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Ma S, Zhang D, Wang Q, Zhu L, Wu X, Ye S, Wang Y. Structure defining of ultrapotent neutralizing nanobodies against MERS-CoV with novel epitopes on receptor binding domain. PLoS Pathog 2024; 20:e1012438. [PMID: 39141662 PMCID: PMC11324105 DOI: 10.1371/journal.ppat.1012438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes severe and fatal acute respiratory disease in humans. High fatality rates and continued infectiousness remain a pressing concern for global health preparedness. Antibodies targeted at the receptor-binding domain (RBD) are major countermeasures against human viral infection. Here, we report four potent nanobodies against MERS-CoV, which are isolated from alpaca, and especially the potency of Nb14 is highest in the pseudotyped virus assay. Structural studies show that Nb14 framework regions (FRs) are mainly involved in interactions targeting a novel epitope, which is entirely distinct from all previously reported antibodies, and disrupt the protein-carbohydrate interaction between residue W535 of RBD and hDPP4 N229-linked carbohydrate moiety (hDPP4-N229-glycan). Different from Nb14, Nb9 targets the cryptic face of RBD, which is distinctive from the hDPP4 binding site and the Nb14 epitope, and it induces the β5-β6 loop to inflect towards a shallow groove of the RBD and dampens the accommodation of a short helix of hDPP4. The particularly striking epitopes endow the two Nbs administrate synergistically in the pseudotyped MERS-CoV assays. These results not only character unprecedented epitopes for antibody recognition but also provide promising agents for prophylaxis and therapy of MERS-CoV infection.
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Affiliation(s)
- Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Doudou Zhang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Qiwei Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Linjing Zhu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Xilin Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, P.R. China
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Kim SH, Kim Y, Jeon S, Park U, Kang JI, Jeon K, Kim HR, Oh S, Rhee JY, Choi JP, Park WB, Park SW, Yang JS, Lee JY, Kang J, Shin HS, Kim Y, Kim S, Kim YS, Lim DG, Cho NH. Rise in broadly cross-reactive adaptive immunity against human β-coronaviruses in MERS-recovered patients during the COVID-19 pandemic. SCIENCE ADVANCES 2024; 10:eadk6425. [PMID: 38416834 PMCID: PMC10901372 DOI: 10.1126/sciadv.adk6425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/23/2024] [Indexed: 03/01/2024]
Abstract
To develop a universal coronavirus (CoV) vaccine, long-term immunity against multiple CoVs, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, Middle East respiratory syndrome (MERS)-CoV, and future CoV strains, is crucial. Following the 2015 Korean MERS outbreak, we conducted a long-term follow-up study and found that although neutralizing antibodies and memory T cells against MERS-CoV declined over 5 years, some recovered patients exhibited increased antibody levels during the COVID-19 pandemic. This likely resulted from cross-reactive immunity induced by SARS-CoV-2 vaccines or infections. A significant correlation in antibody responses across various CoVs indicates shared immunogenic epitopes. Two epitopes-the spike protein's stem helix and intracellular domain-were highly immunogenic after MERS-CoV infection and after SARS-CoV-2 vaccination or infection. In addition, memory T cell responses, especially polyfunctional CD4+ T cells, were enhanced during the pandemic, correlating significantly with MERS-CoV spike-specific antibodies and neutralizing activity. Therefore, incorporating these cross-reactive and immunogenic epitopes into pan-CoV vaccine formulations may facilitate effective vaccine development.
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Affiliation(s)
- So-Hee Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Institute of Endemic Disease, Seoul National University Medical Research, Seoul 03080, Republic of Korea
| | - Sangeun Jeon
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea
| | - Uni Park
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Ju-Il Kang
- Institute of Endemic Disease, Seoul National University Medical Research, Seoul 03080, Republic of Korea
| | - Kyeongseok Jeon
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Hye-Ran Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Songhyeok Oh
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Ji-Young Rhee
- Division of Infectious Diseases, Department of Medicine, Dankook University College of Medicine, Cheonan 31116, Republic of Korea
| | - Jae-Phil Choi
- Department of Internal Medicine, Seoul Medical Center, Seoul 02053, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sang Won Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jeong-Sun Yang
- Center for Emerging Virus Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea
| | - Joo-Yeon Lee
- Center for Emerging Virus Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea
| | - Jihye Kang
- Translational Research Center, Research Institute of Public Health, National Medical Center, Seoul 04564, Republic of Korea
| | - Hyoung-Shik Shin
- Division of Infectious Diseases, Department of Internal Medicine, Daejeon Eulji Medical Center, Eulji University School of Medicine, Daejeon 34824, Republic of Korea
| | - Yeonjae Kim
- Center for Infectious Diseases, National Medical Center, Seoul 04564, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Dong-Gyun Lim
- Translational Research Center, Research Institute of Public Health, National Medical Center, Seoul 04564, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Institute of Endemic Disease, Seoul National University Medical Research, Seoul 03080, Republic of Korea
- Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do 13620, Republic of Korea
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3
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Oh J, Park U, Kim J, Jeon K, Kim C, Cho NH, Choi YS. Enhancing immune protection against MERS-CoV: the synergistic effect of proteolytic cleavage sites and the fusion peptide and RBD domain targeting VLP immunization. Front Immunol 2023; 14:1201136. [PMID: 37275866 PMCID: PMC10235442 DOI: 10.3389/fimmu.2023.1201136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic infectious virus that has caused significant outbreaks in the Middle East and beyond. Due to a highly mortality rate, easy transmission, and rapid spread of the MERS-CoV, it remains as a significant public health treat. There is currently no licensed vaccine available to protect against MERS-CoV. Methods In this study, we investigated whether the proteolytic cleavage sites and fusion peptide domain of the MERS-CoV spike (S) protein could be a vaccine target to elicit the MERS-CoV S protein-specific antibody responses and confer immune protection against MERS-CoV infection. Our results demonstrate that immunization of the proteolytic cleavage sites and the fusion peptide domain using virus-like particle (VLP) induced the MERS-CoV S protein-specific IgG antibodies with capacity to neutralize pseudotyped MERS-CoV infection in vitro. Moreover, proteolytic cleavage sites and the fusion peptide VLP immunization showed a synergistic effect on the immune protection against MERS-CoV infection elicited by immunization with VLP expressing the receptor binding domain (RBD) of the S protein. Additionally, immune evasion of MERS-CoV RBD variants from anti-RBD sera was significantly controlled by anti-proteolytic cleavage sites and the fusion peptide sera. Conclusion and discussion Our study demonstrates the potential of VLP immunization targeting the proteolytic cleavage sites and the fusion peptide and RBD domains of the MERS-CoV S protein for the development of effective treatments and vaccines against MERS-CoV and related variants.
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Affiliation(s)
- Jeein Oh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Uni Park
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Juhyung Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chulwoo Kim
- Deparatment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Republic of Korea
| | - Youn Soo Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Transplantation Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
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Al-Tawfiq JA, Azhar EI, Memish ZA, Zumla A. Middle East Respiratory Syndrome Coronavirus. Semin Respir Crit Care Med 2021; 42:828-838. [PMID: 34918324 DOI: 10.1055/s-0041-1733804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The past two decades have witnessed the emergence of three zoonotic coronaviruses which have jumped species to cause lethal disease in humans: severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. MERS-CoV emerged in Saudi Arabia in 2012 and the origins of MERS-CoV are not fully understood. Genomic analysis indicates it originated in bats and transmitted to camels. Human-to-human transmission occurs in varying frequency, being highest in healthcare environment and to a lesser degree in the community and among family members. Several nosocomial outbreaks of human-to-human transmission have occurred, the largest in Riyadh and Jeddah in 2014 and South Korea in 2015. MERS-CoV remains a high-threat pathogen identified by World Health Organization as a priority pathogen because it causes severe disease that has a high mortality rate, epidemic potential, and no medical countermeasures. MERS-CoV has been identified in dromedaries in several countries in the Middle East, Africa, and South Asia. MERS-CoV-2 causes a wide range of clinical presentations, although the respiratory system is predominantly affected. There are no specific antiviral treatments, although recent trials indicate that combination antivirals may be useful in severely ill patients. Diagnosing MERS-CoV early and implementation infection control measures are critical to preventing hospital-associated outbreaks. Preventing MERS relies on avoiding unpasteurized or uncooked animal products, practicing safe hygiene habits in health care settings and around dromedaries, community education and awareness training for health workers, as well as implementing effective control measures. Effective vaccines for MERS-COV are urgently needed but still under development.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Division of Infectious Disease, Indiana University School of Medicine, Indianapolis, Indiana.,Division of Infectious Disease, Johns Hopkins University, Baltimore, Maryland
| | - Esam I Azhar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziad A Memish
- Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Hubert Department of Global Health, Emory University, Atlanta, Georgia
| | - Alimuddin Zumla
- Division of Infection and Immunity, Department of Infection, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, United Kingdom
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5
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Middle East respiratory syndrome coronavirus Spike protein variants exhibit geographic differences in virulence. Proc Natl Acad Sci U S A 2021; 118:2102983118. [PMID: 34099556 DOI: 10.1073/pnas.2102983118] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Human Middle East respiratory syndrome (MERS) cases were detected primarily in the Middle East before a major outbreak occurred in South Korea in 2015. The Korean outbreak was initiated by a single infected individual, allowing studies of virus evolution in the absence of further MERS-CoV introduction into human populations. In contrast, MERS is primarily a camel disease on the Arabian Peninsula and in Africa, with clinical disease in humans only in the former location. Previous work identified two mutations in the South Korean MERS-CoV, D510G and I529T on the Spike (S) protein, that led to impaired binding to the receptor. However, whether these mutations affected virulence is unknown. To address this question, we constructed isogenic viruses expressing mutations found in the S protein from Korean isolates and showed that isogenic viruses carrying the Korean MERS-CoV mutations, D510G or I529T, were attenuated in mice, resulting in greater survival, less induction of inflammatory cytokines, and less severe lung injury. In contrast, isogenic viruses expressing S proteins from African isolates were nearly fully virulent; other studies showed that West African camel isolates carry mutations in MERS-CoV accessory proteins, which may limit human transmission. These data indicate that following a single-point introduction of the virus, MERS-CoV S protein evolved rapidly in South Korea to adapt to human populations, with consequences on virulence. In contrast, the mutations in S proteins of African isolates did not change virulence, indicating that S protein variation likely does not play a major role in the lack of camel-to-human transmission in Africa.
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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: 6.3] [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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Kim M, Cho H, Lee SH, Park WJ, Kim JM, Moon JS, Kim GW, Lee W, Jung HG, Yang JS, Choi JH, Lee JY, Kim SS, Oh JW. An infectious cDNA clone of a growth attenuated Korean isolate of MERS coronavirus KNIH002 in clade B. Emerg Microbes Infect 2021; 9:2714-2726. [PMID: 33295839 PMCID: PMC7782039 DOI: 10.1080/22221751.2020.1861914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The MERS-CoV isolated during the 2015 nosocomial outbreak in Korea showed distinctive differences in mortality and transmission patterns compared to the prototype MERS-CoV EMC strain belonging to clade A. We established a BAC-based reverse genetics system for a Korean isolate of MERS-CoV KNIH002 in the clade B phylogenetically far from the EMC strain, and generated a recombinant MERS-CoV expressing red fluorescent protein. The virus rescued from the infectious clone and KNIH002 strain displayed growth attenuation compared to the EMC strain. Consecutive passages of the rescued virus rapidly generated various ORF5 variants, highlighting its genetic instability and calling for caution in the use of repeatedly passaged virus in pathogenesis studies and for evaluation of control measures against MERS-CoV. The infectious clone for the KNIH002 in contemporary epidemic clade B would be useful for better understanding of a functional link between molecular evolution and pathophysiology of MERS-CoV by comparative studies with EMC strain.
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Affiliation(s)
- Minwoo Kim
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Hee Cho
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Woo-Jung Park
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Jeong-Min Kim
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Wooseong Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Hae-Gwang Jung
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Jeong-Sun Yang
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Jang-Hoon Choi
- Division of Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Joo-Yeon Lee
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Sung Soon Kim
- Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, Seoul, Korea
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8
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Mishra D, Suri GS, Kaur G, Tiwari M. Comparative insight into the genomic landscape of SARS-CoV-2 and identification of mutations associated with the origin of infection and diversity. J Med Virol 2020; 93:2406-2419. [PMID: 33347622 DOI: 10.1002/jmv.26744] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022]
Abstract
The analyses of 2325 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes revealed 107, 162, and 65 nucleotide substitutions in the coding region of SARS-CoV-2 from the three continents America, Europe, and Asia, respectively. Of these nucleotide substitutions 58, 94, and 37 were nonsynonymous types mostly present in the Nsp2, Nsp3, Spike, and ORF9. A continent-specific phylogram analyses clustered the SARS-CoV-2 in the different group based on the frequency of nucleotide substitutions. Detailed analyses about the continent-specific amino acid changes and their effectiveness by SNAP2 software was investigated. We found 11 common nonsynonymous mutations; among them, two novel effective mutations were identified in ORF9 (S194L and S202N). Intriguingly, ORF9 encodes nucleocapsid phosphoprotein possessing many effective mutations across continents and could be a potential candidate after the spike protein for studying the role of mutation in viral assembly and pathogenesis. Among the two forms of certain frequent mutation, one form is more prevalent in Europe continents (Nsp12:L314, Nsp13:P504, Nsp13:Y541, Spike:G614, and ORF8:L84) while other forms are more prevalent in American (Nsp12:P314, Nsp13:L504, Nsp13:C541, Spike:D614, and ORF8:L84) and Asian continents (Spike:D614), indicating the spatial and temporal dynamics of SARS-CoV-2. We identified highly conserved 38 regions and among these regions, 11 siRNAs were predicted on stringent criteria that can be used to suppress the expression of viral genes and the corresponding reduction of human viral infections. The present investigation provides information on different mutations and will pave the way for differentiating strains based on virulence and their use in the development of better antiviral therapy.
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Affiliation(s)
- Divya Mishra
- Department of Plant Pathology, Kansas State University, Kansas, USA
| | | | - Gurleen Kaur
- California Baptist University, Riverside, California, USA
| | - Manish Tiwari
- Mid-Florida Research and Education Center, University of Florida, Apopka, Florida, USA
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9
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Forni D, Cagliani R, Pontremoli C, Mozzi A, Pozzoli U, Clerici M, Sironi M. Antigenic variation of SARS-CoV-2 in response to immune pressure. Mol Ecol 2020; 30:3548-3559. [PMID: 33289207 PMCID: PMC7753431 DOI: 10.1111/mec.15730] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/30/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
Analysis of the bat viruses most closely related to SARS-CoV-2 indicated that the virus probably required limited adaptation to spread in humans. Nonetheless, since its introduction in human populations, SARS-CoV-2 must have been subject to the selective pressure imposed by the human immune system. We exploited the availability of a large number of high-quality SARS-CoV-2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than nonepitope positions. Similar results were obtained for other human coronaviruses and for sarbecoviruses sampled in bats. Conversely, in the SARS-CoV-2 population, epitopes for CD4+ and CD8+ T cells were not more variable than nonepitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8 and ORF3a). Analysis over longer evolutionary time frames indicated that this effect is not due to differential constraints. These data indicate that SARS-CoV-2 evolves to elude the host humoral immune response, whereas recognition by T cells is not actively avoided by the virus. However, we also found a trend of lower diversity of T cell epitopes for common cold coronaviruses, indicating that epitope conservation per se is not directly linked to disease severity. We suggest that conservation serves to maintain epitopes that elicit tolerizing T cell responses or induce T cells with regulatory activity.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
| | - Mario Clerici
- Department of Physiopathology and TransplantationUniversity of MilanMilanItaly
- Don C. Gnocchi Foundation ONLUSIRCCSMilanItaly
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEABioinformaticsBosisio PariniItaly
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10
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Cimolai N. Applying Immune Instincts and Maternal Intelligence from Comparative Microbiology to COVID-19. ACTA ACUST UNITED AC 2020; 2:2670-2683. [PMID: 33195997 PMCID: PMC7652409 DOI: 10.1007/s42399-020-00634-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 01/02/2023]
Abstract
New data specific to COVID-19 are emerging quickly on key issues of immunity and prevention, but past research in coronavirology and for other human pathogens (e.g., Mycoplasma pneumoniae) has been available and of great relevance. Considerable study of endemic human coronaviruses has shown that neutralizing antibody correlates with protection, but effective clinical protection is variable for subsequent virus exposure. Animal coronavirus research has emphasized the importance of local mucosal protection (especially IgA) and systemic responses. Animal model and human post-infection studies for SARS-CoV and MERS-CoV are largely corroborative. Whether for passive therapeutic strategies or vaccination, these findings provide a template for COVID-19. Many approaches to vaccination have emerged, and there may be more than one vaccine that will be applied, but individualized obstacles and concerns for administration, efficacy, and safety are inevitable. Regardless of safeguards or promises that may be understood from laboratory or vertebrate experiments, observations from large-scale human trials will ultimately prove to shape the medical future. Focus on common mucosal immunity can be underrated, and equally or more, focus on lactogenic immunity may be underestimated. In understanding both passive immunity and protection, the body is already primed to educate us with decisions of what constitutes protection and harm. This review provides key insights that drive hypotheses into how the instinct of immunity and the intelligence of the maternal component of the common mucosal immune system has already guided us and may continue to do so effectively into a bright and safe future.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, BC Canada
- Children’s and Women’s Health Centre of British Columbia, 4480 Oak Street, Vancouver, BC V6H3V4 Canada
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Sironi M, Hasnain SE, Rosenthal B, Phan T, Luciani F, Shaw MA, Sallum MA, Mirhashemi ME, Morand S, González-Candelas F. SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104384. [PMID: 32473976 PMCID: PMC7256558 DOI: 10.1016/j.meegid.2020.104384] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.
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Affiliation(s)
- Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS E. MEDEA, Bosisio Parini (LC), Italy.
| | - Seyed E Hasnain
- JH Institute of Molecular Medicine, Jamia Hamdard, Tughlakabad, New Delhi, India.
| | - Benjamin Rosenthal
- Animal Parasitic Disease Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| | - Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Fabio Luciani
- University of New South Wales, Sydney, 2052, New South Wales, Australia.
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, United Kingdom.
| | - M Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | | | - Serge Morand
- Institute of Evolution Science of Montpellier, Case Courier 064, F-34095 Montpellier, France.
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio) and CIBER in Epidemiology and Public Health, Valencia, Spain.
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Cimolai N. A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19. SN COMPREHENSIVE CLINICAL MEDICINE 2020; 2:2059-2066. [PMID: 32984765 PMCID: PMC7501512 DOI: 10.1007/s42399-020-00533-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
Until either efficacious therapy or vaccination for COVID-19 is achieved, there will be a need to regain world economic stability while yet controlling the pandemic with current approaches. For those infected thus far, there is a prevailing perspective that devising recognition for protective immunity will progressively allow segments of society to return to some functionality more than is existing. At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Serum neutralizing antibody more easily fulfills the latter requisite, but current live virus methods for neutralization prevent large-scale application. It is conceivable that the exposure of previously infected individuals can allow for the definition of protective thresholds of neutralizing antibody. Thereafter, many other antibody assays will be able to screen for surrogate protection after correlations with protective neutralizing antibody are made. Specificity of common antibody tests would benefit from confirmatory blocking systems or confirmatory immunoblotting fingerprints with well-defined antigen(s). The opportunity for the scientific community to make these assessments is evident in the current context of the COVID-19 epidemic given the large numbers of infected individuals worldwide. Such information will also be vital to guide vaccine development and/or immunotherapy.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, Canada
- Children’s and Women’s Health Centre of British Columbia, 4480 Oak Street, Vancouver, BC V6H3V4 Canada
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Al-Ahmadi KH, Alahmadi MH, Al-Zahrani AS, Hemida MG. Spatial variability of Middle East respiratory syndrome coronavirus survival rates and mortality hazard in Saudi Arabia, 2012–2019. PeerJ 2020. [DOI: 10.7717/peerj.9783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
About 83% of laboratory-confirmed Middle East respiratory syndrome coronavirus (MERS-CoV) cases have emerged from Saudi Arabia, which has the highest overall mortality rate worldwide. This retrospective study assesses the impact of spatial/patient characteristics for 14-and 45-day MERS-CoV mortality using 2012–2019 data reported across Saudi regions and provinces. The Kaplan–Meier estimator was employed to estimate MERS-CoV survival rates, Cox proportional-hazards (CPH) models were applied to estimate hazard ratios (HRs) for 14-and 45-day mortality predictors, and univariate local spatial autocorrelation and multivariate spatial clustering analyses were used to assess the spatial correlation. The 14-day, 45-day and overall mortality rates (with estimated survival rates) were 25.52% (70.20%), 32.35% (57.70%) and 37.30% (56.50%), respectively, with no significant rate variations between Saudi regions and provinces. Nationally, the CPH multivariate model identified that being elderly (age ≥ 61), being a non-healthcare worker (non-HCW), and having an underlying comorbidity were significantly related to 14-day mortality (HR = 2.10, 10.12 and 4.11, respectively; p < 0.0001). The 45-day mortality model identified similar risk factors but with an additional factor: patients aged 41–60 (HR = 1.44; p < 0.0001). Risk factors similar to those in the national model were observed in the Central, East and West regions and Riyadh, Makkah, Eastern, Madinah and Qassim provinces but with varying HRs. Spatial clusters of MERS-CoV mortality in the provinces were identified based on the risk factors (r2 = 0.85–0.97): Riyadh (Cluster 1), Eastern, Makkah and Qassim (Cluster 2), and other provinces in the north and south of the country (Cluster 3). The estimated HRs for the 14-and 45-day mortality varied spatially by province. For 45-day mortality, the highest HRs were found in Makkah (age ≥ 61 and non-HCWs), Riyadh (comorbidity) and Madinah (age 41–60). Coming from Makkah (HR = 1.30 and 1.27) or Qassim province (HR = 1.77 and 1.70) was independently related to higher 14-and 45-day mortality, respectively. MERS-CoV patient survival could be improved by implementing appropriate interventions for the elderly, those with comorbidities and non-HCW patients.
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Affiliation(s)
| | | | - Ali Saeed Al-Zahrani
- King Faisal Specialist Hospital and Research Centre, Riyadh, Riyadh, Saudi Arabia
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Al-Hasa, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Kafrelsheikh, Egypt
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Liang WH, Guan WJ, Li CC, Li YM, Liang HR, Zhao Y, Liu XQ, Sang L, Chen RC, Tang CL, Wang T, Wang W, He QH, Chen ZS, Wong SS, Zanin M, Liu J, Xu X, Huang J, Li JF, Ou LM, Cheng B, Xiong S, Xie ZH, Ni ZY, Hu Y, Liu L, Shan H, Lei CL, Peng YX, Wei L, Liu Y, Hu YH, Peng P, Wang JM, Liu JY, Chen Z, Li G, Zheng ZJ, Qiu SQ, Luo J, Ye CJ, Zhu SY, Cheng LL, Ye F, Li SY, Zheng JP, Zhang NF, Zhong NS, He JX. Clinical characteristics and outcomes of hospitalised patients with COVID-19 treated in Hubei (epicentre) and outside Hubei (non-epicentre): a nationwide analysis of China. Eur Respir J 2020; 55:2000562. [PMID: 32269086 PMCID: PMC7144336 DOI: 10.1183/13993003.00562-2020] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/29/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND During the outbreak of coronavirus disease 2019 (COVID-19), consistent and considerable differences in disease severity and mortality rate of patients treated in Hubei province compared to those in other parts of China have been observed. We sought to compare the clinical characteristics and outcomes of patients being treated inside and outside Hubei province, and explore the factors underlying these differences. METHODS Collaborating with the National Health Commission, we established a retrospective cohort to study hospitalised COVID-19 cases in China. Clinical characteristics, the rate of severe events and deaths, and the time to critical illness (invasive ventilation or intensive care unit admission or death) were compared between patients within and outside Hubei. The impact of Wuhan-related exposure (a presumed key factor that drove the severe situation in Hubei, as Wuhan is the epicentre as well the administrative centre of Hubei province) and the duration between symptom onset and admission on prognosis were also determined. RESULTS At the data cut-off (31 January 2020), 1590 cases from 575 hospitals in 31 provincial administrative regions were collected (core cohort). The overall rate of severe cases and mortality was 16.0% and 3.2%, respectively. Patients in Hubei (predominantly with Wuhan-related exposure, 597 (92.3%) out of 647) were older (mean age 49.7 versus 44.9 years), had more cases with comorbidity (32.9% versus 19.7%), higher symptomatic burden, abnormal radiologic manifestations and, especially, a longer waiting time between symptom onset and admission (5.7 versus 4.5 days) compared with patients outside Hubei. Patients in Hubei (severe event rate 23.0% versus 11.1%, death rate 7.3% versus 0.3%, HR (95% CI) for critical illness 1.59 (1.05-2.41)) have a poorer prognosis compared with patients outside Hubei after adjusting for age and comorbidity. However, among patients outside Hubei, the duration from symptom onset to hospitalisation (mean 4.4 versus 4.7 days) and prognosis (HR (95%) 0.84 (0.40-1.80)) were similar between patients with or without Wuhan-related exposure. In the overall population, the waiting time, but neither treated in Hubei nor Wuhan-related exposure, remained an independent prognostic factor (HR (95%) 1.05 (1.01-1.08)). CONCLUSION There were more severe cases and poorer outcomes for COVID-19 patients treated in Hubei, which might be attributed to the prolonged duration of symptom onset to hospitalisation in the epicentre. Future studies to determine the reason for delaying hospitalisation are warranted.
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Affiliation(s)
- Wen-Hua Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Wei-Jie Guan
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Cai-Chen Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Yi-Min Li
- Dept of Pulmonary and Critical Care Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Heng-Rui Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Yi Zhao
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- These authors are joint first authors
| | - Xiao-Qing Liu
- Dept of Pulmonary and Critical Care Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Sang
- Dept of Pulmonary and Critical Care Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Wuhan Jin-yin tan Hospital, Wuhan, China
| | - Ru-Chong Chen
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chun-Li Tang
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tao Wang
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qi-Hua He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zi-Sheng Chen
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Sook-San Wong
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mark Zanin
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Jun Liu
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Huang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Fu Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li-Min Ou
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Cheng
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Xiong
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhan-Hong Xie
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Yu Hu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Liu
- Shenzhen Third People's Hospital, Shenzhen, China
- The Second Affiliated Hospital of Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China
| | - Hong Shan
- The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Chun-Liang Lei
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | | | - Li Wei
- Wuhan No. 1 Hospital, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Yong Liu
- Chengdu Public Health Clinical Medical Center, Chengdu, China
| | - Ya-Hua Hu
- Huangshi Central Hospital of Edong Healthcare Group, Affiliated Hospital of Hubei Polytechnic University, Huangshi, China
| | - Peng Peng
- Wuhan Pulmonary Hospital, Wuhan, China
| | - Jian-Ming Wang
- Tianyou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Ji-Yang Liu
- The First Hospital of Changsha, Changsha, China
| | - Zhong Chen
- The Third People's Hospital of Hainan Province, Sanya, China
| | - Gang Li
- Huanggang Central Hospital, Huanggang, China
| | | | - Shao-Qin Qiu
- The Third People's Hospital of Yichang, Yichang, China
| | - Jie Luo
- Affiliated Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | | | - Shao-Yong Zhu
- The People's Hospital of Huangpi District, Wuhan, China
| | - Lin-Ling Cheng
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Feng Ye
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shi-Yue Li
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jin-Ping Zheng
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nuo-Fu Zhang
- Dept of Respiratory Disease, China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan-Shan Zhong
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Both authors are joint principal authors
| | - Jian-Xing He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Both authors are joint principal authors
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Selection of viral variants during persistent infection of insectivorous bat cells with Middle East respiratory syndrome coronavirus. Sci Rep 2020; 10:7257. [PMID: 32350357 PMCID: PMC7190632 DOI: 10.1038/s41598-020-64264-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are speculated to have originated in bats. The mechanisms by which these viruses are maintained in individuals or populations of reservoir bats remain an enigma. Mathematical models have predicted long-term persistent infection with low levels of periodic shedding as a likely route for virus maintenance and spillover from bats. In this study, we tested the hypothesis that bat cells and MERS coronavirus (CoV) can co-exist in vitro. To test our hypothesis, we established a long-term coronavirus infection model of bat cells that are persistently infected with MERS-CoV. We infected cells from Eptesicus fuscus with MERS-CoV and maintained them in culture for at least 126 days. We characterized the persistently infected cells by detecting virus particles, protein and transcripts. Basal levels of type I interferon in the long-term infected bat cells were higher, relative to uninfected cells, and disrupting the interferon response in persistently infected bat cells increased virus replication. By sequencing the whole genome of MERS-CoV from persistently infected bat cells, we identified that bat cells repeatedly selected for viral variants that contained mutations in the viral open reading frame 5 (ORF5) protein. Furthermore, bat cells that were persistently infected with ΔORF5 MERS-CoV were resistant to superinfection by wildtype virus, likely due to reduced levels of the virus receptor, dipeptidyl peptidase 4 (DPP4) and higher basal levels of interferon in these cells. In summary, our study provides evidence for a model of coronavirus persistence in bats, along with the establishment of a unique persistently infected cell culture model to study MERS-CoV-bat interactions.
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Al-Tawfiq JA, Memish ZA. Middle East Respiratory Syndrome Coronavirus and Severe Acute Respiratory Syndrome Coronavirus. Semin Respir Crit Care Med 2020; 41:568-578. [PMID: 32305045 PMCID: PMC7516363 DOI: 10.1055/s-0040-1709160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Emerging infectious diseases continue to be of a significant importance worldwide with the potential to cause major outbreaks and global pandemics. In 2002, the world had witnessed the appearance of the severe acute respiratory syndrome coronavirus in China which disappeared abruptly within 6 months. About a decade later, a new and emerging novel coronavirus named the Middle East respiratory syndrome coronavirus (MERS-CoV) was described in a patient from Saudi Arabia. These two coronaviruses shared multiple similarities in the epidemiology, clinical presentations, and posed challenges in its prevention and management. Seven years since its discovery, MERS-CoV continues to be a lethal zoonotic pathogen capable of causing severe pneumonia with high case fatality rates and the ability to cause large health care-associated outbreaks.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.,Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ziad A Memish
- Director Research & Innovation Center, Research Center Department, King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia.,Department of Medicine, Al-Faisal University, Riyadh, Saudi Arabia.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
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17
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Vaccination with single plasmid DNA encoding IL-12 and antigens of severe fever with thrombocytopenia syndrome virus elicits complete protection in IFNAR knockout mice. PLoS Negl Trop Dis 2020; 14:e0007813. [PMID: 32196487 PMCID: PMC7112229 DOI: 10.1371/journal.pntd.0007813] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/01/2020] [Accepted: 02/07/2020] [Indexed: 02/01/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease caused by SFTS virus (SFTSV) infection. Despite a gradual increase of SFTS cases and high mortality in endemic regions, no specific viral therapy nor vaccine is available. Here, we developed a single recombinant plasmid DNA encoding SFTSV genes, Gn and Gc together with NP-NS fusion antigen, as a vaccine candidate. The viral antigens were fused with Fms-like tyrosine kinase-3 ligand (Flt3L) and IL-12 gene was incorporated into the plasmid to enhance cell-mediated immunity. Vaccination with the DNA provides complete protection of IFNAR KO mice upon lethal SFTSV challenge, whereas immunization with a plasmid without IL-12 gene resulted in partial protection. Since we failed to detect antibodies against surface glycoproteins, Gn and Gc, in the immunized mice, antigen-specific cellular immunity, as confirmed by enhanced antigen-specific T cell responses, might play major role in protection. Finally, we evaluated the degree of protective immunity provided by protein immunization of the individual glycoprotein, Gn or Gc. Although both protein antigens induced a significant level of neutralizing activity against SFTSV, Gn vaccination resulted in relatively higher neutralizing activity and better protection than Gc vaccination. However, both antigens failed to provide complete protection. Given that DNA vaccines have failed to induce sufficient immunogenicity in human trials when compared to protein vaccines, optimal combinations of DNA and protein elements, proper selection of target antigens, and incorporation of efficient adjuvant, need to be further investigated for SFTSV vaccine development. Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infection endemic to East Asia including China, Korea, and Japan. Gradual rise of disease incidence and relatively high mortality have become a serious public health problem in the endemic countries. In this study, we developed a recombinant plasmid DNA encoding four antigens, Gn, Gc, NP, and NS, of SFTS virus (SFTSV) as a vaccine candidate. In order to enhance cell-mediated immunity, the viral antigens were fused with Flt3L and IL-12 gene was incorporated into the plasmid. Immunization with the DNA vaccine provides complete protection against lethal SFTSV infection in IFNAR KO mice. Antigen-specific T cell responses might play a major role in the protection since we observed enhanced T cell responses specific to the viral antigens but failed to detect neutralizing antibody in the immunized mice. When we immunized with either viral glycoprotein, Gn protein induced relatively higher neutralizing activity and better protection against SFTSV infection than Gc antigen, but neither generated complete protection. Therefore, an optimal combination of DNA and protein elements, as well as proper selection of target antigens, might be required to produce an effective SFTSV vaccine.
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Generation of a Nebulizable CDR-Modified MERS-CoV Neutralizing Human Antibody. Int J Mol Sci 2019; 20:ijms20205073. [PMID: 31614869 PMCID: PMC6829326 DOI: 10.3390/ijms20205073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) induces severe aggravating respiratory failure in infected patients, frequently resulting in mechanical ventilation. As limited therapeutic antibody is accumulated in lung tissue following systemic administration, inhalation is newly recognized as an alternative, possibly better, route of therapeutic antibody for pulmonary diseases. The nebulization process, however, generates diverse physiological stresses, and thus, the therapeutic antibody must be resistant to these stresses, remain stable, and form minimal aggregates. We first isolated a MERS-CoV neutralizing antibody that is reactive to the receptor-binding domain (RBD) of spike (S) glycoprotein. To increase stability, we introduced mutations into the complementarity-determining regions (CDRs) of the antibody. In the HCDRs (excluding HCDR3) in this clone, two hydrophobic residues were replaced with Glu, two residues were replaced with Asp, and four residues were replaced with positively charged amino acids. In LCDRs, only two Leu residues were replaced with Val. These modifications successfully generated a clone with significantly greater stability and equivalent reactivity and neutralizing activity following nebulization compared to the original clone. In summary, we generated a MERS-CoV neutralizing human antibody that is reactive to recombinant MERS-CoV S RBD protein for delivery via a pulmonary route by introducing stabilizing mutations into five CDRs.
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Perlman S, Azhar EI, Memish ZA, Hui DS, Zumla A. Confronting the persisting threat of the Middle East respiratory syndrome to global health security. THE LANCET. INFECTIOUS DISEASES 2019; 20:158-160. [PMID: 31279728 PMCID: PMC7128339 DOI: 10.1016/s1473-3099(19)30347-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Stanley Perlman
- Department of Microbiology and Immunology and Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA.
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre and Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziad A Memish
- Infectious Diseases Division, Department of Medicine and Department of Research, Prince Mohamed Bin Abdulaziz Hospital, Riyadh, Saudi Arabia; Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - David S Hui
- Division of Respiratory Medicine and Stanley Ho Center for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong, China
| | - Alimuddin Zumla
- Division of Infection and Immunity, Center for Clinical Microbiology, University College London, London, UK; NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
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