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Li X, Mi Z, Liu Z, Rong P. SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines. Front Microbiol 2024; 15:1334152. [PMID: 38939189 PMCID: PMC11208693 DOI: 10.3389/fmicb.2024.1334152] [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: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.
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Affiliation(s)
- Xi Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenguo Liu
- Department of Infectious Disease, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
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Pisharodi M. Portable and Air Conditioner-Based Bio-Protection Devices to Prevent Airborne Infections in Acute and Long-Term Healthcare Facilities, Public Gathering Places, Public Transportation, and Similar Entities. Cureus 2024; 16:e55950. [PMID: 38469370 PMCID: PMC10926937 DOI: 10.7759/cureus.55950] [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] [Accepted: 03/11/2024] [Indexed: 03/13/2024] Open
Abstract
The nature in which the coronavirus disease 2019 (COVID-19) pandemic started and spread all over the world has surprised and shocked experts and the general population alike. This has brought out a worldwide desire and serious efforts to prevent, or at least reduce, the severity of another airborne viral infection and protect individuals gathering for various reasons. Toward this main purpose, a novel method to disinfect the air, using graded, predictable, safe, and reliable dosage of ultraviolet C (UVC), with specially designed devices, is described here. Individuals exclusively breathing this disinfected air can prevent infection, thus destroying the airborne virus or any other pathogens outside the human body to prevent acute and chronic damage to the organs and provide a sense of security to congregate, use public transport, and be protected in acute and long-term healthcare facilities. The study involved designing and testing a unit with one UVC chamber and another unit with six UVC chambers both enclosed in UVC-opaque housings that could be used to destroy airborne pathogens. Wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used as a representative pathogen. The virus was fed into these units and in both units, the virus was destroyed to undetectable levels. Such disinfected air can be made available for individuals to breathe at an individual and a community level. The two units that were studied were able to destroy the SARS-CoV-2 virus completely in UVC-opaque housings, making them safe for human use. By employing the air to bring the virus to the UVC, the problem of the virus getting protected behind structures was avoided. The individuals get to breathe totally disinfected air through a mask or a ventilator. To protect individuals who are unable or unwilling to use these units meant for individual use, the same principle can be expanded for use with air conditioners to provide community protection. It is envisaged that this method can prevent airborne infections from turning into pandemics and is a clear example of advocating prevention, rather than treatment. These units are expandable and the UVC dosage to the pathogen can be adjusted and predictable, thereby making it a standard technique to study the dosage needed to inactivate different pathogens.
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3
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Boggiano-Ayo T, Palacios-Oliva J, Lozada-Chang S, Relova-Hernandez E, Gomez-Perez J, Oliva G, Hernandez L, Bueno-Soler A, Montes de Oca D, Mora O, Machado-Santisteban R, Perez-Martinez D, Perez-Masson B, Cabrera Infante Y, Calzadilla-Rosado L, Ramirez Y, Aymed-Garcia J, Ruiz-Ramirez I, Romero Y, Gomez T, Espinosa LA, Gonzalez LJ, Cabrales A, Guirola O, de la Luz KR, Pi-Estopiñan F, Sanchez-Ramirez B, Garcia-Rivera D, Valdes-Balbin Y, Rojas G, Leon-Monzon K, Ojito-Magaz E, Hardy E. Development of a scalable single process for producing SARS-CoV-2 RBD monomer and dimer vaccine antigens. Front Bioeng Biotechnol 2023; 11:1287551. [PMID: 38050488 PMCID: PMC10693982 DOI: 10.3389/fbioe.2023.1287551] [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: 09/01/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
We have developed a single process for producing two key COVID-19 vaccine antigens: SARS-CoV-2 receptor binding domain (RBD) monomer and dimer. These antigens are featured in various COVID-19 vaccine formats, including SOBERANA 01 and the licensed SOBERANA 02, and SOBERANA Plus. Our approach involves expressing RBD (319-541)-His6 in Chinese hamster ovary (CHO)-K1 cells, generating and characterizing oligoclones, and selecting the best RBD-producing clones. Critical parameters such as copper supplementation in the culture medium and cell viability influenced the yield of RBD dimer. The purification of RBD involved standard immobilized metal ion affinity chromatography (IMAC), ion exchange chromatography, and size exclusion chromatography. Our findings suggest that copper can improve IMAC performance. Efficient RBD production was achieved using small-scale bioreactor cell culture (2 L). The two RBD forms - monomeric and dimeric RBD - were also produced on a large scale (500 L). This study represents the first large-scale application of perfusion culture for the production of RBD antigens. We conducted a thorough analysis of the purified RBD antigens, which encompassed primary structure, protein integrity, N-glycosylation, size, purity, secondary and tertiary structures, isoform composition, hydrophobicity, and long-term stability. Additionally, we investigated RBD-ACE2 interactions, in vitro ACE2 recognition of RBD, and the immunogenicity of RBD antigens in mice. We have determined that both the monomeric and dimeric RBD antigens possess the necessary quality attributes for vaccine production. By enabling the customizable production of both RBD forms, this unified manufacturing process provides the required flexibility to adapt rapidly to the ever-changing demands of emerging SARS-CoV-2 variants and different COVID-19 vaccine platforms.
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Affiliation(s)
- Tammy Boggiano-Ayo
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | | | | | - Gonzalo Oliva
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Alexi Bueno-Soler
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Osvaldo Mora
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Dayana Perez-Martinez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Beatriz Perez-Masson
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Yaima Ramirez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Judey Aymed-Garcia
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Yamile Romero
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Tania Gomez
- Quality Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Annia Cabrales
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | | | | | | | | | | | - Gertrudis Rojas
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Kalet Leon-Monzon
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Eugenio Hardy
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
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4
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Zhou H, Xie P, Qiu M, Dong S, Xia X, Yang Z, Yuan Y, Shen L. Arbidol increases the survival rate by mitigating inflammation in suckling mice infected with human coronavirus OC43 virus. J Med Virol 2023; 95:e29052. [PMID: 37650132 DOI: 10.1002/jmv.29052] [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: 03/09/2023] [Revised: 07/20/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) often causes common cold and is able to neuroinvasive, but it can also induce lower respiratory tract infections (LRTI) especially in children and the elderly adults with underlying diseases. HCoV-OC43 infections currently have no approved antiviral treatment. Arbidol (ARB) is a broad-spectrum antiviral and is an antiviral medication for the treatment of influenza used in Russia and China. Due to its multiple mechanisms of action, such as inhibition of viral fusion and entry, immunomodulation, and modulation of host cell signaling pathways, ARB has the potential to be an effective treatment option for viral infections. Therefore, the study aims to investigate the activities of ARB against HCoV-OC43 infections. Suckling mice were infected with HCoV-OC43 and treated with ARB (50, 25 and 12.5 mg/kg/d) by gavage once daily for 4 days. the survival rates and body weight were recorded, the viral titer was measured by real-time quantitative polymerase chain reaction, cytokine levels were measured by Bio-Plex assays. Histopathological changes of the lungs and brain were analyzed. Our results show ARB increased the survival rate, reduced viral copy numbers in the lung, mitigated pro-inflammatory cytokine production, and improved brain and lung histopathology significantly without any significant toxicity or side effects in vivo. Our results suggest ARB could be a promising approach for the prevention and treatment of HCoV-OC43 while further studies are needed to address these possibilities and the underlying mechanism.
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Affiliation(s)
- Hongxia Zhou
- Department of Critical Care Medicine, Dongguan Institute of Respiratory and Critical Care Medicine, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Southern Medical University, Dongguan, China
| | - Peifang Xie
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Minshan Qiu
- Department of Critical Care Medicine, Dongguan Institute of Respiratory and Critical Care Medicine, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Southern Medical University, Dongguan, China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yaoqin Yuan
- Dongguan Institute of Respiratory and Critical Care Medicine, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Southern Medical University, Dongguan, China
| | - Lihan Shen
- Department of Critical Care Medicine, Dongguan Institute of Respiratory and Critical Care Medicine, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Southern Medical University, Dongguan, China
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5
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Xue S, Xu W, Wang L, Wang X, Duan Q, Calcul L, Wang S, Liu W, Sun X, Lu L, Jiang S, Cai J. An HR2-Mimicking Sulfonyl-γ-AApeptide Is a Potent Pan-coronavirus Fusion Inhibitor with Strong Blood-Brain Barrier Permeability, Long Half-Life, and Promising Oral Bioavailability. ACS CENTRAL SCIENCE 2023; 9:1046-1058. [PMID: 37252367 PMCID: PMC10184535 DOI: 10.1021/acscentsci.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 05/31/2023]
Abstract
Neutralizing antibodies and fusion inhibitory peptides have the potential required to combat the global pandemic caused by SARS-CoV-2 and its variants. However, the lack of oral bioavailability and enzymatic susceptibility limited their application, necessitating the development of novel pan-CoV fusion inhibitors. Herein we report a series of helical peptidomimetics, d-sulfonyl-γ-AApeptides, which effectively mimic the key residues of heptad repeat 2 and interact with heptad repeat 1 in the SARS-CoV-2 S2 subunit, resulting in inhibiting SARS-CoV-2 spike protein-mediated fusion between virus and cell membranes. The leads also displayed broad-spectrum inhibitory activity against a panel of other human CoVs and showed strong potency in vitro and in vivo. Meanwhile, they also demonstrated complete resistance to proteolytic enzymes or human sera and exhibited extremely long half-life in vivo and highly promising oral bioavailability, delineating their potential as pan-CoV fusion inhibitors with the potential to combat SARS-CoV-2 and its variants.
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Affiliation(s)
- Songyi Xue
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Wei Xu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of
Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic
Microbes and Infection, Shanghai Institute of Infectious Disease and
Biosecurity, Fudan University, Shanghai 200433, China
| | - Lei Wang
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Xinling Wang
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of
Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic
Microbes and Infection, Shanghai Institute of Infectious Disease and
Biosecurity, Fudan University, Shanghai 200433, China
| | - Qianyu Duan
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of
Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic
Microbes and Infection, Shanghai Institute of Infectious Disease and
Biosecurity, Fudan University, Shanghai 200433, China
| | - Laurent Calcul
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Shaohui Wang
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
| | - Wenqi Liu
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Xingmin Sun
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
| | - Lu Lu
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of
Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic
Microbes and Infection, Shanghai Institute of Infectious Disease and
Biosecurity, Fudan University, Shanghai 200433, China
| | - Shibo Jiang
- Key
Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of
Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic
Microbes and Infection, Shanghai Institute of Infectious Disease and
Biosecurity, Fudan University, Shanghai 200433, China
| | - Jianfeng Cai
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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6
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Abouhajar F, Chaudhuri R, Valiulis SN, Stuart DD, Malinick AS, Xue M, Cheng Q. Label-Free Analysis of Binding and Inhibition of SARS-Cov-19 Spike Proteins to ACE2 Receptor with ACE2-Derived Peptides by Surface Plasmon Resonance. ACS APPLIED BIO MATERIALS 2023; 6:182-190. [PMID: 36550079 PMCID: PMC9797021 DOI: 10.1021/acsabm.2c00832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has been shown to enter and infect human cells via interactions between spike protein (S glycoprotein) and angiotensin-converting enzyme 2 (ACE2). As such, it may be possible to suppress the infection of the virus via the blocking of this binding interaction through the use of specific peptides that can mimic the human ACE 2 peptidase domain (PD) α 1-helix. Herein, we report the use of competitive assays along with surface plasmon resonance (SPR) to investigate the effect of peptide sequence and length on spike protein inhibition. The characterization of these binding interactions helps us understand the mechanisms behind peptide-based viral blockage and develop SPR methodologies to quickly screen disease inhibitors. This work not only helps further our understanding of the important biological interactions involved in viral inhibition but will also aid in future studies that focus on the development of therapeutics and drug options. Two peptides of different sequence lengths, [30-42] and [22-44], based on the α 1-helix of ACE2 PD were selected for this fundamental investigation. In addition to characterizing their inhibitory behavior, we also identified the critical amino acid residues of the RBD/ACE2-derived peptides by combining experimental results and molecular docking modeling. While both investigated peptides were found to effectively block the RBD residues known to bind to ACE2 PD, our investigation showed that the shorter peptide was able to reach a maximal inhibition at lower concentrations. These inhibition results matched with molecular docking models and indicated that peptide length and composition are key in the development of an effective peptide for inhibiting biophysical interactions. The work presented here emphasizes the importance of inhibition screening and modeling, as longer peptides are not always more effective.
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Affiliation(s)
- Fatimah Abouhajar
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rohit Chaudhuri
- Department of Chemistry, University of California, Riverside, CA 92521
| | | | - Daniel D. Stuart
- Department of Chemistry, University of California, Riverside, CA 92521
| | | | - Min Xue
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, CA 92521
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7
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An engineered SARS-CoV-2 receptor-binding domain produced in Pichia pastoris as a candidate vaccine antigen. N Biotechnol 2022; 72:11-21. [PMID: 35953030 PMCID: PMC9359770 DOI: 10.1016/j.nbt.2022.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 06/26/2022] [Accepted: 08/07/2022] [Indexed: 01/07/2023]
Abstract
Developing affordable and easily manufactured SARS-CoV-2 vaccines will be essential to achieve worldwide vaccine coverage and long-term control of the COVID-19 pandemic. Here the development is reported of a vaccine based on the SARS-CoV-2 receptor-binding domain (RBD), produced in the yeast Pichia pastoris. The RBD was modified by adding flexible N- and C-terminal amino acid extensions that modulate protein/protein interactions and facilitate protein purification. A fed-batch methanol fermentation with a yeast extract-based culture medium in a 50 L fermenter and an immobilized metal ion affinity chromatography-based downstream purification process yielded 30-40 mg/L of RBD. Correct folding of the purified protein was demonstrated by mass spectrometry, circular dichroism, and determinations of binding affinity to the angiotensin-converting enzyme 2 (ACE2) receptor. The RBD antigen also exhibited high reactivity with sera from convalescent individuals and Pfizer-BioNTech or Sputnik V vaccinees. Immunization of mice and non-human primates with 50 µg of the recombinant RBD adjuvanted with alum induced high levels of binding antibodies as assessed by ELISA with RBD produced in HEK293T cells, and which inhibited RBD binding to ACE2 and neutralized infection of VeroE6 cells by SARS-CoV-2. Additionally, the RBD protein stimulated IFNγ, IL-2, IL-6, IL-4 and TNFα secretion in splenocytes and lung CD3+-enriched cells of immunized mice. The data suggest that the RBD recombinant protein produced in yeast P. pastoris is suitable as a vaccine candidate against COVID-19.
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8
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Ávalos I, Lao T, Rodríguez EM, Zamora Y, Rodríguez A, Ramón A, Lemos G, Cabrales A, Bequet-Romero M, Casillas D, Andújar I, Espinosa LA, González LJ, Alvarez Y, Carpio Y, Estrada MP. Chimeric Antigen by the Fusion of SARS-CoV-2 Receptor Binding Domain with the Extracellular Domain of Human CD154: A Promising Improved Vaccine Candidate. Vaccines (Basel) 2022; 10:897. [PMID: 35746505 PMCID: PMC9228316 DOI: 10.3390/vaccines10060897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
COVID-19 is a respiratory viral disease caused by a new coronavirus called SARS-CoV-2. This disease has spread rapidly worldwide with a high rate of morbidity and mortality. The receptor-binding domain (RBD) of protein spike (S) mediates the attachment of the virus to the host's cellular receptor. The RBD domain constitutes a very attractive target for subunit vaccine development due to its ability to induce a neutralizing antibody response against the virus. With the aim of boosting the immunogenicity of RBD, it was fused to the extracellular domain of CD154, an immune system modulator molecule. To obtain the chimeric protein, stable transduction of HEK-293 was carried out with recombinant lentivirus and polyclonal populations and cell clones were obtained. RBD-CD was purified from culture supernatant and further characterized by several techniques. RBD-CD immunogenicity evaluated in mice and non-human primates (NHP) indicated that recombinant protein was able to induce a specific and high IgG response after two doses. NHP sera also neutralize SARS-CoV-2 infection of Vero E6 cells. RBD-CD could improve the current vaccines against COVID-19, based in the enhancement of the host humoral and cellular response. Further experiments are necessary to confirm the utility of RBD-CD as a prophylactic vaccine and/or booster purpose.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yamila Carpio
- Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/158 y 190, Havana 10600, Cuba; (I.Á.); (T.L.); (E.M.R.); (Y.Z.); (A.R.); (A.R.); (G.L.); (A.C.); (M.B.-R.); (D.C.); (I.A.); (L.A.E.); (L.J.G.); (Y.A.)
| | - Mario Pablo Estrada
- Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/158 y 190, Havana 10600, Cuba; (I.Á.); (T.L.); (E.M.R.); (Y.Z.); (A.R.); (A.R.); (G.L.); (A.C.); (M.B.-R.); (D.C.); (I.A.); (L.A.E.); (L.J.G.); (Y.A.)
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9
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Lazo L, Bequet-Romero M, Lemos G, Musacchio A, Cabrales A, Bruno AJ, Ariel Espinosa L, Saloheimo M, Vitikainen M, Hernández A, Emalfarb M, Tchelet R, Suzarte E, Guillén G. A recombinant SARS-CoV-2 receptor-binding domain expressed in an engineered fungal strain of Thermothelomyces heterothallica induces a functional immune response in mice. Vaccine 2022; 40:1162-1169. [PMID: 35078661 PMCID: PMC8783260 DOI: 10.1016/j.vaccine.2022.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 12/15/2022]
Abstract
Since the beginning of the COVID-19 pandemic, the development of effective vaccines against this pathogen has been a priority for the scientific community. Several strategies have been developed including vaccines based on recombinant viral protein fragments. The receptor-binding domain (RBD) in the S1 subunit of S protein has been considered one of the main targets of neutralizing antibodies. In this study we assess the potential of a vaccine formulation based on the recombinant RBD domain of SARS-CoV-2 expressed in the thermophilic filamentous fungal strain Thermothelomyces heterothallica and the hepatitis B virus (HBV) core protein. Functional humoral and cellular immune responses were detected in mice. To our knowledge, this is the first report on the immune evaluation of a biomedical product obtained in the fungal strain T. heterothallica. These results together with the intrinsic advantages of this expression platform support its use for the development of biotechnology products for medical purpose.
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10
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Sypabekova M, Tosi D, Vangelista L. Perspectives on Assembling Coronavirus Spikes on Fiber Optics to Reveal Broadly Recognizing Antibodies and Generate a Universal Coronavirus Detector. Front Bioeng Biotechnol 2021; 9:637715. [PMID: 34900951 PMCID: PMC8661133 DOI: 10.3389/fbioe.2021.637715] [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: 12/04/2020] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
In time of COVID-19 biological detection technologies are of crucial relevance. We propose here the use of state of the art optical fiber biosensors to address two aspects of the fight against SARS-CoV-2 and other pandemic human coronaviruses (HCoVs). Fiber optic biosensors functionalized with HCoV spikes could be used to discover broadly neutralizing antibodies (bnAbs) effective against known HCoVs (SARS-CoV, MERS-CoV and SARS-CoV-2) and likely future ones. In turn, identified bnAbs, once immobilized onto fiber optic biosensors, should be capable to detect HCoVs as diagnostic and environmental sensing devices. The therapeutic and preventative value of bnAbs is immense as they can be used for passive immunization and for the educated development of a universal vaccine (active immunization). Hence, HCoV bnAbs represent an extremely important resource for future preparedness against coronavirus-borne pandemics. Furthermore, the assembly of bnAb-based biosensors constitutes an innovative approach to counteract public health threats, as it bears diagnostic competence additional to environmental detection of a range of pandemic strains. This concept can be extended to different pandemic viruses, as well as bio-warfare threats that entail existing, emerging and extinct viruses (e.g., the smallpox-causing Variola virus). We report here the forefront fiber optic biosensor technology that could be implemented to achieve these aims.
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Affiliation(s)
| | - Daniele Tosi
- School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan.,Laboratory of Biosensors and Bioinstruments, National Laboratory Astana, Nur-Sultan, Kazakhstan
| | - Luca Vangelista
- School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
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11
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Han F, Liu Y, Mo M, Chen J, Wang C, Yang Y, Wu J. Current treatment strategies for COVID‑19 (Review). Mol Med Rep 2021; 24:858. [PMID: 34664677 PMCID: PMC8548951 DOI: 10.3892/mmr.2021.12498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022] Open
Abstract
The spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) emerged suddenly at the end of 2019 and the disease came to be known as coronavirus disease 2019 (COVID‑19). To date, there is no specific therapy established to treat COVID‑19. Identifying effective treatments is urgently required to treat patients and stop the transmission of SARS‑CoV‑2 in humans. For the present review, >100 publications on therapeutic agents for COVID‑19, including in vitro and in vivo animal studies, case reports, retrospective analyses and meta‑analyses were retrieved from PubMed and analyzed, and promising therapeutic agents that may be used to combat SARS‑CoV‑2 infection were highlighted. Since the outbreak of COVID‑19, different drugs have been repurposed for its treatment. Existing drugs, including chloroquine (CQ), its derivative hydroxychloroquine (HCQ), remdesivir and nucleoside analogues, monoclonal antibodies, convalescent plasma, Chinese herbal medicine and natural compounds for treating COVID‑19 evaluated in experimental and clinical studies were discussed. Although early clinical studies suggested that CQ/HCQ produces antiviral action, later research indicated certain controversy regarding their use for treating COVID‑19. The molecular mechanisms of these therapeutic agents against SARS‑CoV2 have been investigated, including inhibition of viral interactions with angiotensin‑converting enzyme 2 receptors in human cells, viral RNA‑dependent RNA polymerase, RNA replication and the packaging of viral particles. Potent therapeutic options were reviewed and future challenges to accelerate the development of novel therapeutic agents to treat and prevent COVID‑19 were acknowledged.
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Affiliation(s)
- Fabin Han
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Laboratory for Stem Cell and Regenerative Medicine, Institute for Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong 252000, P.R. China
| | - Yanming Liu
- Laboratory for Stem Cell and Regenerative Medicine, Institute for Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong 252000, P.R. China
| | - Mei Mo
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Juanli Chen
- Laboratory for Stem Cell and Regenerative Medicine, Institute for Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong 252000, P.R. China
| | - Cheng Wang
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Department of Research and Development, Shandong Meijia Therapeutic Biotechnology Co., Ltd., Jinan, Shandong 250100, P.R. China
| | - Yong Yang
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Jibiao Wu
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
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12
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Haynes WA, Kamath K, Bozekowski J, Baum-Jones E, Campbell M, Casanovas-Massana A, Daugherty PS, Dela Cruz CS, Dhal A, Farhadian SF, Fitzgibbons L, Fournier J, Jhatro M, Jordan G, Klein J, Lucas C, Kessler D, Luchsinger LL, Martinez B, Catherine Muenker M, Pischel L, Reifert J, Sawyer JR, Waitz R, Wunder EA, Zhang M, Iwasaki A, Ko A, Shon JC. High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. Commun Biol 2021; 4:1317. [PMID: 34811480 PMCID: PMC8608966 DOI: 10.1038/s42003-021-02835-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally infected patients can guide the development of effective vaccines and therapies. Since traditional epitope identification tools are dependent upon pre-defined peptide sequences, they are not readily adaptable to diverse viral proteomes. The Serum Epitope Repertoire Analysis (SERA) platform leverages a high diversity random bacterial display library to identify proteome-independent epitope binding specificities which are then analyzed in the context of organisms of interest. When evaluating immune response in the context of SARS-CoV-2, we identify dominant epitope regions and motifs which demonstrate potential to classify mild from severe disease and relate to neutralization activity. We highlight SARS-CoV-2 epitopes that are cross-reactive with other coronaviruses and demonstrate decreased epitope signal for mutant SARS-CoV-2 strains. Collectively, the evolution of SARS-CoV-2 mutants towards reduced antibody response highlight the importance of data-driven development of the vaccines and therapies to treat COVID-19.
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Affiliation(s)
| | | | | | | | - Melissa Campbell
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Charles S Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Shelli F Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | - John Fournier
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren Pischel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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13
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Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG. Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem 2021; 297:101175. [PMID: 34499924 PMCID: PMC8421091 DOI: 10.1016/j.jbc.2021.101175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.
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Affiliation(s)
- Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Lucas A Defelipe
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lucio Aliperti
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Christian Löw
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María García-Alai
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Ignacio E Sánchez
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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14
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Bojadzic D, Alcazar O, Chen J, Chuang ST, Capcha JMC, Shehadeh LA, Buchwald P. Small-Molecule Inhibitors of the Coronavirus Spike: ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2. ACS Infect Dis 2021; 7:1519-1534. [PMID: 33979123 PMCID: PMC8130611 DOI: 10.1021/acsinfecdis.1c00070] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and human ACE2 (hACE2), which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than that with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable/less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound library focused around the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel druglike compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50's of 0.2-3.0 μM), whereas control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs of interest identified here bind SARS-CoV-2-S and not hACE2. While dyes seemed to be promiscuous inhibitors, DRI-C23041 showed some selectivity and inhibited the entry of two different SARS-CoV-2-S expressing pseudoviruses into hACE2-expressing cells in a concentration-dependent manner with low micromolar IC50's (6-7 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for SARS-CoV-2 attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.
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Affiliation(s)
- Damir Bojadzic
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Oscar Alcazar
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jinshui Chen
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Sung-Ting Chuang
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jose M. Condor Capcha
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
| | - Lina A. Shehadeh
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miami, Florida, USA
| | - Peter Buchwald
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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15
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Moscato G, Mazzetti P, Lucenteforte E, Rosellini A, Cara A, Quaranta P, Mainardi V, Villa P, Focosi D, Lanza M, Bianco I, Mazzoni A, Falcone M, Menichetti F, Maggi F, Lai M, Freer G, Pistello M. Assessment of automated high-throughput serological assays for prediction of high-titer SARS-CoV-2 neutralizing antibody. JOURNAL OF CLINICAL VIROLOGY PLUS 2021; 1:100016. [PMID: 35262004 PMCID: PMC8093006 DOI: 10.1016/j.jcvp.2021.100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/08/2021] [Accepted: 04/20/2021] [Indexed: 12/28/2022] Open
Abstract
COVID19 convalescent patient plasma units with high titer neutralizing antibody can be used to treat patients with severe disease. Therefore, in order to select suitable donors, neutralizing antibody titer against SARS CoV-2 needs to be determined. Because the neutralization assay is highly demanding from several points of view, a pre-selection of sera would be desirable to minimize the number of sera to be tested. In this study, a total of 140 serum samples that had been titrated for SARS-CoV-2 neutralizing antibody by microneutralization assay were also tested for the presence of anti-SARS-CoV2 antibody using 5 different tests: Architect® immunoassay (Abbott Diagnostics), detecting IgG against the nucleocapsid protein, LIAISON XL® (Diasorin) detecting IgG against a recombinant form of the S1/S2 subunits of the spike protein, VITROS® (Ortho Clinical Diagnostics), detecting IgG against a recombinant form of the spike protein, and ELISA (Euroimmun AG), detecting IgA or IgG against a recombinant form of the S1 subunit. To determine which immunoassay had the highest chance to detect sera with neutralizing antibodies above a certain threshold, we compared the results obtained from the five immunoassays with the titers obtained by microneutralization assay by linear regression analysis and by using receiver operating characteristic curve and Youden's index. Our results indicate that the most suitable method to predict sera with high Nab titer is Euroimmun® IgG, followed closely by Ortho VITROS® Anti-SARS-CoV-2 IgG.
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Affiliation(s)
| | - Paola Mazzetti
- Virology Unit, Pisa University Hospital, Pisa, Italy
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
| | - Ersilia Lucenteforte
- Department of Experimental and Clinical Medicine, University of Pisa, Pisa, Italy
| | | | - Alice Cara
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | - Paola Quaranta
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
| | | | - Pietro Villa
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Maria Lanza
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Irene Bianco
- Transfusion Medicine and Transplant Biology, Pisa University Hospital, Pisa, Italy
| | - Alessandro Mazzoni
- Transfusion Medicine and Transplant Biology, Pisa University Hospital, Pisa, Italy
| | - Marco Falcone
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesco Menichetti
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Fabrizio Maggi
- Virology Unit, Pisa University Hospital, Pisa, Italy
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
| | - Michele Lai
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
| | - Giulia Freer
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
| | - Mauro Pistello
- Virology Unit, Pisa University Hospital, Pisa, Italy
- Retrovirus Center, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via del Brennero 2, Pisa I-56127, Italy
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16
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Costanzo M, De Giglio MAR, Roviello GN. Anti-Coronavirus Vaccines: Past Investigations on SARS-CoV-1 and MERS-CoV, the Approved Vaccines from BioNTech/Pfizer, Moderna, Oxford/AstraZeneca and others under Development Against SARS-CoV-2 Infection. Curr Med Chem 2021; 29:4-18. [PMID: 34355678 DOI: 10.2174/0929867328666210521164809] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 11/22/2022]
Abstract
The aim of this review article is to summarize the knowledge available to date on prophylaxis achievements to fight against Coronavirus. This work will give an overview of what is reported in the most recent literature on vaccines (under investigation or already developed like BNT162b2, mRNA-1273, and ChAdOx1-S) effective against the most pathogenic Coronaviruses (SARS-CoV-1, MERS-CoV-1, and SARS-CoV-2), with of course particular attention paid to those under development or already in use to combat the current COVID-19 (COronaVIrus Disease 19) pandemic. Our main objective is to make a contribution to the comprehension, additionally at a molecular level, of what is currently ready for anti-SARS-CoV-2 prophylactic intervention, as well as to provide the reader with an overall picture of the most innovative approaches for the development of vaccines that could be of general utility in the fight against the most pathogenic Coronaviruses.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples 'Federico II', Via S. Pansini 5, I-80131 Naples, Italy
| | | | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16; I-80134 Naples, Italy
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17
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Ashraf MU, Sharif S, Ahmad MU, Zahid MN, Mukhtar H. A review on clinical, pathological characteristics and drug designing for COVID-19. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1080/25765299.2020.1836812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Muhammad Usama Ashraf
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sundas Sharif
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Muhammad Usman Ahmad
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Muhammad Nauman Zahid
- Department of Biology, College of Science, University of Bahrain, Zallaq, Kingdom of Bahrain
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
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18
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Kruse RL, Huang Y, Smetana H, Gehrie EA, Amukele TK, Tobian AA, Mostafa HH, Wang ZZ. A rapid, point-of-care red blood cell agglutination assay detecting antibodies against SARS-CoV-2. Biochem Biophys Res Commun 2021; 553:165-171. [PMID: 33773139 PMCID: PMC7959259 DOI: 10.1016/j.bbrc.2021.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic has caused significant morbidity and mortality. There is an urgent need for serological tests to detect antibodies against SARS-CoV-2, which could be used to assess past infection, evaluate responses to vaccines in development, and determine individuals who may be protected from future infection. Current serological tests developed for SARS-CoV-2 rely on traditional technologies such as enzyme-linked immunosorbent assays (ELISA) and lateral flow assays, which have not scaled to meet the demand of hundreds of millions of antibody tests so far. Herein, we present an alternative method of antibody testing that depends on one protein reagent being added to patient serum/plasma or whole blood with direct, visual readout. Two novel fusion proteins, RBD-2E8 and B6-CH1-RBD, were designed to bind red blood cells (RBCs) via a single-chain variable fragment (scFv), thereby displaying the receptor-binding domain (RBD) of SARS-CoV-2 spike protein on the surface of RBCs. Mixing mammalian-derived RBD-2E8 and B6-CH1-RBD with convalescent COVID-19 patient serum and RBCs led to visible hemagglutination, indicating the presence of antibodies against SARS-CoV-2 RBD. B6-CH1-RBD made in bacteria was not as effective in inducing agglutination, indicating better recognition of RBD epitopes from mammalian cells. Given that our hemagglutination test uses methods routinely used in hospital clinical labs across the world for blood typing, we anticipate the test can be rapidly deployed at minimal cost. We anticipate our hemagglutination assay may find extensive use in low-resource settings for detecting SARS-CoV-2 antibodies.
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Affiliation(s)
- Robert L. Kruse
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Corresponding author. Carnegie Building, Room 401, Johns Hopkins Hospital, 600N Wolfe St, Baltimore, MD, 21287, USA
| | - Yuting Huang
- Department of Medicine, University of Maryland Medical Center Midtown Campus, Baltimore, MD, USA,Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heather Smetana
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eric A. Gehrie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Timothy K. Amukele
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heba H. Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zack Z. Wang
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Corresponding author
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19
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Li C, Tian X, Jia X, Wan J, Lu L, Jiang S, Lan F, Lu Y, Wu Y, Ying T. The impact of receptor-binding domain natural mutations on antibody recognition of SARS-CoV-2. Signal Transduct Target Ther 2021; 6:132. [PMID: 33758169 PMCID: PMC7985591 DOI: 10.1038/s41392-021-00536-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Affiliation(s)
- Cheng Li
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaolong Tian
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaodong Jia
- Department of Comprehensive Liver Cancer, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jinkai Wan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lu Lu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shibo Jiang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yinying Lu
- Department of Comprehensive Liver Cancer, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China.
| | - Yanling Wu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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20
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Obajuluwa AO, Okiki PA, Obajuluwa TM, Afolabi OB. In-silico nucleotide and protein analyses of S-gene region in selected zoonotic coronaviruses reveal conserved domains and evolutionary emergence with trajectory course of viral entry from SARS-CoV-2 genomic data. Pan Afr Med J 2021; 37:285. [PMID: 33654512 PMCID: PMC7896521 DOI: 10.11604/pamj.2020.37.285.24663] [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: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 11/24/2022] Open
Abstract
Introduction the recent zoonotic coronavirus virus outbreak of a novel type (COVID-19) has necessitated the adequate understanding of the evolutionary pathway of zoonotic viruses which adversely affects human populations for therapeutic constructs to combat the pandemic now and in the future. Methods we analyzed conserved domains of the severe acute respiratory coronavirus 2 (SARS-CoV-2) for possible targets of viral entry inhibition in host cells, evolutionary relationship of human coronavirus (229E) and zoonotic coronaviruses with SARS-CoV-2 as well as evolutionary relationship between selected SARS-CoV-2 genomic data. Results conserved domains with antagonistic action on host innate antiviral cellular mechanisms in SARS-CoV-2 include nsp 11, nsp 13 etc. Also, multiple sequence alignments of the spike (S) gene protein of selected candidate zoonotic coronaviruses alongside the S gene protein of the SARS-CoV-2 revealed closest evolutionary relationship (95.6%) with pangolin coronaviruses (S) gene. Clades formed between Wuhan SARS-CoV-2 phylogeny data and five others suggests viral entry trajectory while revealing genomic and protein SARS-CoV-2 data from Philippines as early ancestors. Conclusion phylogeny of SARS-CoV-2 genomic data suggests profiling in diverse populations with and without the outbreak alongside migration history and racial background for mutation tracking and dating of viral subtype divergence which is essential for effective management of present and future zoonotic coronavirus outbreaks.
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Affiliation(s)
- Adejoke Olukayode Obajuluwa
- Biotechnology Unit, Department of Biological Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
| | - Pius Abimbola Okiki
- Biotechnology Unit, Department of Biological Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
| | | | - Olakunle Bamikole Afolabi
- Biochemistry Unit, Department of Chemical Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
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21
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Molaei S, Dadkhah M, Asghariazar V, Karami C, Safarzadeh E. The immune response and immune evasion characteristics in SARS-CoV, MERS-CoV, and SARS-CoV-2: Vaccine design strategies. Int Immunopharmacol 2021; 92:107051. [PMID: 33429331 PMCID: PMC7522676 DOI: 10.1016/j.intimp.2020.107051] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 01/25/2023]
Abstract
The worldwide outbreak of SARS-CoV-2, severe acute respiratory syndrome coronavirus 2 as a novel human coronavirus, was the worrying news at the beginning of 2020. Since its emergence complicated more than 870,000 individuals and led to more than 43,000 deaths worldwide. Considering to the potential threat of a pandemic and transmission severity of it, there is an urgent need to evaluate and realize this new virus's structure and behavior and the immunopathology of this disease to find potential therapeutic protocols and to design and develop effective vaccines. This disease is able to agitate the response of the immune system in the infected patients, so ARDS, as a common consequence of immunopathological events for infections with Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2, could be the main reason for death. Here, we summarized the immune response and immune evasion characteristics in SARS-CoV, MERS-CoV, and SARS-CoV-2 and therapeutic and prophylactic strategies with a focus on vaccine development and its challenges.
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Affiliation(s)
- Soheila Molaei
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, Iran; Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Masoomeh Dadkhah
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran; Department of Pharmacology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Chiman Karami
- Department of Microbiology, Parasitology, and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elham Safarzadeh
- Department of Microbiology, Parasitology, and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran.
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22
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Tompa DR, Immanuel A, Srikanth S, Kadhirvel S. Trends and strategies to combat viral infections: A review on FDA approved antiviral drugs. Int J Biol Macromol 2021; 172:524-541. [PMID: 33454328 PMCID: PMC8055758 DOI: 10.1016/j.ijbiomac.2021.01.076] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022]
Abstract
The infectious microscopic viruses invade living cells to reproduce themselves, and causes chronic infections such as HIV/AIDS, hepatitis B and C, flu, etc. in humans which may lead to death if not treated. Different strategies have been utilized to develop new and superior antiviral drugs to counter the viral infections. The FDA approval of HIV nucleoside reverse transcriptase inhibitor, zidovudine in 1987 boosted the development of antiviral agents against different viruses. Currently, there are a number of combination drugs developed against various viral infections to arrest the activity of same or different viral macromolecules at multiple stages of its life cycle; among which majority are targeted to interfere with the replication of viral genome. Besides these, other type of antiviral molecules includes entry inhibitors, integrase inhibitors, protease inhibitors, interferons, immunomodulators, etc. The antiviral drugs can be toxic to human cells, particularly in case of administration of combination drugs, and on the other hand viruses can grow resistant to the antiviral drugs. Furthermore, emergence of new viruses like Ebola, coronaviruses (SARS-CoV, SARS-CoV-2) emphasizes the need for more innovative strategies to develop better antiviral drugs to fight the existing and the emerging viral infections. Hence, we reviewed the strategic enhancements in developing antiviral drugs for the treatment of different viral infections over the years.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Aruldoss Immanuel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Srimari Srikanth
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India.
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23
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Zhou D, Tian X, Qi R, Peng C, Zhang W. Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: Implications for vaccination and antibody therapeutics. Glycobiology 2021; 31:69-80. [PMID: 32518941 PMCID: PMC7313968 DOI: 10.1093/glycob/cwaa052] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins. The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown. Glycosylation by insect cells differs from the native form produced in human cells, but insect cell-derived influenza vaccines have been approved by the US Food and Drug Administration. In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1-4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites. We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures and available antibodies that bind to SARS-CoV-1. All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans. MS/MS fragmentation clearly established the glycopeptide identities. Electron densities of glycans cover most of the spike receptor-binding domain of SARS-CoV-2, except YQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ, similar to a region FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ in SARS-CoV-1. Other surface-exposed domains include those located on central helix, connecting region, heptad repeats and N-terminal domain. Because the majority of antibody paratopes bind to the peptide portion with or without sugar modification, we propose a snake-catching model for predicted paratopes: a minimal length of peptide is first clamped by a paratope and sugar modifications close to the peptide either strengthen or do not hinder the binding.
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Affiliation(s)
- Dapeng Zhou
- Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China.,Shanghai Pudong New Area Mental Health Center affiliated with Tongji University School of Medicine, 165 Sanlin Road, Shanghai 200124, China
| | - Xiaoxu Tian
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, 333 Haike Road, Shanghai 201210, China
| | - Ruibing Qi
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, 518 Ziyue Road, Shanghai 200241, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, 333 Haike Road, Shanghai 201210, China
| | - Wen Zhang
- Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, 200433 Gongwei Road, Shanghai, China.,Department of Systems Biology for Medicine, Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
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24
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Ward D, Higgins M, Phelan JE, Hibberd ML, Campino S, Clark TG. An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Genome Med 2021; 13:4. [PMID: 33413610 PMCID: PMC7790334 DOI: 10.1186/s13073-020-00822-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online "immuno-analytics" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).
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Affiliation(s)
- Daniel Ward
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Matthew Higgins
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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25
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Hassert M, Geerling E, Stone ET, Steffen TL, Feldman MS, Dickson AL, Class J, Richner JM, Brien JD, Pinto AK. mRNA induced expression of human angiotensin-converting enzyme 2 in mice for the study of the adaptive immune response to severe acute respiratory syndrome coronavirus 2. PLoS Pathog 2020; 16:e1009163. [PMID: 33326500 PMCID: PMC7773324 DOI: 10.1371/journal.ppat.1009163] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/30/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic. Critical to the rapid evaluation of vaccines and antivirals against SARS-CoV-2 is the development of tractable animal models to understand the adaptive immune response to the virus. To this end, the use of common laboratory strains of mice is hindered by significant divergence of the angiotensin-converting enzyme 2 (ACE2), which is the receptor required for entry of SARS-CoV-2. In the current study, we designed and utilized an mRNA-based transfection system to induce expression of the hACE2 receptor in order to confer entry of SARS-CoV-2 in otherwise non-permissive cells. By employing this expression system in an in vivo setting, we were able to interrogate the adaptive immune response to SARS-CoV-2 in type 1 interferon receptor deficient mice. In doing so, we showed that the T cell response to SARS-CoV-2 is enhanced when hACE2 is expressed during infection. Moreover, we demonstrated that these responses are preserved in memory and are boosted upon secondary infection. Importantly, using this system, we functionally identified the CD4+ and CD8+ structural peptide epitopes targeted during SARS-CoV-2 infection in H2b restricted mice and confirmed their existence in an established model of SARS-CoV-2 pathogenesis. We demonstrated that, identical to what has been seen in humans, the antigen-specific CD8+ T cells in mice primarily target peptides of the spike and membrane proteins, while the antigen-specific CD4+ T cells target peptides of the nucleocapsid, membrane, and spike proteins. As the focus of the immune response in mice is highly similar to that of the humans, the identification of functional murine SARS-CoV-2-specific T cell epitopes provided in this study will be critical for evaluation of vaccine efficacy in murine models of SARS-CoV-2 infection.
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Affiliation(s)
- Mariah Hassert
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Tara L. Steffen
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Madi S. Feldman
- Department of Biomedical Engineering, Saint Louis University, St. Louis, Missouri, United States of America
| | - Alexandria L. Dickson
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Jacob Class
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - Justin M. Richner
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, St. Louis, Missouri, United States of America
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26
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Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A 2020; 117:28046-28055. [PMID: 33093202 PMCID: PMC7668070 DOI: 10.1073/pnas.2016093117] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2-pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.
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Affiliation(s)
- Anum Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Daniel Limonta
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Matthew A Nix
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Nicholas J Rettko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Shoshana Zha
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Rachel Yamin
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Kevin Kao
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Tom C Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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27
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Dasari CM, Bhukya R. Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104432. [PMID: 32592845 PMCID: PMC7314694 DOI: 10.1016/j.meegid.2020.104432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022]
Abstract
The genetic code contains information that impacts the efficiency and rate of translation. Translation elongation plays a crucial role in determining the composition of the proteome, errors within a protein contributes towards disease processes. It is important to analyze the novel coronavirus (2019-nCoV) at the codon level to find similarities and variations in hosts to compare with other human coronavirus (CoVs). This requires a comparative and comprehensive study of various human and zoonotic nature CoVs relating to codon usage bias, relative synonymous codon usage (RSCU), proportions of slow codons, and slow di-codons, the effective number of codons (ENC), mutation bias, codon adaptation index (CAI), and codon frequencies. In this work, seven different CoVs were analyzed to determine the protein synthesis rate and the adaptation of these viruses to the host cell. The result reveals that the proportions of slow codons and slow di-codons in human host of 2019-nCoV and SARS-CoV found to be similar and very less compared to the other five coronavirus types, which suggest that the 2019-nCoV and SARS-CoV have faster protein synthesis rate. Zoonotic CoVs have high RSCU and codon adaptation index than human CoVs which implies the high translation rate in zoonotic viruses. All CoVs have more AT% than GC% in genetic codon compositions. The average ENC values of seven CoVs ranged between 38.36 and 49.55, which implies the CoVs are highly conserved and are easily adapted to host cells. The mutation rate of 2019-nCoV is comparatively less than MERS-CoV and NL63 that shows an evidence for genetic diversity. Host-specific codon composition analysis portrays the relation between viral host sequences and the capability of novel virus replication in host cells. Moreover, the analysis provides useful measures for evaluating a virus-host adaptation, transmission potential of novel viruses, and thus contributes to the strategies of anti-viral drug design.
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Affiliation(s)
- Chandra Mohan Dasari
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
| | - Raju Bhukya
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
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28
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Khan N, Chen X, Geiger JD. Role of Endolysosomes in Severe Acute Respiratory Syndrome Coronavirus-2 Infection and Coronavirus Disease 2019 Pathogenesis: Implications for Potential Treatments. Front Pharmacol 2020; 11:595888. [PMID: 33324224 PMCID: PMC7723437 DOI: 10.3389/fphar.2020.595888] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an enveloped, single-stranded RNA virus. Humans infected with SARS-CoV-2 develop a disease known as coronavirus disease 2019 (COVID-19) with symptoms and consequences including acute respiratory distress syndrome (ARDS), cardiovascular disorders, and death. SARS-CoV-2 appears to infect cells by first binding viral spike proteins with host protein angiotensin-converting enzyme 2 (ACE2) receptors; the virus is endocytosed following priming by transmembrane protease serine 2 (TMPRSS2). The process of virus entry into endosomes and its release from endolysosomes are key features of enveloped viruses. Thus, it is important to focus attention on the role of endolysosomes in SARS-CoV-2 infection. Indeed, coronaviruses are now known to hijack endocytic machinery to enter cells such that they can deliver their genome at replication sites without initiating host detection and immunological responses. Hence, endolysosomes might be good targets for developing therapeutic strategies against coronaviruses. Here, we focus attention on the involvement of endolysosomes in SARS-CoV-2 infection and COVID-19 pathogenesis. Further, we explore endolysosome-based therapeutic strategies to restrict SARS-CoV-2 infection and COVID-19 pathogenesis.
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Affiliation(s)
| | | | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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29
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Dinnon KH, Leist SR, Schäfer A, Edwards CE, Martinez DR, Montgomery SA, West A, Yount BL, Hou YJ, Adams LE, Gully KL, Brown AJ, Huang E, Bryant MD, Choong IC, Glenn JS, Gralinski LE, Sheahan TP, Baric RS. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature 2020; 586:560-566. [PMID: 32854108 PMCID: PMC8034761 DOI: 10.1038/s41586-020-2708-8] [Citation(s) in RCA: 475] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Coronaviruses are prone to transmission to new host species, as recently demonstrated by the spread to humans of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic1. Small animal models that recapitulate SARS-CoV-2 disease are needed urgently for rapid evaluation of medical countermeasures2,3. SARS-CoV-2 cannot infect wild-type laboratory mice owing to inefficient interactions between the viral spike protein and the mouse orthologue of the human receptor, angiotensin-converting enzyme 2 (ACE2)4. Here we used reverse genetics5 to remodel the interaction between SARS-CoV-2 spike protein and mouse ACE2 and designed mouse-adapted SARS-CoV-2 (SARS-CoV-2 MA), a recombinant virus that can use mouse ACE2 for entry into cells. SARS-CoV-2 MA was able to replicate in the upper and lower airways of both young adult and aged BALB/c mice. SARS-CoV-2 MA caused more severe disease in aged mice, and exhibited more clinically relevant phenotypes than those seen in Hfh4-ACE2 transgenic mice, which express human ACE2 under the control of the Hfh4 (also known as Foxj1) promoter. We demonstrate the utility of this model using vaccine-challenge studies in immune-competent mice with native expression of mouse ACE2. Finally, we show that the clinical candidate interferon-λ1a (IFN-λ1a) potently inhibits SARS-CoV-2 replication in primary human airway epithelial cells in vitro-both prophylactic and therapeutic administration of IFN-λ1a diminished SARS-CoV-2 replication in mice. In summary, the mouse-adapted SARS-CoV-2 MA model demonstrates age-related disease pathogenesis and supports the clinical use of pegylated IFN-λ1a as a treatment for human COVID-196.
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MESH Headings
- Aging/immunology
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/drug therapy
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Disease Models, Animal
- Female
- Forkhead Transcription Factors/genetics
- Humans
- Interferon-alpha/administration & dosage
- Interferon-alpha/pharmacology
- Interferon-alpha/therapeutic use
- Interferons/administration & dosage
- Interferons/pharmacology
- Interferons/therapeutic use
- Interleukins/administration & dosage
- Interleukins/pharmacology
- Interleukins/therapeutic use
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Models, Molecular
- Pandemics/prevention & control
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/genetics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- SARS-CoV-2
- Viral Vaccines/immunology
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Affiliation(s)
- Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily E Adams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ariane J Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Huang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Jeffrey S Glenn
- Departments of Medicine and Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill, NC, USA.
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30
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Hassert M, Geerling E, Stone ET, Steffen TL, Dickson A, Feldman MS, Class J, Richner JM, Brien JD, Pinto AK. mRNA induced expression of human angiotensin-converting enzyme 2 in mice for the study of the adaptive immune response to severe acute respiratory syndrome coronavirus 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32793909 DOI: 10.1101/2020.08.07.241877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic resulting in nearly 20 million infections across the globe, as of August 2020. Critical to the rapid evaluation of vaccines and antivirals is the development of tractable animal models of infection. The use of common laboratory strains of mice to this end is hindered by significant divergence of the angiotensin-converting enzyme 2 (ACE2), which is the receptor required for entry of SARS-CoV-2. In the current study, we designed and utilized an mRNA-based transfection system to induce expression of the hACE2 receptor in order to confer entry of SARS-CoV-2 in otherwise non-permissive cells. By employing this expression system in an in vivo setting, we were able to interrogate the adaptive immune response to SARS-CoV-2 in type 1 interferon receptor deficient mice. In doing so, we showed that the T cell response to SARS-CoV-2 is enhanced when hACE2 is expressed during infection. Moreover, we demonstrated that these responses are preserved in memory and are boosted upon secondary infection. Interestingly, we did not observe an enhancement of SARS-CoV-2 specific antibody responses with hACE2 induction. Importantly, using this system, we functionally identified the CD4+ and CD8+ peptide epitopes targeted during SARS-CoV-2 infection in H2b restricted mice. Antigen-specific CD8+ T cells in mice of this MHC haplotype primarily target peptides of the spike and membrane proteins, while the antigen-specific CD4+ T cells target peptides of the nucleocapsid, membrane, and spike proteins. The functional identification of these T cell epitopes will be critical for evaluation of vaccine efficacy in murine models of SARS-CoV-2. The use of this tractable expression system has the potential to be used in other instances of emerging infections in which the rapid development of an animal model is hindered by a lack of host susceptibility factors.
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31
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Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Lim SA, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.31.231746. [PMID: 32766586 PMCID: PMC7402043 DOI: 10.1101/2020.07.31.231746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the 10-100 ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.
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Affiliation(s)
- Anum Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Daniel Limonta
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - Matthew A. Nix
- Department of Laboratory Medicine, University of California at San Francisco, CA
| | - Nicholas J. Rettko
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Shoshana Zha
- Department of Medicine, University of California at San Francisco, CA
| | - Rachel Yamin
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Kevin Kao
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Oren S. Rosenberg
- Department of Medicine, University of California at San Francisco, CA
| | - Jeffrey V. Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Arun P. Wiita
- Department of Laboratory Medicine, University of California at San Francisco, CA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Tom C. Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Canada
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA
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32
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Abstract
A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) is causing the global coronavirus disease 2019 (COVID-19) pandemic. Understanding how SARS-CoV-2 enters human cells is a high priority for deciphering its mystery and curbing its spread. A virus surface spike protein mediates SARS-CoV-2 entry into cells. To fulfill its function, SARS-CoV-2 spike binds to its receptor human ACE2 (hACE2) through its receptor-binding domain (RBD) and is proteolytically activated by human proteases. Here we investigated receptor binding and protease activation of SARS-CoV-2 spike using biochemical and pseudovirus entry assays. Our findings have identified key cell entry mechanisms of SARS-CoV-2. First, SARS-CoV-2 RBD has higher hACE2 binding affinity than SARS-CoV RBD, supporting efficient cell entry. Second, paradoxically, the hACE2 binding affinity of the entire SARS-CoV-2 spike is comparable to or lower than that of SARS-CoV spike, suggesting that SARS-CoV-2 RBD, albeit more potent, is less exposed than SARS-CoV RBD. Third, unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Successful intervention strategies must target both the potency of SARS-CoV-2 and its evasiveness.
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Affiliation(s)
- Jian Shang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Yushun Wan
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Chuming Luo
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Gang Ye
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Qibin Geng
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Ashley Auerbach
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108
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33
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Zhang JY, Yan YY, Li JJ, Adhikari R, Fu LW. PD-1/PD-L1 Based Combinational Cancer Therapy: Icing on the Cake. Front Pharmacol 2020; 11:722. [PMID: 32528284 PMCID: PMC7247431 DOI: 10.3389/fphar.2020.00722] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer has been a major global health problem due to its high morbidity and mortality. While many chemotherapy agents have been studied and applied in clinical trials or in clinic, their application is limited due to its toxic side effects and poor tolerability. Monoclonal antibodies specific to the PD-1 and PD-L1 immune checkpoints have been approved for the treatment of various tumors. However, the application of PD-1/PD-L1 inhibitors remains suboptimal and thus another strategy comes in to our sight involving the combination of checkpoint inhibitors with other agents, enhancing the therapeutic efficacy. Various novel promising approaches are now in clinical trials, just as icing on the cake. This review summarizes relevant investigations on combinatorial therapeutics based on PD-1/PD-L1 inhibition.
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Affiliation(s)
- Jian-Ye Zhang
- State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan-Yan Yan
- Institute of Respiratory and Occupational Diseases, Collaborative Innovation Center for Cancer, Medical College, Shanxi Datong University, Datong, China
| | - Jia-Jun Li
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Li-Wu Fu
- State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-Sen University, Guangzhou, China
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34
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Dinnon KH, Leist SR, Schäfer A, Edwards CE, Martinez DR, Montgomery SA, West A, Yount BL, Hou YJ, Adams LE, Gully KL, Brown AJ, Huang E, Bryant MD, Choong IC, Glenn JS, Gralinski LE, Sheahan TP, Baric RS. A mouse-adapted SARS-CoV-2 model for the evaluation of COVID-19 medical countermeasures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.06.081497. [PMID: 32511406 PMCID: PMC7263553 DOI: 10.1101/2020.05.06.081497] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronaviruses are prone to emergence into new host species most recently evidenced by SARS-CoV-2, the causative agent of the COVID-19 pandemic. Small animal models that recapitulate SARS-CoV-2 disease are desperately needed to rapidly evaluate medical countermeasures (MCMs). SARS-CoV-2 cannot infect wildtype laboratory mice due to inefficient interactions between the viral spike (S) protein and the murine ortholog of the human receptor, ACE2. We used reverse genetics to remodel the S and mACE2 binding interface resulting in a recombinant virus (SARS-CoV-2 MA) that could utilize mACE2 for entry. SARS-CoV-2 MA replicated in both the upper and lower airways of both young adult and aged BALB/c mice. Importantly, disease was more severe in aged mice, and showed more clinically relevant phenotypes than those seen in hACE2 transgenic mice. We then demonstrated the utility of this model through vaccine challenge studies in immune competent mice with native expression of mACE2. Lastly, we show that clinical candidate interferon (IFN) lambda-1a can potently inhibit SARS-CoV-2 replication in primary human airway epithelial cells in vitro , and both prophylactic and therapeutic administration diminished replication in mice. Our mouse-adapted SARS-CoV-2 model demonstrates age-related disease pathogenesis and supports the clinical use of IFN lambda-1a treatment in human COVID-19 infections.
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35
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Abstract
A key to curbing SARS-CoV-2 is to understand how it enters cells. SARS-CoV-2 and SARS-CoV both use human ACE2 as entry receptor and human proteases as entry activators. Using biochemical and pseudovirus entry assays and SARS-CoV as a comparison, we have identified key cell entry mechanisms of SARS-CoV-2 that potentially contribute to the immune evasion, cell infectivity, and wide spread of the virus. This study also clarifies conflicting reports from recent studies on cell entry of SARS-CoV-2. Finally, by highlighting the potency and the evasiveness of SARS-CoV-2, the study provides insight into intervention strategies that target its cell entry mechanisms. A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) is causing the global coronavirus disease 2019 (COVID-19) pandemic. Understanding how SARS-CoV-2 enters human cells is a high priority for deciphering its mystery and curbing its spread. A virus surface spike protein mediates SARS-CoV-2 entry into cells. To fulfill its function, SARS-CoV-2 spike binds to its receptor human ACE2 (hACE2) through its receptor-binding domain (RBD) and is proteolytically activated by human proteases. Here we investigated receptor binding and protease activation of SARS-CoV-2 spike using biochemical and pseudovirus entry assays. Our findings have identified key cell entry mechanisms of SARS-CoV-2. First, SARS-CoV-2 RBD has higher hACE2 binding affinity than SARS-CoV RBD, supporting efficient cell entry. Second, paradoxically, the hACE2 binding affinity of the entire SARS-CoV-2 spike is comparable to or lower than that of SARS-CoV spike, suggesting that SARS-CoV-2 RBD, albeit more potent, is less exposed than SARS-CoV RBD. Third, unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Successful intervention strategies must target both the potency of SARS-CoV-2 and its evasiveness.
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36
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Srinivasan S, Cui H, Gao Z, Liu M, Lu S, Mkandawire W, Narykov O, Sun M, Korkin D. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins. Viruses 2020; 12:v12040360. [PMID: 32218151 PMCID: PMC7232164 DOI: 10.3390/v12040360] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/22/2022] Open
Abstract
During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge, we leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.
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Affiliation(s)
- Suhas Srinivasan
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Hongzhu Cui
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Ziyang Gao
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Ming Liu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Senbao Lu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Winnie Mkandawire
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Oleksandr Narykov
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Mo Sun
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Dmitry Korkin
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Correspondence:
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37
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Sheikh A, Al-Taher A, Al-Nazawi M, Al-Mubarak AI, Kandeel M. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. J Virol Methods 2020; 277:113806. [PMID: 31911390 PMCID: PMC7119019 DOI: 10.1016/j.jviromet.2019.113806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
Abstract
The nucleotide variations among the N genes of 13 different coronaviruses (CoVs) were interpreted. Overall, 18 amino acids observed with varying preferred codons. The effective number of codon values ranged from 40.43 to 53.85, revealing a slight codon bias. A highly significant correlation between GC3s and ENc values was observed in porcine epidemic diarrhea CoV, followed by Middle East respiratory syndrome CoV.
The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus’s genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus’s host adaptation, evolution and is thus of value to vaccine design strategies.
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Affiliation(s)
- Abdullah Sheikh
- The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdulla Al-Taher
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdullah I Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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38
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Kim MH, Kim HJ, Chang J. Superior immune responses induced by intranasal immunization with recombinant adenovirus-based vaccine expressing full-length Spike protein of Middle East respiratory syndrome coronavirus. PLoS One 2019; 14:e0220196. [PMID: 31329652 PMCID: PMC6645677 DOI: 10.1371/journal.pone.0220196] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes an acute and severe lower respiratory illness as well as vomiting, diarrhea, and renal failure. Because no licensed MERS-CoV vaccines are currently available, preventive and therapeutic measures are urgently needed. The surface spike (S) glycoprotein of MERS-CoV, which binds to the cellular receptor dipeptidyl peptidase 4 (DPP4), is considered as a major target for MERS-CoV vaccine development. Here, we designed recombinant replication-deficient adenovirus-based vaccines expressing the N-terminal domain (rAd/NTD) and receptor-binding domain (rAd/RBD) of the MERS-CoV S1 subunit and full-length Spike protein (rAd/Spike). We found that immunization with candidate vaccines via intranasal route induced S1-specific IgG antibodies and neutralizing antibodies against MERS spike pseudotyped virus. Especially, rAd/Spike induced the highest neutralizing antibody titer and the strongest cytokine-induced T cell responses among the three candidate vaccines. To compare the immune responses induced by different administration routes, rAd/Spike was administered via intranasal, sublingual, or intramuscular route. All these administration routes exhibited neutralizing effects in the serum. MERS-CoV-specific neutralizing IgA antibodies in the bronchoalveolar lavage fluid were only induced by intranasal and sublingual administration but not by intramuscular administration. Intranasal administration with rAd/Spike also created resident memory CD8 T cells in the airway and lung parenchyma. Taken together, our results showed that both the humoral and cellular immune responses are highly induced by rAd/Spike administration, suggesting that rAd/Spike may confer protection against MERS-CoV infection.
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Affiliation(s)
- Myung Hee Kim
- Graduate School of Pharmaceutical Sciences, Ewha Woman’s University, Seoul, Republic of Korea
| | - Hyun Jik Kim
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jun Chang
- Graduate School of Pharmaceutical Sciences, Ewha Woman’s University, Seoul, Republic of Korea
- * E-mail:
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39
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Xia S, Yan L, Xu W, Agrawal AS, Algaissi A, Tseng CTK, Wang Q, Du L, Tan W, Wilson IA, Jiang S, Yang B, Lu L. A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. SCIENCE ADVANCES 2019; 5:eaav4580. [PMID: 30989115 PMCID: PMC6457931 DOI: 10.1126/sciadv.aav4580] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/14/2019] [Indexed: 05/07/2023]
Abstract
Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site.
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Affiliation(s)
- Shuai Xia
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China
| | - Lei Yan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Wei Xu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China
| | - Anurodh Shankar Agrawal
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abdullah Algaissi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Qian Wang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Wenjie Tan
- MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ian A. Wilson
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA
- Corresponding author. (I.A.W.); (S.J.); (B.Y.); (L.L.)
| | - Shibo Jiang
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
- Corresponding author. (I.A.W.); (S.J.); (B.Y.); (L.L.)
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Corresponding author. (I.A.W.); (S.J.); (B.Y.); (L.L.)
| | - Lu Lu
- Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China
- Corresponding author. (I.A.W.); (S.J.); (B.Y.); (L.L.)
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Abstract
Introduction: The highly pathogenic coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are lethal zoonotic viruses that have emerged into human populations these past 15 years. These coronaviruses are associated with novel respiratory syndromes that spread from person-to-person via close contact, resulting in high morbidity and mortality caused by the progression to Acute Respiratory Distress Syndrome (ARDS). Areas covered: The risks of re-emergence of SARS-CoV from bat reservoir hosts, the persistence of MERS-CoV circulation, and the potential for future emergence of novel coronaviruses indicate antiviral drug discovery will require activity against multiple coronaviruses. In this review, approaches that antagonize viral nonstructural proteins, neutralize structural proteins, or modulate essential host elements of viral infection with varying levels of efficacy in models of highly pathogenic coronavirus disease are discussed. Expert opinion: Treatment of SARS and MERS in outbreak settings has focused on therapeutics with general antiviral activity and good safety profiles rather than efficacy data provided by cellular, rodent, or nonhuman primate models of highly pathogenic coronavirus infection. Based on lessons learned from SARS and MERS outbreaks, lack of drugs capable of pan-coronavirus antiviral activity increases the vulnerability of public health systems to a highly pathogenic coronavirus pandemic.
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Affiliation(s)
- Allison L Totura
- a Division of Molecular and Translational Sciences , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD , USA
| | - Sina Bavari
- a Division of Molecular and Translational Sciences , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD , USA
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Veit S, Jany S, Fux R, Sutter G, Volz A. CD8+ T Cells Responding to the Middle East Respiratory Syndrome Coronavirus Nucleocapsid Protein Delivered by Vaccinia Virus MVA in Mice. Viruses 2018; 10:v10120718. [PMID: 30558354 PMCID: PMC6316859 DOI: 10.3390/v10120718] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV), a novel infectious agent causing severe respiratory disease and death in humans, was first described in 2012. Antibodies directed against the MERS-CoV spike (S) protein are thought to play a major role in controlling MERS-CoV infection and in mediating vaccine-induced protective immunity. In contrast, relatively little is known about the role of T cell responses and the antigenic targets of MERS-CoV that are recognized by CD8+ T cells. In this study, the highly conserved MERS-CoV nucleocapsid (N) protein served as a target immunogen to elicit MERS-CoV-specific cellular immune responses. Modified Vaccinia virus Ankara (MVA), a safety-tested strain of vaccinia virus for preclinical and clinical vaccine research, was used for generating MVA-MERS-N expressing recombinant N protein. Overlapping peptides spanning the whole MERS-CoV N polypeptide were used to identify major histocompatibility complex class I/II-restricted T cell responses in BALB/c mice immunized with MVA-MERS-N. We have identified a H2-d restricted decamer peptide epitope in the MERS-N protein with CD8+ T cell antigenicity. The identification of this epitope, and the availability of the MVA-MERS-N candidate vaccine, will help to evaluate MERS-N-specific immune responses and the potential immune correlates of vaccine-mediated protection in the appropriate murine models of MERS-CoV infection.
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Affiliation(s)
- Svenja Veit
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany.
| | - Sylvia Jany
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany.
| | - Robert Fux
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany.
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany.
- German Center for Infection Research (DZIF), partner site Munich, 80539 Munich, Germany.
| | - Asisa Volz
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany.
- German Center for Infection Research (DZIF), partner site Munich, 80539 Munich, Germany.
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42
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Wang L, Shi W, Chappell JD, Joyce MG, Zhang Y, Kanekiyo M, Becker MM, van Doremalen N, Fischer R, Wang N, Corbett KS, Choe M, Mason RD, Van Galen JG, Zhou T, Saunders KO, Tatti KM, Haynes LM, Kwong PD, Modjarrad K, Kong WP, McLellan JS, Denison MR, Munster VJ, Mascola JR, Graham BS. Importance of Neutralizing Monoclonal Antibodies Targeting Multiple Antigenic Sites on the Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein To Avoid Neutralization Escape. J Virol 2018; 92:e02002-17. [PMID: 29514901 PMCID: PMC5923077 DOI: 10.1128/jvi.02002-17] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/19/2018] [Indexed: 01/01/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes a highly lethal pulmonary infection with ∼35% mortality. The potential for a future pandemic originating from animal reservoirs or health care-associated events is a major public health concern. There are no vaccines or therapeutic agents currently available for MERS-CoV. Using a probe-based single B cell cloning strategy, we have identified and characterized multiple neutralizing monoclonal antibodies (MAbs) specifically binding to the receptor-binding domain (RBD) or S1 (non-RBD) regions from a convalescent MERS-CoV-infected patient and from immunized rhesus macaques. RBD-specific MAbs tended to have greater neutralizing potency than non-RBD S1-specific MAbs. Six RBD-specific and five S1-specific MAbs could be sorted into four RBD and three non-RBD distinct binding patterns, based on competition assays, mapping neutralization escape variants, and structural analysis. We determined cocrystal structures for two MAbs targeting the RBD from different angles and show they can bind the RBD only in the "out" position. We then showed that selected RBD-specific, non-RBD S1-specific, and S2-specific MAbs given prophylactically prevented MERS-CoV replication in lungs and protected mice from lethal challenge. Importantly, combining RBD- and non-RBD MAbs delayed the emergence of escape mutations in a cell-based virus escape assay. These studies identify MAbs targeting different antigenic sites on S that will be useful for defining mechanisms of MERS-CoV neutralization and for developing more effective interventions to prevent or treat MERS-CoV infections.IMPORTANCE MERS-CoV causes a highly lethal respiratory infection for which no vaccines or antiviral therapeutic options are currently available. Based on continuing exposure from established reservoirs in dromedary camels and bats, transmission of MERS-CoV into humans and future outbreaks are expected. Using structurally defined probes for the MERS-CoV spike glycoprotein (S), the target for neutralizing antibodies, single B cells were sorted from a convalescent human and immunized nonhuman primates (NHPs). MAbs produced from paired immunoglobulin gene sequences were mapped to multiple epitopes within and outside the receptor-binding domain (RBD) and protected against lethal MERS infection in a murine model following passive immunization. Importantly, combining MAbs targeting distinct epitopes prevented viral neutralization escape from RBD-directed MAbs. These data suggest that antibody responses to multiple domains on CoV spike protein may improve immunity and will guide future vaccine and therapeutic development efforts.
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Affiliation(s)
- Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle M Becker
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Neeltje van Doremalen
- Virus Ecology Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Robert Fischer
- Virus Ecology Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Nianshuang Wang
- Department of Biochemistry and Cellular Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph G Van Galen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin O Saunders
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathleen M Tatti
- Division of Viral Disease, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lia M Haynes
- Division of Viral Disease, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kayvon Modjarrad
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason S McLellan
- Department of Biochemistry and Cellular Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Mark R Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vincent J Munster
- Virus Ecology Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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43
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Excler JL, Delvecchio CJ, Wiley RE, Williams M, Yoon IK, Modjarrad K, Boujelal M, Moorthy VS, Hersi AS, Kim JH. Toward Developing a Preventive MERS-CoV Vaccine-Report from a Workshop Organized by the Saudi Arabia Ministry of Health and the International Vaccine Institute, Riyadh, Saudi Arabia, November 14-15, 2015. Emerg Infect Dis 2018; 22. [PMID: 27439020 PMCID: PMC4982192 DOI: 10.3201/eid2208.160229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Middle East respiratory syndrome (MERS) remains a serious international public health threat. With the goal of accelerating the development of countermeasures against MERS coronavirus (MERS-CoV), funding agencies, nongovernmental organizations, and researchers across the world assembled in Riyadh, Saudi Arabia, on November 14-15, 2015, to discuss vaccine development challenges. The meeting was spearheaded by the Saudi Ministry of Health and co-organized by the International Vaccine Institute, South Korea. Accelerating the development of a preventive vaccine requires a better understanding of MERS epidemiology, transmission, and pathogenesis in humans and animals. A combination of rodent and nonhuman primate models should be considered in evaluating and developing preventive and therapeutic vaccine candidates. Dromedary camels should be considered for the development of veterinary vaccines. Several vaccine technology platforms targeting the MERS-CoV spike protein were discussed. Mechanisms to maximize investment, provide robust data, and affect public health are urgently needed.
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Johnson BA, Graham RL, Menachery VD. Viral metagenomics, protein structure, and reverse genetics: Key strategies for investigating coronaviruses. Virology 2017; 517:30-37. [PMID: 29279138 PMCID: PMC5869085 DOI: 10.1016/j.virol.2017.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022]
Abstract
Viral metagenomics, modeling of protein structure, and manipulation of viral genetics are key approaches that have laid the foundations of our understanding of coronavirus biology. In this review, we discuss the major advances each method has provided and discuss how future studies should leverage these strategies synergistically to answer novel questions.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
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45
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Cho H, Excler JL, Kim JH, Yoon IK. Development of Middle East Respiratory Syndrome Coronavirus vaccines - advances and challenges. Hum Vaccin Immunother 2017; 14:304-313. [PMID: 29048984 DOI: 10.1080/21645515.2017.1389362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging pathogen with the potential to pose a threat to global public health. Sporadic cases and outbreaks continue to be reported in the Middle East, and case fatality rates remain high at approximately 36% globally. No specific preventive or therapeutic countermeasures currently exist. A safe and effective vaccine could play an important role in protecting against the threat from MERS-CoV. This review discusses human vaccine candidates currently under development, and explores viral characteristics, molecular epidemiology and immunology relevant to MERS-CoV vaccine development. At present, a DNA vaccine candidate has begun a human clinical trial, while two vector-based candidates will very soon begin human trials. Protein-based vaccines are still at pre-clinical stage. Challenges to successful development include incomplete understanding of viral transmission, pathogenesis and immune response (in particular at the mucosal level), no optimal animal challenge models, lack of standardized immunological assays, and insufficient sustainable funding.
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Affiliation(s)
- Heeyoun Cho
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - Jean-Louis Excler
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - Jerome H Kim
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - In-Kyu Yoon
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
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46
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Wong AHM, Tomlinson ACA, Zhou D, Satkunarajah M, Chen K, Sharon C, Desforges M, Talbot PJ, Rini JM. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nat Commun 2017; 8:1735. [PMID: 29170370 PMCID: PMC5701055 DOI: 10.1038/s41467-017-01706-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/06/2017] [Indexed: 02/08/2023] Open
Abstract
RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding. Coronaviruses have a relatively high mutation rate, potentially allowing fast adaptation to changing pressures. Here, Wong et al. provide the structure of the receptor-binding domain (RBD) of the human coronavirus HCoV-229E and its receptor and analyze the evolution of the RBD over the past 50 years.
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Affiliation(s)
- Alan H M Wong
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Aidan C A Tomlinson
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Dongxia Zhou
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Malathy Satkunarajah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Kevin Chen
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Chetna Sharon
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - James M Rini
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8. .,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.
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47
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Sun Y, Zhang H, Shi J, Zhang Z, Gong R. Identification of a Novel Inhibitor against Middle East Respiratory Syndrome Coronavirus. Viruses 2017; 9:v9090255. [PMID: 28906430 PMCID: PMC5618021 DOI: 10.3390/v9090255] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/28/2022] Open
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated in 2012, and circulated worldwide with high mortality. The continual outbreaks of MERS-CoV highlight the importance of developing antiviral therapeutics. Here, we rationally designed a novel fusion inhibitor named MERS-five-helix bundle (MERS-5HB) derived from the six-helix bundle (MERS-6HB) which was formed by the process of membrane fusion. MERS-5HB consists of three copies of heptad repeat 1 (HR1) and two copies of heptad repeat 2 (HR2) while MERS-6HB includes three copies each of HR1 and HR2. As it lacks one HR2, MERS-5HB was expected to interact with viral HR2 to interrupt the fusion step. What we found was that MERS-5HB could bind to HR2P, a peptide derived from HR2, with a strong affinity value (KD) of up to 0.24 nM. Subsequent assays indicated that MERS-5HB could inhibit pseudotyped MERS-CoV entry effectively with 50% inhibitory concentration (IC50) of about 1 μM. In addition, MERS-5HB significantly inhibited spike (S) glycoprotein-mediated syncytial formation in a dose-dependent manner. Further biophysical characterization showed that MERS-5HB was a thermo-stable α-helical secondary structure. The inhibitory potency of MERS-5HB may provide an attractive basis for identification of a novel inhibitor against MERS-CoV, as a potential antiviral agent.
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Affiliation(s)
- Yaping Sun
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huaidong Zhang
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Jian Shi
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Zhe Zhang
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
| | - Rui Gong
- Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan 430071, China.
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48
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Cell Attachment Domains of the Porcine Epidemic Diarrhea Virus Spike Protein Are Key Targets of Neutralizing Antibodies. J Virol 2017; 91:JVI.00273-17. [PMID: 28381581 DOI: 10.1128/jvi.00273-17] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/24/2017] [Indexed: 01/12/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes enteric disease in pigs, resulting in significant economic losses to the swine industry worldwide. Current vaccination approaches against this emerging coronavirus are only partially effective, though natural infection protects pigs against reinfection and provides lactogenic immunity to suckling piglets. The viral spike (S) glycoprotein, responsible for receptor binding and cell entry, is the major target for neutralizing antibodies. However, knowledge of antibody epitopes, their nature and location in the spike structure, and the mechanisms by which the antibodies interfere with infection is scarce. Here we describe the generation and characterization of 10 neutralizing and nonneutralizing mouse monoclonal antibodies raised against the S1 receptor binding subunit of the S protein. By expression of different S1 protein fragments, six antibody epitope classes distributed over the five structural domains of the S1 subunit were identified. Characterization of antibodies for cross-reactivity and cross-neutralization revealed antigenic differences among PEDV strains. The epitopes of potent neutralizing antibodies segregated into two epitope classes and mapped within the N-terminal sialic acid binding domain and in the more C-terminal receptor binding domain. Antibody neutralization escape mutants displayed single amino acid substitutions that impaired antibody binding and neutralization and defined the locations of the epitopes. Our observations picture the antibody epitope landscape of the PEDV S1 subunit and reveal that its cell attachment domains are key targets of neutralizing antibodies.IMPORTANCE Porcine epidemic diarrhea virus (PEDV), an emerging porcine coronavirus, causes an economically important enteric disease in pigs. Effective PEDV vaccines for disease control are currently lacking. The spike (S) glycoprotein on the virion surface is the key player in virus cell entry and, therefore, the main target of neutralizing antibodies. To understand the antigenic landscape of the PEDV spike protein, we developed monoclonal antibodies against the spike protein's S1 receptor binding region and characterized their epitopes, neutralizing activity, and cross-reactivity toward multiple PEDV strains. Epitopes of antibodies segregated into six epitope classes dispersed over the multidomain S1 structure. Monoclonal antibodies revealed antigenic variability in B-cell epitopes between PEDV strains. The epitopes of neutralizing antibodies mapped to two distinct domains in S1 that are involved in binding to carbohydrate and proteinaceous cell surface molecules, respectively, indicating the importance of these cell attachment sites on the PEDV spike protein in eliciting a protective humoral immune response.
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49
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Okba NM, Raj VS, Haagmans BL. Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches. Curr Opin Virol 2017; 23:49-58. [PMID: 28412285 PMCID: PMC7102752 DOI: 10.1016/j.coviro.2017.03.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/20/2017] [Indexed: 12/26/2022]
Abstract
MERS-CoV vaccines for dromedary camels and their human contacts can potentially stop virus transmission in the community. Both neutralizing antibody and T-cell responses are required for protection MERS-CoV vaccines should aim at inducing (long term) mucosal immunity in the different target populations. The spike protein induces both neutralizing antibodies and T-cell responses and is the main target of the current vaccine candidates. Epitope-based vaccines, focusing at (cross)-protective epitopes, could induce higher and/or broader responses.
Middle East respiratory syndrome coronavirus (MERS-CoV) is a cause of severe respiratory infection in humans, specifically the elderly and people with comorbidities. The re-emergence of lethal coronaviruses calls for international collaboration to produce coronavirus vaccines, which are still lacking to date. Ongoing efforts to develop MERS-CoV vaccines should consider the different target populations (dromedary camels and humans) and the correlates of protection. Extending on our current knowledge of MERS, vaccination of dromedary camels to induce mucosal immunity could be a promising approach to diminish MERS-CoV transmission to humans. In addition, it is equally important to develop vaccines for humans that induce broader reactivity against various coronaviruses to be prepared for a potential next CoV outbreak.
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Affiliation(s)
- Nisreen Ma Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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50
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Wang Y, Tai W, Yang J, Zhao G, Sun S, Tseng CTK, Jiang S, Zhou Y, Du L, Gao J. Receptor-binding domain of MERS-CoV with optimal immunogen dosage and immunization interval protects human transgenic mice from MERS-CoV infection. Hum Vaccin Immunother 2017; 13:1615-1624. [PMID: 28277821 DOI: 10.1080/21645515.2017.1296994] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Middle East respiratory syndrome (MERS) continues to raise worldwide concerns due to its pandemic potential. Increased MERS cases and no licensed MERS vaccines highlight the need to develop safe and effective vaccines against MERS. We have previously demonstrated that a receptor-binding domain (RBD) fragment containing residues 377-588 of MERS-coronavirus (MERS-CoV) spike protein is a critical neutralizing domain and an important vaccine target. Nevertheless, its optimal immunogen dosage and immunization interval, key factors for human-used vaccines that induce protective immunity, have never been investigated. In this study, we optimized these criteria using a recombinant MERS-CoV RBD protein fused with Fc (S377-588-Fc) and utilized the optimal immunization schedule to evaluate the protective efficacy of RBD against MERS-CoV infection in human dipeptidyl peptidase 4 transgenic (hDPP4-Tg) mice. Compared with one dose and 2 doses at 1-, 2-, and 3-week intervals, a regimen of 2 doses of this protein separated by an interval of 4 weeks induced the strongest antibody response and neutralizing antibodies against MERS-CoV infection, and maintained at a high level during the detection period. Notably, RBD protein at the optimal dosage and interval protected hDPP4-Tg mice against lethal MERS-CoV challenge, and the protection was positively correlated with serum neutralizing antibodies. Taken together, the optimal immunogen dosage and immunization interval identified in this study will provide useful guidelines for further development of MERS-CoV RBD-based vaccines for human use.
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Affiliation(s)
- Yufei Wang
- a School of Medical Laboratory Science , Wenzhou Medical University , Wenzhou , Zhejiang , China.,b Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA.,c State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Wanbo Tai
- b Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA.,c State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Jie Yang
- b Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA
| | - Guangyu Zhao
- c State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Shihui Sun
- c State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Chien-Te K Tseng
- d Department of Microbiology and Immunology and Center for Biodefense and Emerging Disease , University of Texas Medical Branch , Galveston , TX , USA
| | - Shibo Jiang
- b Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA.,e Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Basic Medical College and Institute of Medical Microbiology , Fudan University , Shanghai , China
| | - Yusen Zhou
- a School of Medical Laboratory Science , Wenzhou Medical University , Wenzhou , Zhejiang , China.,c State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Lanying Du
- b Lindsley F. Kimball Research Institute , New York Blood Center , New York , NY , USA
| | - Jimin Gao
- a School of Medical Laboratory Science , Wenzhou Medical University , Wenzhou , Zhejiang , China
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