID: 34836774 PMCID: PMC8604694 DOI: 10.1016/j.smim.2021.101533] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 02/04/2023]
Abstract
Responsible for more than 4.9 million deaths so far, COVID-19, caused by SARS-CoV-2, is instigating devastating effects on the global health care system whose impacts could be longer for the years to come. Acquiring a comprehensive knowledge of host-virus interaction is critical for designing effective vaccines and/or drugs. Understanding the evolution of the virus and the impact of genetic variability on host immune evasion and vaccine efficacy is helpful to design novel strategies to minimize the effects of the emerging variants of concern (VOC). Most vaccines under development and/or in current use target the spike protein owning to its unique function of host receptor binding, relatively conserved nature, potent immunogenicity in inducing neutralizing antibodies, and being a good target of T cell responses. However, emerging SARS-CoV-2 strains are exhibiting variability on the spike protein which could affect the efficacy of vaccines and antibody-based therapies in addition to enhancing viral immune evasion mechanisms. Currently, the degree to which mutations on the spike protein affect immunity and vaccination, and the ability of the current vaccines to confer protection against the emerging variants attracts much attention. This review discusses the implications of SARS-CoV-2 spike protein mutations on immune evasion and vaccine-induced immunity and forward directions which could contribute to future studies focusing on designing effective vaccines and/or immunotherapies to consider viral evolution. Combining vaccines derived from different regions of the spike protein that boost both the humoral and cellular wings of adaptive immunity could be the best options to cope with the emerging VOC.
Collapse
Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Arnaud John Kombe Kombe
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Daniel Mekonnen
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China
| | - Abtie Abebaw
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Melese Getachew
- Department of Clinical Pharmacy, College of Health Science, Debre Markos University, Debre Markos, 269, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui, 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, 200031, China.
| |
Collapse
|
39
|
Pandey U, Yee R, Shen L, Judkins AR, Bootwalla M, Ryutov A, Maglinte DT, Ostrow D, Precit M, Biegel JA, Bender JM, Gai X, Dien Bard J. High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Open Forum Infect Dis 2021; 8:ofaa551. [PMID: 34095334 PMCID: PMC7717363 DOI: 10.1093/ofid/ofaa551] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children. METHODS Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity. RESULTS Higher viral load was detected in symptomatic patients (P = .0007) and in children <5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California. CONCLUSIONS Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.
Collapse
Affiliation(s)
- Utsav Pandey
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Rebecca Yee
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Lishuang Shen
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Moiz Bootwalla
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Alex Ryutov
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Dennis T Maglinte
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Mimi Precit
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jeffrey M Bender
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Xiaowu Gai
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
40
|
He L, Chaudhary A, Lin X, Sou C, Alkutkar T, Kumar S, Ngo T, Kosviner E, Ozorowski G, Stanfield RL, Ward AB, Wilson IA, Zhu J. Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Nat Commun 2021; 12:2633. [PMID: 33976149 DOI: 10.1101/2020.08.22.262634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 05/27/2023] Open
Abstract
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.
Collapse
MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antigens, Viral/administration & dosage
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/ultrastructure
- B-Lymphocytes/immunology
- Crystallography, X-Ray
- Disease Models, Animal
- Ebola Vaccines/administration & dosage
- Ebola Vaccines/genetics
- Ebola Vaccines/immunology
- Ebolavirus/genetics
- Ebolavirus/immunology
- Epitopes, T-Lymphocyte/administration & dosage
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/ultrastructure
- Female
- Glycoproteins/administration & dosage
- Glycoproteins/genetics
- Glycoproteins/immunology
- Glycoproteins/ultrastructure
- Hemorrhagic Fever, Ebola/blood
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/therapy
- Hemorrhagic Fever, Ebola/virology
- Humans
- Mice
- Nanoparticles/chemistry
- Protein Domains/genetics
- Protein Domains/immunology
- Protein Engineering
- Protein Multimerization/genetics
- Protein Multimerization/immunology
- Protein Stability
- Rabbits
- T-Lymphocytes, Helper-Inducer/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Viral Proteins/administration & dosage
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/ultrastructure
Collapse
Affiliation(s)
- Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anshul Chaudhary
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kosviner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
41
|
González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Viruses 2021; 13:883. [PMID: 34064904 PMCID: PMC8151058 DOI: 10.3390/v13050883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
Collapse
Affiliation(s)
- Jorge González-Puelma
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Marco Montes de Oca
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Mónica Pinto
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | | | - Diego Alvarez-Saravia
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Hermy Álvarez
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Gonzalo Encina
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
- Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
| | - Rodrigo Muñoz
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile;
- Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Marcelo A. Navarrete
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| |
Collapse
|
42
|
He L, Chaudhary A, Lin X, Sou C, Alkutkar T, Kumar S, Ngo T, Kosviner E, Ozorowski G, Stanfield RL, Ward AB, Wilson IA, Zhu J. Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Nat Commun 2021; 12:2633. [PMID: 33976149 PMCID: PMC8113551 DOI: 10.1038/s41467-021-22867-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display. Ebola virus glycoprotein (GP) is a major target for vaccine design. Here, the authors identify mutations to improve GP stability and yield, design two multilayered nanoparticle carriers, and demonstrate good immunogenicity of the modified GP on nanoparticles in mice and rabbits.
Collapse
Affiliation(s)
- Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anshul Chaudhary
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kosviner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
43
|
Song DH, Garcia G, Situ K, Chua BA, Hong MLO, Do EA, Ramirez CM, Harui A, Arumugaswami V, Morizono K. Development of a blocker of the universal phosphatidylserine- and phosphatidylethanolamine-dependent viral entry pathways. Virology 2021; 560:17-33. [PMID: 34020328 DOI: 10.1016/j.virol.2021.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022]
Abstract
Envelope phosphatidylserine (PtdSer) and phosphatidylethanolamine (PtdEtr) have been shown to mediate binding of enveloped viruses. However, commonly used PtdSer binding molecules such as Annexin V cannot block PtdSer-mediated viral infection. Lack of reagents that can conceal envelope PtdSer and PtdEtr and subsequently inhibit infection hinders elucidation of the roles of the envelope phospholipids in viral infection. Here, we developed sTIM1dMLDR801, a reagent capable of blocking PtdSer- and PtdEtr-dependent infection of enveloped viruses. Using sTIM1dMLDR801, we found that envelope PtdSer and/or PtdEtr can support ZIKV infection of not only human but also mosquito cells. In a mouse model for ZIKV infection, sTIM1dMLDR801 reduced ZIKV load in serum and the spleen, indicating envelope PtdSer and/or PtdEtr support in viral infection in vivo. sTIM1dMLDR801 will enable elucidation of the roles of envelope PtdSer and PtdEtr in infection of various virus species, thereby facilitating identification of their receptors and transmission mechanisms.
Collapse
Affiliation(s)
- Da-Hoon Song
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Kathy Situ
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Bernadette A Chua
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Madeline Lauren O Hong
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Elyza A Do
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Christina M Ramirez
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | - Airi Harui
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
| | - Kouki Morizono
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA; UCLA AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
44
|
Kinganda-Lusamaki E, Black A, Mukadi DB, Hadfield J, Mbala-Kingebeni P, Pratt CB, Aziza A, Diagne MM, White B, Bisento N, Nsunda B, Akonga M, Faye M, Faye O, Edidi-Atani F, Matondo-Kuamfumu M, Mambu-Mbika F, Bulabula J, Di Paola N, Pauthner MG, Andersen KG, Palacios G, Delaporte E, Sall AA, Peeters M, Wiley MR, Ahuka-Mundeke S, Bedford T, Tamfum JJM. Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo. Nat Med 2021; 27:710-716. [PMID: 33846610 PMCID: PMC8549801 DOI: 10.1038/s41591-021-01302-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 03/02/2021] [Indexed: 12/29/2022]
Abstract
On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale (INRB) implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis and dissemination of genomic epidemiologic results to frontline public health workers. We report 744 new genomes sampled between 27 July 2018 and 27 April 2020 generated by this surveillance effort. Together with previously available sequence data (n = 48 genomes), these data represent almost 24% of all laboratory-confirmed Ebola virus (EBOV) infections in DRC in the period analyzed. We inferred spatiotemporal transmission dynamics from the genomic data as new sequences were generated, and disseminated the results to support epidemiologic response efforts. Here we provide an overview of how this genomic surveillance system functioned, present a full phylodynamic analysis of 792 Ebola genomes from the Nord Kivu outbreak and discuss how the genomic surveillance data informed response efforts and public health decision making.
Collapse
Affiliation(s)
- Eddy Kinganda-Lusamaki
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo.
| | - Allison Black
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel B Mukadi
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Catherine B Pratt
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Bailey White
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nella Bisento
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bibiche Nsunda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Marceline Akonga
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | | | - Francois Edidi-Atani
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Meris Matondo-Kuamfumu
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Fabrice Mambu-Mbika
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Junior Bulabula
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Matthias G Pauthner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | | | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Michael R Wiley
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Jean-Jacques Muyembe Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| |
Collapse
|
45
|
Dolzhikova IV, Shcherbinin DN, Logunov DY, Gintsburg AL. [Ebola virus ( Filoviridae: Ebolavirus: Zaire ebolavirus): fatal adaptation mutations]. Vopr Virusol 2021; 66:7-16. [PMID: 33683061 DOI: 10.36233/0507-4088-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/07/2021] [Indexed: 01/13/2023]
Abstract
Ebola virus disease (EVD) (former Ebola hemorrhagic fever) is one of the most dangerous infectious diseases affecting humans and primates. Since the identification of the first outbreak in 1976, there have been more than 25 outbreaks worldwide, the largest of which escalated into an epidemic in 2014-2016 and caused the death of more than 11,000 people. There are currently 2 independent outbreaks of this disease in the eastern and western parts of the Democratic Republic of the Congo (DRC) at the same time. Bats (Microchiroptera) are supposed to be the natural reservoir of EVD, but the infectious agent has not yet been isolated from them. Most animal viruses are unable to replicate in humans. They have to develop adaptive mutations (AM) to become infectious for humans. In this review based on the results of a number of studies, we hypothesize that the formation of AM occurs directly in the human and primate population and subsequently leads to the development of EVD outbreaks.
Collapse
Affiliation(s)
- I V Dolzhikova
- FSBI National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya of the Ministry of Health of Russia
| | - D N Shcherbinin
- FSBI National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya of the Ministry of Health of Russia
| | - D Yu Logunov
- FSBI National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya of the Ministry of Health of Russia
| | - A L Gintsburg
- FSBI National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya of the Ministry of Health of Russia
| |
Collapse
|
46
|
Al Awaidy ST, Asghar RJ, Omais S, Salman M, Zaraket H. Implications of the Emerging SARS-CoV-2 Variant: Caution is the Key. Oman Med J 2021; 36:e235. [PMID: 33768966 PMCID: PMC7961681 DOI: 10.5001/omj.2021.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022] Open
Affiliation(s)
| | | | - Saad Omais
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Muhammad Salman
- Public Health Laboratory Division, National Institutes of Health, Islamabad, Pakistan
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology and Microbiology, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
47
|
Misasi J, Sullivan NJ. Immunotherapeutic strategies to target vulnerabilities in the Ebolavirus glycoprotein. Immunity 2021; 54:412-436. [PMID: 33691133 DOI: 10.1016/j.immuni.2021.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
The 2014 Ebola virus disease (EVD) outbreak in West Africa and the subsequent outbreaks of 2018-2020 in Equator and North Kivu provinces of the Democratic Republic of the Congo illustrate the public health challenges of emerging and reemerging viruses. EVD has a high case fatality rate with a rapidly progressing syndrome of fever, rash, vomiting, diarrhea, and bleeding diathesis. Recently, two monoclonal-antibody-based therapies received United States Food and Drug Administration (FDA) approval, and there are several other passive immunotherapies that hold promise as therapeutics against other species of Ebolavirus. Here, we review concepts needed to understand mechanisms of action, present an expanded schema to define additional sites of vulnerability on the viral glycoprotein, and review current antibody-based therapeutics. The concepts described are used to gain insights into the key characteristics that represent functional targets for immunotherapies against Zaire Ebolavirus and other emerging viruses within the Ebolavirus genus.
Collapse
Affiliation(s)
- John Misasi
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
48
|
A Glycoprotein Mutation That Emerged during the 2013-2016 Ebola Virus Epidemic Alters Proteolysis and Accelerates Membrane Fusion. mBio 2021; 12:mBio.03616-20. [PMID: 33593971 PMCID: PMC8545129 DOI: 10.1128/mbio.03616-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genomic surveillance of viral isolates during the 2013–2016 Ebola virus epidemic in Western Africa, the largest and most devastating filovirus outbreak on record, revealed several novel mutations. The responsible strain, named Makona, carries an A-to-V substitution at position 82 (A82V) in the glycoprotein (GP), which is associated with enhanced infectivity in vitro. Here, we investigated the mechanistic basis for this enhancement as well as the interplay between A82V and a T-to-I substitution at residue 544 of GP, which also modulates infectivity in cell culture. We found that both 82V and 544I destabilize GP, with the residue at position 544 impacting overall stability, while 82V specifically destabilizes proteolytically cleaved GP. Both residues also promote faster kinetics of lipid mixing of the viral and host membranes in live cells, individually and in tandem, which correlates with faster times to fusion following colocalization with the viral receptor Niemann-Pick C1 (NPC1). Furthermore, GPs bearing 82V are more sensitive to proteolysis by cathepsin L (CatL), a key host factor for viral entry. Intriguingly, CatL processed 82V variant GPs to a novel product with a molecular weight of approximately 12,000 (12K), which we hypothesize corresponds to a form of GP that is pre-triggered for fusion. We thus propose a model in which 82V promotes more efficient GP processing by CatL, leading to faster viral fusion kinetics and higher levels of infectivity.
Collapse
|
49
|
Majid S, Khan MS, Rashid S, Niyaz A, Farooq R, Bhat SA, Wani HA, Qureshi W. COVID-19: Diagnostics, Therapeutic Advances, and Vaccine Development. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021; 8:152-166. [PMID: 33614398 PMCID: PMC7883962 DOI: 10.1007/s40588-021-00157-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 02/06/2023]
Abstract
Purpose of Review Human race is currently facing the wrath of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a highly transmittable and pathogenic RNA virus, causing coronavirus disease 2019 (COVID-19), the worst ever global pandemic. Coronaviruses (CoVs) have emerged as a major public health concern. Urgent global response to COVID-19 outbreak has been to limit spread of SARS-CoV-2 via extensive monitoring and containment. Various treatment regimens have been adopted to manage COVID-19, with known drugs and drug combinations used to decrease the morbidity and mortality associated with COVID-19. Intensive research on various fronts including studying molecular and structural aspects of these viruses and unraveling the pathophysiology and mechanistic basis of COVID-19 aimed at developing effective prophylactic, therapeutic agents and vaccines has been carried out globally. Recent Findings No approved antiviral treatment except remdesivir exists for SARS-CoV-2 till date though novel drug targets have been identified. However, worldwide frantic and competitive vaccine development pharmaceutical race has borne fruit in the form of a number of promising candidate vaccines, out of which few have already received emergency use authorization by regulatory bodies in record time. Summary This review highlights the painstaking efforts of healthcare workers and scientific community to successfully address the COVID-19 pandemic—though damage in the form of severe illness, loss of lives, and livelihood has left a serious mark. Focusing on extensive research on various therapeutic options and antiviral strategies including neutralizing antibodies, potential drugs, and drug targets, light has been shed on various diagnostic options and the amazing vaccine development process as well.
Collapse
Affiliation(s)
- Sabhiya Majid
- Department of Biochemistry, Government Medical College Srinagar and Associated SMHS and Super Speciality Hospital and Research Centre, University of Kashmir Srinagar, Srinagar, J&K 190010 India
| | - Mosin S. Khan
- Department of Biochemistry, Government Medical College Srinagar and Associated SMHS and Super Speciality Hospital and Research Centre, University of Kashmir Srinagar, Srinagar, J&K 190010 India
| | - Samia Rashid
- Department of Medicine, Government Medical College Srinagar and Associated SMHS and Super Speciality Hospital, Srinagar, J&K 190010 India
| | - Ayesha Niyaz
- SHKM Government Medical College, Mewat, Haryana India
| | - Rabia Farooq
- Department of Basic Medical Sciences, College of Medicine, University of Bisha, Bisha, 67714 Saudi Arabia
| | - Showkat A. Bhat
- Department of Biochemistry, Government Medical College Doda, Doda, J&K 182202 India
| | - Hilal A. Wani
- Department of Higher Education, Government of Jammu & Kashmir, Jammu, India
| | - Waseem Qureshi
- Registrar Academics, Government Medical College Srinagar, Srinagar, J&K 190010 India
| |
Collapse
|
50
|
Villoutreix BO, Calvez V, Marcelin AG, Khatib AM. In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Int J Mol Sci 2021; 22:1695. [PMID: 33567580 PMCID: PMC7915722 DOI: 10.3390/ijms22041695] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike-ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure-function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.
Collapse
Affiliation(s)
- Bruno O. Villoutreix
- Integrative Computational Pharmacology and Data Mining, INSERM UMR 1141, NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Abdel-Majid Khatib
- Université de Bordeaux, INSERM, LAMC, U1029, F-33600 Pessac, France
- Institut Bergonié, 33000 Bordeaux, France
| |
Collapse
|