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Jiang Y, Cheng X, Gao M, Yu Y, Dou X, Shen H, Tang M, Zhou S, Peng D. Two mutations on S2 subunit were critical for Vero cell tropism expansion of infectious bronchitis virus HV80. Vet Microbiol 2024; 294:110134. [PMID: 38820725 DOI: 10.1016/j.vetmic.2024.110134] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Infectious bronchitis virus (IBV) restricts cell tropism. Except for the Beaudette strain, other IBVs cannot infect mammalian cell lines. The limited cell tropism of other IBVs has hindered IBV vaccine development and research on the mechanisms of IBV infection. A novel Vero cell-adapted strain, HV80, has been previously reported. In this study, we constructed recombinants expressing the chimeric S glycoprotein, S1 or S2 subunit of strain H120 and demonstrated that mutations on S2 subunit are associated with the strain HV80 Vero cell adaptation. R687P or P687R substitution recombinants were constructed with the genome backbone of strains HV80 or H120. We found that the RRRR690/S motif at the S2' cleavage site is crucial to the Vero cell adaptation of strain HV80. Another six amino acid substitutions in the S2 subunit of the recombinants showed that the Q855H mutation induced syncytium formation. A transient transfection assay demonstrated the S glycoprotein with the PRRR690/S motif at the S2' cleavage site induced low-level cell-cell fusion, while H855Q substitution hindered cell-cell fusion and blocked cleavage event with S20 product. This study provides a basis for the construction of IBV recombinants capable of replicating in Vero cells, thus contributing to the advancement in the development of genetically engineered cell-based IBV vaccines.
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Affiliation(s)
- Yi Jiang
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xu Cheng
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Mingyan Gao
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Yan Yu
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xinhong Dou
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Haiyu Shen
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Mengjun Tang
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Sheng Zhou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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2
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McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 2024:S0092-8674(24)00646-9. [PMID: 38964328 DOI: 10.1016/j.cell.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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3
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Du W, Debski-Antoniak O, Drabek D, van Haperen R, van Dortmondt M, van der Lee J, Drulyte I, van Kuppeveld FJM, Grosveld F, Hurdiss DL, Bosch BJ. Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun 2024; 15:5330. [PMID: 38909062 PMCID: PMC11193727 DOI: 10.1038/s41467-024-49693-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Oliver Debski-Antoniak
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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4
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Meng X, Zhang J, Wan Z, Li T, Xie Q, Qin A, Shao H, Zhang H, Ye J. Molecular epidemiology of infectious bronchitis virus in eastern and southern China during 2021-2023. Poult Sci 2024; 103:103939. [PMID: 38909507 DOI: 10.1016/j.psj.2024.103939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/25/2024] Open
Abstract
As a highly infectious and contagious pathogen in chickens, infectious bronchitis virus (IBV) is currently grouped into nine genotypes (GI to GIX). However, the classification of serotypes of IBV is still not clear. In this study, 270 field strains of IBV were isolated from dead or diseased chicken flocks in eastern and southern China during January 2021 to April 2023. These isolated IBV strains could be classified into 2 genotypes, GI (including 5 lineages GI-1, GI-13, GI-19, GI-22, and GI-28) and GVI based on the complete S1 sequence. Further analysis showed that the GI-19, GI-13, GI-22, GI-28, and GVI were the dominant genotypes with the proportions of 61.48, 8.89, 8.89, 7.78, and 8.89% respectively, and the homology of S1 protein of these isolates ranged from 86.85 to 100% in GI-19, 92.22 to 100% in GI-13, 83.1 to 100% in GI-22, 94.81 to 100% in GI-28 and 90.0 to 99.8% in GVI, respectively. Moreover, cross-neutralization test with sera revealed that these isolates in GI-19 lineage could be classified into at least 3 serotypes according to the antigenic relationship. In addition, structure assay using PyMOL indicated that one mutation such as S120 in receptor binding site (RBD) of GI-19 might alter the antigenicity and conformation of S protein of IBV. Overall, our data demonstrate that not only multiple genotypes, but also multiple serotypes in a single genotype or lineage have been co-circulated in eastern and southern China, providing novel insights into the molecular evolution of the antigenicity of IBV and highlighting the significance of the selection of the dominant isolate for vaccine development in IBV endemic region.
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Affiliation(s)
- Xianchen Meng
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Biotechnology Research laboratory, Jiangsu Lihua Animal Husbandry Co., Ltd., Changzhou, Jiangsu, 213168, China
| | - Jianjun Zhang
- Sinopharm Yangzhou VAC Biological Engineering Co., Ltd., Yangzhou, Jiangsu, 225000, China
| | - Zhimin Wan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Tuofan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Quan Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Haitao Zhang
- Biotechnology Research laboratory, Jiangsu Lihua Animal Husbandry Co., Ltd., Changzhou, Jiangsu, 213168, China.
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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Cuadrado C, Breedlove C, van Santen E, Joiner KS, van Santen VL, Toro H. Protection Against Infectious Bronchitis Virus Vaccine Recombinants and Chicken-Selected Vaccine Subpopulations. Avian Dis 2024; 68:89-98. [PMID: 38885050 DOI: 10.1637/aviandiseases-d-23-00064] [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: 09/11/2023] [Accepted: 02/12/2024] [Indexed: 06/20/2024]
Abstract
Outbreaks of infectious bronchitis (IB) continue to occur from novel variants of IB virus (IBV) emerging from selection of vaccine subpopulations and/or naturally occurring recombination events. S1 sequencing of Arkansas (Ark) -type viruses obtained from clinical cases in Alabama broilers and backyard chickens shows both Ark Delmarva Poultry Industry (ArkDPI) vaccine subpopulations as well as Ark vaccine viruses showing recombination with other IB vaccine viruses. IB Ark-type isolates AL5, most similar to an ArkDPI vaccine subpopulation selected in chickens, AL4, showing a cluster of three nonsynonymous changes from ArkDPI subpopulations selected in chickens, and AL9, showing recombination with Massachusetts (Mass) -type IBV, were examined for pathogenicity and ability to break through immunity elicited by vaccination with a commercial ArkDPI vaccine. Analysis of predicted S1 protein structures indicated the changes were in regions previously shown to comprise neutralizing epitopes. Thus, they were expected to contribute to immune escape and possibly virulence. Based on clinical signs, viral load, and histopathology, all three isolates caused disease in naïve chickens, although AL9 and AL5 viral loads in trachea were statistically significantly higher (30- and 40-fold) than AL4. S1 gene sequencing confirmed the stability of the relevant changes in the inoculated viruses in the chickens, although virus in some individual chickens exhibited additional S1 changes. A single amino acid deletion in the S1 NTD was identified in some individual chickens. The location of this deletion in the predicted structure of S1 suggested the possibility that it was a compensatory change for the reduced ability of AL4 to replicate in the trachea of naïve chickens. Chickens vaccinated with a commercial ArkDPI vaccine at day of hatch and challenged at 21 days of age showed that vaccination provided incomplete protection against challenge with these viruses. Moreover, based on viral RNA copy numbers in trachea, differences were detected in the ability of the vaccine to protect against these IBV isolates, with the vaccine protecting the most poorly against AL4. These results provide additional evidence supporting that IBV attenuated vaccines, especially ArkDPI vaccines, contribute to perpetuating the problem of IB in commercial chickens.
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Affiliation(s)
- Camila Cuadrado
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36830
| | - Cassandra Breedlove
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36830
| | - Edzard van Santen
- Statistical Consulting Unit and Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611
| | - Kelly S Joiner
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36830
| | - Vicky L van Santen
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36830
| | - Haroldo Toro
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL 36830,
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6
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Chen Y, Feng C, Huang C, Shi Y, Omar SM, Zhang B, Cai G, Liu P, Guo X, Gao X. Preparation of polyclonal antibodies to chicken P62 protein and its application in nephropathogenic infectious bronchitis virus-infected chickens. Int J Biol Macromol 2024; 271:132515. [PMID: 38768912 DOI: 10.1016/j.ijbiomac.2024.132515] [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: 04/12/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
p62, also known as SQSTM1, has been shown to be closely related to the coronavirus. However, it remains unclear on the relationship between p62 and NIBV infection. Moreover, there are no available antibodies against the chicken p62 protein. Thus, this study aimed to prepare p62 polyclonal antibody and investigate the correlation between the p62 protein and NIBV infection. Here, PET-32a-p62 prokaryotic fusion expression vector was constructed for prokaryotic protein expression, and then p62 polyclonal antibody was prepared by immunizing rabbits. Lastly, these antibodies were then utilized in Western blotting (WB), immunohistochemistry (IHC), and immunofluorescence (IF) assays. The results showed that we successfully prepared chicken p62 polyclonal antibody. Meanwhile, WB and IF demonstrated that the expression of p62 showed a trend of first increase and then decrease after NIBV infection. IHC showed that the expression of p62 in the spleen, lung, kidney, bursa of Fabricius and trachea of chickens infected with NIBV in 11 dpi was significantly higher than that of normal chickens. Taken together, this study successfully prepared a polyclonal antibody for chicken p62 protein and confirmed its application and expression in chickens, as well as the expression of p62 in tissues after NIBV infection.
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Affiliation(s)
- Yunfeng Chen
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Chenlu Feng
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Cheng Huang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yan Shi
- School of Computer and Information Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Salma Mbarouk Omar
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Bingqing Zhang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Gaofeng Cai
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Xiaona Gao
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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7
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Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [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: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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8
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Franzo G, Faustini G, Tucciarone CM, Poletto F, Tonellato F, Cecchinato M, Legnardi M. The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus. Viruses 2024; 16:481. [PMID: 38543846 PMCID: PMC10974917 DOI: 10.3390/v16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the "Old World". Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each with distinct production systems and control strategies. This study leverages this scenario to explore how different environments may influence virus evolution. Through the analysis of the complete S1 sequence, four datasets were identified, comprising strains of monophyletic clades circulating in different continents or countries (e.g., Asia vs. Europe and China vs. Thailand), indicative of single introduction events and independent evolution. The population dynamics and evolutionary rate variation over time, as well as the presence and intensity of selective pressures, were estimated and compared across these datasets. Since the lineage origin (approximately in the mid-20th century), a more persistent and stable viral population was estimated in Asia and China, while in Europe and Thailand, a sharp increase following the introduction (i.e., 2005 and 2007, respectively) of GI-19 was observed, succeeded by a rapid decline. Although a greater number of sites on the S1 subunit were under diversifying selection in the Asian and Chinese datasets, more focused and stronger pressures were evident in both the European (positions 2, 52, 54, 222, and 379 and Thai (i.e., positions 10, 12, 32, 56, 62, 64, 65, 78, 95, 96, 119, 128, 140, 182, 292, 304, 320, and 323) strains, likely reflecting a more intense and uniform application of vaccines in these regions. This evidence, along with the analysis of control strategies implemented in different areas, suggests a strong link between effective, systematic vaccine implementation and infection control. However, while the overall evolutionary rate was estimated at approximately 10-3 to 10-4, a significant inverse correlation was found between viral population size and the rate of viral evolution over time. Therefore, despite the stronger selective pressure imposed by vaccination, effectively constraining the former through adequate control strategies can efficiently prevent viral evolution and the emergence of vaccine-escaping variants.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (G.F.); (C.M.T.); (F.P.); (F.T.); (M.C.); (M.L.)
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9
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Keep S, Stevenson-Leggett P, Webb I, Fones A, Kirk J, Britton P, Bickerton E. The spike protein of the apathogenic Beaudette strain of avian coronavirus can elicit a protective immune response against a virulent M41 challenge. PLoS One 2024; 19:e0297516. [PMID: 38265985 PMCID: PMC10807761 DOI: 10.1371/journal.pone.0297516] [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: 11/08/2023] [Accepted: 01/07/2024] [Indexed: 01/26/2024] Open
Abstract
The avian Gammacoronavirus infectious bronchitis virus (IBV) causes major economic losses in the poultry industry as the aetiological agent of infectious bronchitis, a highly contagious respiratory disease in chickens. IBV causes major economic losses to poultry industries across the globe and is a concern for global food security. IBV vaccines are currently produced by serial passage, typically 80 to 100 times in chicken embryonated eggs (CEE) to achieve attenuation by unknown molecular mechanisms. Vaccines produced in this manner present a risk of reversion as often few consensus level changes are acquired. The process of serial passage is cumbersome, time consuming, solely dependent on the supply of CEE and does not allow for rapid vaccine development in response to newly emerging IBV strains. Both alternative rational attenuation and cell culture-based propagation methods would therefore be highly beneficial. The majority of IBV strains are however unable to be propagated in cell culture proving a significant barrier to the development of cell-based vaccines. In this study we demonstrate the incorporation of a heterologous Spike (S) gene derived from the apathogenic Beaudette strain of IBV into a pathogenic M41 genomic backbone generated a recombinant IBV denoted M41K-Beau(S) that exhibits Beaudette's unique ability to replicate in Vero cells, a cell line licenced for vaccine production. The rIBV M41K-Beau(S) additionally exhibited an attenuated in vivo phenotype which was not the consequence of the presence of a large heterologous gene demonstrating that the Beaudette S not only offers a method for virus propagation in cell culture but also a mechanism for rational attenuation. Although historical research suggested that Beaudette, and by extension the Beaudette S protein was poorly immunogenic, vaccination of chickens with M41K-Beau(S) induced a complete cross protective immune response in terms of clinical disease and tracheal ciliary activity against challenge with a virulent IBV, M41-CK, belonging to the same serogroup as Beaudette. This implies that the amino acid sequence differences between the Beaudette and M41 S proteins have not distorted important protective epitopes. The Beaudette S protein therefore offers a significant avenue for vaccine development, with the advantage of a propagation platform less reliant on CEE.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Surrey, United Kingdom
| | | | - Isobel Webb
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, The University of Bristol, Bristol, United Kingdom
| | | | - James Kirk
- The Pirbright Institute, Surrey, United Kingdom
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10
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McCallum M, Park YJ, Stewart C, Sprouse KR, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574565. [PMID: 38260518 PMCID: PMC10802434 DOI: 10.1101/2024.01.09.574565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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11
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Saleem W, Vereecke N, Zaman MG, Afzal F, Reman I, Khan SUH, Nauwynck H. Genotyping and phylogeography of infectious bronchitis virus isolates from Pakistan show unique linkage to GI-24 lineage. Poult Sci 2024; 103:103236. [PMID: 37980750 PMCID: PMC10685022 DOI: 10.1016/j.psj.2023.103236] [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: 05/02/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/21/2023] Open
Abstract
Infectious bronchitis virus (IBV) is prevalent in Pakistan causing enormous economic losses. To date no clear data are available on circulating genotypes and phylogeographic spread of the virus. Hence current study assessed these parameters for all available IBV Pakistani isolates, based on the 9 new sequences, with respect to other Asian and non-Asian countries. Results indicated that all Pakistani isolates belonged to genotype I (GI), with more than half of them (16/27) belonging to the GI-24 lineage, against which no vaccine is available. Three possible introduction events of the GI-13 IBV lineage into Pakistan, based on the estimated IBV population using isolates from this study, were observed possibly from Afghanistan, China, and/or Egypt. These events were further analyzed on the S1 amino acid level which showed unique alterations (S250H, T270K, and Q298S) in 1 isolate (IBV4, GI-13) when compared to GI-1 lineage. Both GI-1 and GI-13 Pakistani strains showed close homology with homologous vaccine strains that are used in Pakistan. For GI-24 strains, none of the used vaccines showed substantial homology, necessitating the need for further exploration of this lineage and vaccine design. In addition, our findings highlight the importance of genomic surveillance to support phylogeographical studies on IBV in genotyping and molecular epidemiology.
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Affiliation(s)
- Waqar Saleem
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium.
| | - Nick Vereecke
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Pathosense BV, Lier 2500, Belgium
| | - Muhammad Goher Zaman
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, 54770 Islamabad, Pakistan
| | - Farhan Afzal
- Disease Diagnostic Laboratory, Poultry Research Institute, 46000 Rawalpindi, Pakistan
| | - Iqra Reman
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, 54770 Islamabad, Pakistan
| | - Saeed Ul-Hasan Khan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, 54770 Islamabad, Pakistan
| | - Hans Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Pathosense BV, Lier 2500, Belgium
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12
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Zhang Y, Han Z, Li H, Liu S. Development of a Recombinant Enzyme-Linked Immunosorbent Assay for the Detection of Antibodies Against Infectious Bronchitis Virus. Viral Immunol 2023; 36:649-658. [PMID: 37903239 DOI: 10.1089/vim.2023.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023] Open
Abstract
Infectious bronchitis virus (IBV), a gammacoronavirus within the Coronaviridae family, is an economically important etiological disease agent in chickens. Both early diagnosis and determination of the immune status of chickens are important for controlling IBV outbreaks in chicken flocks. The N protein is the most abundantly expressed virus-derived protein during IBV infection and can induce a strong immune response by producing antibodies during early infection or immunization. In this study, we found that the amino acid sequences of the N protein between CK/CH/LJL/04I and the other 22 IBVs were conserved, especially in the 1-160 amino acid region. Based on the sequence similarities, the three recombinant proteins, rN160 (amino acid positions 1-160), rN266 (144-409), and rN409 (1-409), were expressed using the Escherichia coli system and subsequently purified. The results demonstrated that the antigenicity and reactivity of rN160 were better than those of rN266 and rN409. As a result, an indirect enzyme-linked immunosorbent assay (ELISA) (rN160 ELISA) was developed to detect the IBV antibody based on the rN160 protein. Using 1,500 clinical field serum samples, the relative sensitivity, specificity, and accuracy of the rN160 ELISA were 98.97%, 92.34%, and 97.93%, respectively, compared to those of a commercial ELISA kit (IDEXX), indicating a strong positive correlation between the two methods. Taken together, these results reveal that the rN160 ELISA is a rapid, simple, and sensitive method for detecting group-specific IBV antibodies for epidemiological investigation and antibody-level monitoring.
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Affiliation(s)
- Yu Zhang
- Division of Avian Infectious Diseases, State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, the People's Republic of China
| | - Zongxi Han
- Division of Avian Infectious Diseases, State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, the People's Republic of China
| | - Huixin Li
- Division of Avian Infectious Diseases, State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, the People's Republic of China
| | - Shengwang Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, the People's Republic of China
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13
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Geng Q, Wan Y, Hsueh FC, Shang J, Ye G, Bu F, Herbst M, Wilkens R, Liu B, Li F. Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. eLife 2023; 12:e74060. [PMID: 37991488 PMCID: PMC10695562 DOI: 10.7554/elife.74060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
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Affiliation(s)
- Qibin Geng
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Yushun Wan
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Jian Shang
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Rowan Wilkens
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Bin Liu
- Hormel Institute, University of MinnesotaAustinUnited States
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
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14
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Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X. Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. Life Sci Alliance 2023; 6:e202201796. [PMID: 37402591 PMCID: PMC10320017 DOI: 10.26508/lsa.202201796] [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: 11/02/2022] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.
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Affiliation(s)
- Xixi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yutong Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lutang Fu
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Peiyi Wang
- Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China
| | - Xiaolin Zhong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Liang Jin
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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15
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Hong SM, Kim SJ, An SH, Kim J, Ha EJ, Kim H, Kwon HJ, Choi KS. Receptor binding motif surrounding sites in the spike 1 protein of infectious bronchitis virus have high susceptibility to mutation related to selective pressure. J Vet Sci 2023; 24:e51. [PMID: 37532296 PMCID: PMC10404704 DOI: 10.4142/jvs.23039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. OBJECTIVE This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. METHODS The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). RESULTS Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. CONCLUSIONS Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.
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Affiliation(s)
- Seung-Min Hong
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Se-Hee An
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jiye Kim
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Eun-Jin Ha
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Howon Kim
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hyuk-Joon Kwon
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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16
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You R, Liu K, Huang M, Tang L, Zhang X, Huang Y, Zhao J, Zhao Y, Ye L, Zhang G. Identification and Comparison of the Sialic Acid-Binding Domain Characteristics of Avian Coronavirus Infectious Bronchitis Virus Spike Protein. J Virol 2023; 97:e0048923. [PMID: 37097156 PMCID: PMC10231253 DOI: 10.1128/jvi.00489-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
Infectious bronchitis virus (IBV) infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host factors and fuses the viral and cell membranes. The N-terminal domain of the S1 subunit of IBV S protein binds to sialic acids, but the precise location of the sialic acid binding domain (SABD) and the role of the SABD in IBV-infected chickens remain unclear. Here, we identify the S1 N-terminal amino acid (aa) residues 19 to 227 (209 aa total) of IBV strains SD (GI-19) and GD (GI-7), and the corresponding region of M41 (GI-1), as the minimal SABD using truncated protein histochemistry and neuraminidase assays. Both α-2,3- and α-2,6-linked sialic acids on the surfaces of CEK cells can be used as attachment receptors by IBV, leading to increased infection efficiency. However, 9-O acetylation of the sialic acid glycerol side chain inhibits IBV S1 and SABD protein binding. We further constructed recombinant strains in which the S1 gene or the SABD in the GD and SD genomes were replaced with the corresponding region from M41 by reverse genetics. Infecting chickens with these viruses revealed that the virulence and nephrotropism of rSDM41-S1, rSDM41-206, rGDM41-S1, and rGDM41-206 strains were decreased to various degrees compared to their parental strains. A positive sera cross-neutralization test showed that the serotypes were changed for the recombinant viruses. Our results provide insight into IBV infection of host cells that may aid vaccine design. IMPORTANCE To date, only α-2,3-linked sialic acid has been identified as a potential host binding receptor for IBV. Here, we show the minimum region constituting the sialic acid binding domain (SABD) and the binding characteristics of the S1 subunit of spike (S) protein of IBV strains SD (GI-19), GD (GI-7), and M41 (GI-1) to various sialic acids. The 9-O acetylation modification partially inhibits IBV from binding to sialic acid, while the virus can also bind to sialic acid molecules linked to host cells through an α-2,6 linkage, serving as another receptor determinant. Substitution of the putative SABD from strain M41 into strains SD and GD resulted in reduced virulence, nephrotropism, and a serotype switch. These findings suggest that sialic acid binding has diversified during the evolution of γ-coronaviruses, impacting the biological properties of IBV strains. Our results offer insight into the mechanisms by which IBV invades host cells.
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Affiliation(s)
- Renrong You
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kangchengyin Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Min Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Lihua Tang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Xuehui Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yahui Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, People’s Republic of China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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17
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Yan W, Yang Q, Huang S, Liu S, Wang K, Tang Y, Lei C, Wang H, Yang X. Insights on genetic characterization and pathogenesis of a GI-19 (QX-like) infectious bronchitis virus isolated in China. Poult Sci 2023; 102:102719. [PMID: 37156078 DOI: 10.1016/j.psj.2023.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/29/2023] [Accepted: 04/09/2023] [Indexed: 05/10/2023] Open
Abstract
Infectious bronchitis virus (IBV) causes respiratory diseases in chickens, incurring great losses to the poultry industry worldwide. In this study, we isolated an IBV strain, designated as AH-2020, from the chickens vaccinated with H120 and 4/91 in Anhui, China. The sequence homology analysis based on the S1 gene revealed that AH-2020 shares low similarities with the 3 vaccine strains, namely, H120, LDT3-A, and 4/91 (78.19, 80.84, and 81.6%, respectively). Phylogenetic analysis based on the S1 gene revealed that AH-2020 clustered with the GI-19 type. Furthermore, protein modeling revealed that the mutations in the amino acids in AH-2020 were mainly located in the N-terminal domain of S1 (S1-NTD), and the pattern of deletion and insertion mutations in the S1 protein may have influenced the structural changes on the surface of S1. Further, approximately 7-day-old SPF chickens were inoculated with AH-2020 at 106.0 EID50. These chickens exhibited clinical signs of the infection such as listlessness, huddling, and head-shaking, accompanied by depression and 40% mortality. Serum antibody test demonstrated that in response to the AH-2020 infection, the antibody level increased the fastest at 7 dpi, with virus shedding rate of cloaca being 100% at 14 dpi. The viral titer in various tissues was detected using hematoxylin and eosin staining and immunohistochemistry, which revealed that AH-2020 infection can damage the kidney, trachea, lung, cecal tonsil, and bursa of Fabricius. Our study provided evidence that the GI-19-type IBV is undergoing more complex mutations, and effective measures are urgently needed to prevent the spread of these variant strains.
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Affiliation(s)
- Wenjun Yan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Qingcheng Yang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Siyu Huang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Song Liu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Kailu Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Yizhi Tang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Cangwei Lei
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Hongning Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xin Yang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu 610064, China.
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18
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A novel S2-derived peptide-based ELISA for broad detection of antibody against infectious bronchitis virus. Poult Sci 2023; 102:102661. [PMID: 37037098 PMCID: PMC10120374 DOI: 10.1016/j.psj.2023.102661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Avian infectious bronchitis (IB) is a highly contagious disease caused by infectious bronchitis virus (IBV). Vaccination is an effective approach for controlling IBV. Therefore, reliable immune monitoring for IB is critical for poultry. In this study, a novel peptide derived from S2 protein was used to develop an enzyme-linked immunosorbent assay (ELISA) for the detection of broadly cross-reactive antibodies against IBV. The peptide-based ELISA (pELISA) showed good specificity and sensitivity in detecting IBV antibodies against different serotypes. A semilogarithmic regression method for determining IBV antibody titers was also established. Antibody titers detected by pELISA and calculated with this equation were statistically similar to those evaluated by indirect fluorescence assay (IFA). Moreover, the comparison analysis showed a 96.07% compatibility between the pELISA and IDEXX ELISA. All these data demonstrate that the pELISA generated here can be as a rapid and reliable serological surveillance tool for monitoring IBV infection or vaccination.
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Vermeulen CJ, Dijkman R, de Wit JJS, Bosch BJ, Heesterbeek JAPH, van Schaik G. Genetic analysis of infectious bronchitis virus (IBV) in vaccinated poultry populations over a period of 10 years. Avian Pathol 2023; 52:157-167. [PMID: 36745131 DOI: 10.1080/03079457.2023.2177140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infectious bronchitis virus (IBV) is an avian pathogen from the Coronavirus family causing major health issues in poultry flocks worldwide. Because of its negative impact on health, performance, and bird welfare, commercial poultry are routinely vaccinated by administering live attenuated virus. However, field strains are capable of rapid adaptation and may evade vaccine-induced immunity. We set out to describe dynamics within and between lineages and assess potential escape from vaccine-induced immunity. We investigated a large nucleotide sequence database of over 1700 partial sequences of the S1 spike protein gene collected from clinical samples of Dutch chickens submitted to the laboratory of Royal GD between 2011 and 2020. Relative frequencies of the two major lineages GI-13 (793B) and GI-19 (QX) did not change in the investigated period, but we found a succession of distinct GI-19 sublineages. Analysis of dN/dS ratio over all sequences demonstrated episodic diversifying selection acting on multiple sites, some of which overlap predicted N-glycosylation motifs. We assessed several measures that would indicate divergence from vaccine strains, both in the overall database and in the two major lineages. However, the frequency of vaccine-homologous lineages did not decrease, no increase in genetic variation with time was detected, and the sequences did not grow more divergent from vaccine sequences in the examined time window. Concluding, our results show sublineage turnover within the GI-19 lineage and we demonstrate episodic diversifying selection acting on the partial sequence, but we cannot confirm nor rule out escape from vaccine-induced immunity.RESEARCH HIGHLIGHTSSuccession of GI-19 IBV variants in broiler populations.IBV lineages overrepresented in either broiler, or layer production chickens.Ongoing episodic selection at the IBV S1 spike protein gene sequence.Several positively selected codons coincident with N-glycosylation motifs.
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Affiliation(s)
- Cornelis J Vermeulen
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Royal GD (GD Animal Health), Deventer, The Netherlands
| | - Remco Dijkman
- Royal GD (GD Animal Health), Deventer, The Netherlands
| | - J J Sjaak de Wit
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Royal GD (GD Animal Health), Deventer, The Netherlands
| | - Berend-Jan Bosch
- Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - J A P Hans Heesterbeek
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gerdien van Schaik
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Royal GD (GD Animal Health), Deventer, The Netherlands
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20
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Li SY, Shen YX, Xiang XL, Li YX, Li NL, Wang AD, Cui M, Han XF, Huang Y, Xia J. The conserved L1089 in the S2 subunit of avian infectious bronchitis virus determines viral kidney tropism by disrupting virus-cell fusion. Vet Microbiol 2023; 277:109619. [PMID: 36525909 DOI: 10.1016/j.vetmic.2022.109619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
The virulence of avian gamma-coronavirus infectious bronchitis viruses (IBV) for the kidney has led to high mortality in dominant-genotype isolations, but the key sites of viral protein that determine kidney tropism are still not fully clear. In this study, the amino acid sequences of the S2 subunit of IBVs with opposing adaptivity to chicken embryonic kidney cells (CEKs) were aligned to identify putative sites associated with differences in viral adaptability. The S2 gene and the putative sites of the non-adapted CN strain were introduced into the CEKs-adapted SczyC30 strain to rescue seven mutants. Analysis of growth characteristics showed that the replacement of the entire S2 subunit and the L1089I substitution in the S2 subunit entirely abolished the proliferation of recombinant IBV in CEKs as well as in primary chicken oviduct epithelial cells. Pathogenicity assays also support the decisive role of this L1089 for viral nephrotropism, and this non-nephrotropic L1089I substitution significantly attenuates pathogenicity. Analysis of the putative cause of proliferation inhibition in CEKs suggests that the L1089I substitution affects neither virus attachment nor endocytosis, but instead fails to form double-membrane vesicles to initiate the viral replication and translation. Position 1089 of the IBV S2 subunit is conservative and predicted to lie in heptad repeat 2 domains. It is therefore reasonable to conclude that the L1089I substitution alters the nephrotropism of parent strain by affecting virus-cell fusion. These findings provide crucial insights into the adaptive mechanisms of IBV and have applications in the development of vaccines and drugs against IB.
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Affiliation(s)
- Shu-Yun Li
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Yu-Xi Shen
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Xue-Lian Xiang
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Yong-Xin Li
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Nian-Ling Li
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - An-Dong Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Min Cui
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Xin-Feng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
| | - Jing Xia
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road, Wenjiang, Chengdu, Sichuan 611130, P. R. China.
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21
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Ardicli O, Carli KT, Satitsuksanoa P, Dreher A, Cusini A, Hutter S, Mirer D, Rückert B, Jonsdottir H, Weber B, Cervia C, Akdis M, Boyman O, Eggel A, Brüggen M, Akdis C, van de Veen W. Exposure to avian coronavirus vaccines is associated with increased levels of SARS-CoV-2-cross-reactive antibodies. Allergy 2022; 77:3648-3662. [PMID: 35869837 PMCID: PMC9467642 DOI: 10.1111/all.15441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/01/2022] [Accepted: 07/09/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Although avian coronavirus infectious bronchitis virus (IBV) and SARS-CoV-2 belong to different genera of the Coronaviridae family, exposure to IBV may result in the development of cross-reactive antibodies to SARS-CoV-2 due to homologous epitopes. We aimed to investigate whether antibody responses to IBV cross-react with SARS-CoV-2 in poultry farm personnel who are occupationally exposed to aerosolized IBV vaccines. METHODS We analyzed sera from poultry farm personnel, COVID-19 patients, and pre-pandemic controls. IgG levels against the SARS-CoV-2 antigens S1, RBD, S2, and N and peptides corresponding to the SARS-CoV-2 ORF3a, N, and S proteins as well as whole virus antigens of the four major S1-genotypes 4/91, IS/1494/06, M41, and D274 of IBV were investigated by in-house ELISAs. Moreover, live-virus neutralization test (VNT) was performed. RESULTS A subgroup of poultry farm personnel showed elevated levels of specific IgG for all tested SARS-CoV-2 antigens compared with pre-pandemic controls. Moreover, poultry farm personnel, COVID-19 patients, and pre-pandemic controls showed specific IgG antibodies against IBV strains. These antibody titers were higher in long-term vaccine implementers. We observed a strong correlation between IBV-specific IgG and SARS-CoV-2 S1-, RBD-, S2-, and N-specific IgG in poultry farm personnel compared with pre-pandemic controls and COVID-19 patients. However, no neutralization was observed for these cross-reactive antibodies from poultry farm personnel using the VNT. CONCLUSION We report here for the first time the detection of cross-reactive IgG antibodies against SARS-CoV-2 antigens in humans exposed to IBV vaccines. These findings may be useful for further studies on the adaptive immunity against COVID-19.
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Affiliation(s)
- Ozge Ardicli
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
- Department of Microbiology, Faculty of Veterinary MedicineBursa Uludag UniversityBursaTurkey
| | - K. Tayfun Carli
- Department of Microbiology, Faculty of Veterinary MedicineBursa Uludag UniversityBursaTurkey
| | | | - Anita Dreher
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Alexia Cusini
- Division of Infectious DiseasesCantonal Hospital of GrisonsChurSwitzerland
| | - Sandra Hutter
- Central LaboratoryCantonal Hospital of GrisonsChurSwitzerland
| | - David Mirer
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
| | - Beate Rückert
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
| | - Hulda R. Jonsdottir
- Spiez Laboratory, Federal Office for Civil ProtectionSpiezSwitzerland
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
- Department of BioMedical ResearchUniversity of BernBernSwitzerland
| | - Benjamin Weber
- Spiez Laboratory, Federal Office for Civil ProtectionSpiezSwitzerland
| | - Carlo Cervia
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Mubeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
| | - Onur Boyman
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
- Faculty of MedicineUniversity of ZurichZurichSwitzerland
| | - Alexander Eggel
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
- Department of BioMedical ResearchUniversity of BernBernSwitzerland
| | - Marie‐Charlotte Brüggen
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
- Faculty of MedicineUniversity of ZurichZurichSwitzerland
- Department of DermatologyUniversity Hospital ZurichZurichSwitzerland
| | - Cezmi A. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
- Christine Kühne‐Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland
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22
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Genotyping and In Silico Analysis of Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Spike 1 (S1) Glycoprotein. Genes (Basel) 2022; 13:genes13091617. [PMID: 36140785 PMCID: PMC9498812 DOI: 10.3390/genes13091617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Genetic diversity and evolution of infectious bronchitis virus (IBV) are mainly impacted by mutations in the spike 1 (S1) gene. This study focused on whole genome sequencing of an IBV isolate (IBV/Ck/Can/2558004), which represents strains highly prevalent in Canadian commercial poultry, especially concerning features related to its S1 gene and protein sequences. Based on the phylogeny of the S1 gene, IBV/Ck/Can/2558004 belongs to the GI-17 lineage. According to S1 gene and protein pairwise alignment, IBV/Ck/Can/2558004 had 99.44–99.63% and 98.88–99.25% nucleotide (nt) and deduced amino acid (aa) identities, respectively, with five Canadian Delmarva (DMV/1639) IBVs isolated in 2019, and it also shared 96.63–97.69% and 94.78–97.20% nt and aa similarities with US DMV/1639 IBVs isolated in 2011 and 2019, respectively. Further homology analysis of aa sequences showed the existence of some aa substitutions in the hypervariable regions (HVRs) of the S1 protein of IBV/Ck/Can/2558004 compared to US DMV/1639 isolates; most of these variant aa residues have been subjected to positive selection pressure. Predictive analysis of potential N-glycosylation and phosphorylation motifs showed either loss or acquisition in the S1 glycoprotein of IBV/Ck/Can/2558004 compared to S1 of US DMV/1639 IBV. Furthermore, bioinformatic analysis showed some of the aa changes within the S1 protein of IBV/Ck/Can/2558004 have been predicted to impact the function and structure of the S1 protein, potentially leading to a lower binding affinity of the S1 protein to its relevant ligand (sialic acid). In conclusion, these findings revealed that the DMV/1639 IBV isolates are under continuous evolution among Canadian poultry.
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23
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Tian G, Shi Y, Cao X, Chen W, Gu Y, Li N, Huang C, Zhuang Y, Li G, Liu P, Hu G, Gao X, Guo X. Preparation of the RIPK3 Polyclonal Antibody and Its Application in Immunoassays of Nephropathogenic Infectious Bronchitis Virus-Infected Chickens. Viruses 2022; 14:v14081747. [PMID: 36016369 PMCID: PMC9412573 DOI: 10.3390/v14081747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
Receptor interacting protein kinase 3 (RIPK3) is a vital serine/threonine kinase in regulating the programmed destruction of infected cells to defend against RNA viruses. Although the role of RIPK3 in viruses in mice is well characterized, it remains unclear where in nephropathogenic infectious bronchitis virus (NIBV) in chickens. Here, we use a self-prepared polyclonal antibody to clarify the abundance of RIPK3 in tissues and define the contributions of RIPK3 in tissue damage caused by NIBV infection in chickens. Western blot analyses showed that RIPK3 polyclonal antibody can specifically recognize RIPK3 in the vital tissues of Hy-Line brown chicks and RIPK3 protein is abundantly expressed in the liver and kidney. Moreover, NIBV significantly upregulated the expression levels of RIPK3 in the trachea and kidney of chicks in a time-dependent manner. In addition, the activation of necroptosis in response to NIBV infection was demonstrated by the coimmunoprecipitation (CoIP) experiments through RIPK3 in the necrosome, which phosphorylates its downstream mixed-spectrum kinase structural domain-like protein (MLKL). Our findings offered preliminary insights into the key role of RIPK3 protein in studying the underlying mechanism of organ failure caused by NIBV infection.
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Affiliation(s)
- Guanming Tian
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yan Shi
- School of Computer and Information Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xianhong Cao
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wei Chen
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yueming Gu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ning Li
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Cheng Huang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yu Zhuang
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaona Gao
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (X.G.); (X.G.); Tel.: +86-13870917561 (X.G.); +86-15195717316 (X.G.)
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (X.G.); (X.G.); Tel.: +86-13870917561 (X.G.); +86-15195717316 (X.G.)
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Liang H, Zhang W, Chen Z, Chen X. Visualizing a Field of Research for the Coronavirus Replication in Humans with Knowledge Mapping: Evidence from Web of Science. Interdiscip Sci 2022; 14:471-484. [PMID: 35150388 PMCID: PMC8853024 DOI: 10.1007/s12539-022-00504-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/05/2022] [Accepted: 01/18/2022] [Indexed: 11/26/2022]
Abstract
Background The outbreak of COVID-19 sweeping the globe in 2020 has caused widespread fear and threatened global health security. Compared to SARS and MERS, COVID-19 also causes severe respiratory diseases and even fatal diseases but have many differences, such as the unidentified gene sequence and replication mechanism. From SARS to MERS, and then to COVID-19, coronaviruses have significant variations in host adaptation, virus evolution, infectivity, spread, and pathogenicity due to its unique replication mechanism. Methods A field of research for the coronavirus replication in humans was visualized with a database covering 9177 kinds of literature in Web of Science from 2002 through October 2021 to provide cognitive direction for the epidemic situation of virus infection. Knowledge Mapping by CiteSpace and Bibliometrix Package in R Software was drawn to depict the underlying features of viral replication and changing trends of studies, with these analyses including co-citation, density visualization, keyword clustering, and time zone. Results The keyword frequencies of "replication," ''infection," and ''spike protein" repeatedly appeared in published papers. Coronavirus can promote or inhibit apoptosis, depending on the balance between viral protein and apoptotic factors. When the living environment of cells is irreversibly damaged by the virus, cells have to start the apoptosis mechanism to prevent the replication, transmission, and spread of the virus. The replication, assembly and transmission of coronavirus can inhibit cells from entering the apoptosis prematurely with the fusion of spike protein and cell receptor in human. Conclusion Our results indicated that "viral infection," spike protein," and "mutation" might be future research hotspots on coronavirus replication in humans. The attention should be paid to the mutations of S protein and these mutants carrying mutations. Graphical abstract ![]()
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25
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Li S, Fan S, Li N, Shen Y, Xiang X, Chen W, Xia J, Han X, Cui M, Huang Y. The N1038S Substitution and 1153EQTRPKKSV 1162 Deletion of the S2 Subunit of QX-Type Avian Infectious Bronchitis Virus Can Synergistically Enhance Viral Proliferation. Front Microbiol 2022; 13:829218. [PMID: 35432239 PMCID: PMC9006875 DOI: 10.3389/fmicb.2022.829218] [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: 12/05/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The S2 subunit of infectious bronchitis virus (IBV) plays a critical role in the process of IBV infection. A comparison between the S2 subunit sequence of chicken embryo kidney cell (CEK) adapted virulent QX-like IBV strain SczyC30 (hereafter referred to as zy30) and its CEK-attenuated strain, SczyC100, revealed an N1038S substitution in S2 subunit and a 1154EQTRPKKSV1162 residue deletion in the C-terminus of the S2 subunit. In order to explore whether these two mutations are related to changes in the biological characteristics of IBV, we firstly constructed an infectious clone of zy30 using a bacterial artificial chromosome (BAC), which combines the transcription of infectious IBV genomic RNA in non-susceptible BHK-21 cells with the amplification of rescued virus rzy30 in CEK cells. Then, three recombinant viruses, including an rzy30S2-N1038S strain that contained the N1038S substitution, an rzy30S2-CT9△ strain that contained the 1154EQTRPKKSV1162 deletion, and an rzy30S2-N1038S-CT9△ strain that contained both mutations, were constructed using rescued virus rzy30 as the backbone. The results showed that each mutation did not significantly affect the replication titer in CEK cells but reduced pathogenicity in chickens, while in combination, the N1038S substitution and 1154EQTRPKKSV1162 deletion improved the proliferation efficiency in CEK cells and reduced pathogenicity, compared to rzy30 strain. The contribution made by the 1154EQTRPKKSV1162 deletion in reducing pathogenicity was higher than that of N1038S substitution. Our results revealed that the N1038S substitution and 1154EQTRPKKSV1162 deletion in S2 subunit were deeply involved in the replication efficiency of IBV and contributed to reduction of viral pathogenicity.
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Affiliation(s)
- Shuyun Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shunyi Fan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Nianning Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuxi Shen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuelian Xiang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wen Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Xia
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Min Cui
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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26
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Phillygenin activates PKR/eIF2α pathway and induces stress granule to exert anti-avian infectious bronchitis virus. Int Immunopharmacol 2022; 108:108764. [PMID: 35421804 DOI: 10.1016/j.intimp.2022.108764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/22/2022]
Abstract
The prevalence of avian infectious bronchitis virus (IBV) is still one of causes inducing severe losses of production in the poultry industry worldwide. Vaccination does not completely prevent IBV infection and spread due to immune failure and viral mutations. ForsythiaeFructus and its compounds have been widely used in a lot of prescriptions of the traditional Chinese medicine for a long history, and it is well-known as safety and efficiency in heat-clearing and detoxifying. This study aims to investigate the anti-IBV activity and mechanism of phillygenin. The results showed that phillygenin inhibited IBV replication by disturbing multiple stages of the virus life cycle, including viral adsorption, invasion, internalization, and release in Vero cells. After being treated with 100, 125 and 150 μg/mL phillygenin, the expression of G3BP1 was significantly increased and the phosphorylation of PKR/eIF2α was activated, which increased stress granule, thereby triggering the antiviral response in Vero cells. The anti-virus activity of PHI was decreased when G3BP1 was interfered by si-RNA, and G3BP1 was down-regulated when PKR/eIF2α was interfered by si-RNA. In conclusion, our findings indicate that phillygenin activates PKR/eIF2α pathway and induces stress granule formation to exert anti-IBV, which holds promise to develop into a novel anti-IBV drug. Further study in vivo is needed to explore phillygenin as a potential and effective drug to prevent IB in poultry.
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27
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Genetic Analysis of the Complete S1 Gene in Japanese Infectious Bronchitis Virus Strains. Viruses 2022; 14:v14040716. [PMID: 35458447 PMCID: PMC9029843 DOI: 10.3390/v14040716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
The complete nucleotide sequence of the S1 glycoprotein gene of the Japanese infectious bronchitis virus (IBV) strains was determined and genetically analyzed. A total of 61 Japanese IBV strains were classified into seven genotypes, namely GI-1, 3, 7, 13, 18, 19, and GVI-1 using the classification scheme that was proposed by Valastro et al, with three exceptions. These genotypes practically corresponded to those defined in Japan, namely Mass, Gray, JP-II, 4/91, JP-I, JP-III, and JP-IV, which have been identified through their partial nucleotide sequences containing hypervariable regions 1 and 2. In addition, three exceptive strains were considered to be derived from recombination within the S1 gene of IBV strains G1-13 and GI-19. By analyzing the amino acid polymorphism of the S1 glycoprotein among Japanese genotypes, a diversity was observed based on the genotype-specific amino acid residue, the proteolytic cleavage motif at the S1/S2 cleavage site, and the position of the potential N-glycosylation sites.
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Ye G, Liu B, Li F. Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain. Nat Commun 2022; 13:1214. [PMID: 35241675 PMCID: PMC8894419 DOI: 10.1038/s41467-022-28882-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
The omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we determined the 3.0 Å cryo-EM structure of the omicron spike protein ectodomain. In contrast to the original strain of SARS-CoV-2 where the receptor-binding domain (RBD) of the spike protein takes a mixture of open ("standing up") and closed ("lying down") conformations, the omicron spike molecules are predominantly in the open conformation, with one upright RBD ready for receptor binding. The open conformation of the omicron spike is stabilized by enhanced inter-domain and inter-subunit packing, which involves new mutations in the omicron strain. Moreover, the omicron spike has undergone extensive mutations in RBD regions where known neutralizing antibodies target, allowing the omicron variant to escape immune surveillance aimed at the original viral strain. The stable open conformation of the omicron spike sheds light on the cell entry and immune evasion mechanisms of the omicron variant.
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Affiliation(s)
- Gang Ye
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA.,Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA
| | - Bin Liu
- Hormel Institute, University of Minnesota, Austin, MN, USA.
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA. .,Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA.
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29
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Masuda A, Lee JM, Miyata T, Mon H, Sato K, Oyama K, Sakurai Y, Yasuda J, Takahashi D, Ueda T, Kato Y, Nishida M, Karasaki N, Kakino K, Ebihara T, Nagasato T, Hino M, Nakashima A, Suzuki K, Tonooka Y, Tanaka M, Moriyama T, Nakatake H, Fujita R, Kusakabe T. Optimization of SARS-CoV-2 Spike Protein Expression in the Silkworm and Induction of Efficient Protective Immunity by Inoculation With Alum Adjuvants. Front Immunol 2022; 12:803647. [PMID: 35095889 PMCID: PMC8789674 DOI: 10.3389/fimmu.2021.803647] [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: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a spread of coronavirus disease 2019 (COVID-19) globally. In order to end the COVID-19 pandemic, an effective vaccine against SARS-CoV-2 must be produced at low cost and disseminated worldwide. The spike (S) protein of coronaviruses plays a pivotal role in the infection to host cells. Therefore, targeting the S protein is one of the most rational approaches in developing vaccines and therapeutic agents. In this study, we optimized the expression of secreted trimerized S protein of SARS-CoV-2 using a silkworm-baculovirus expression vector system and evaluated its immunogenicity in mice. The results showed that the S protein forming the trimeric structure was the most stable when the chicken cartilage matrix protein was used as the trimeric motif and could be purified in large amounts from the serum of silkworm larvae. The purified S protein efficiently induced antigen-specific antibodies in mouse serum without adjuvant, but its ability to induce neutralizing antibodies was low. After examining several adjuvants, the use of Alum adjuvant was the most effective in inducing strong neutralizing antibody induction. We also examined the adjuvant effect of paramylon from Euglena gracilis when administered with the S protein. Our results highlight the effectiveness and suitable construct design of the S protein produced in silkworms for the subunit vaccine development against SARS-CoV-2.
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Affiliation(s)
- Akitsu Masuda
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Jae Man Lee
- Laboratory of Creative Science for Insect Industries, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Miyata
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Keita Sato
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | - Kosuke Oyama
- Laboratory of Protein Structure, Function and Design, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Daisuke Takahashi
- Laboratory of Protein Structure, Function and Design, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tadashi Ueda
- Laboratory of Protein Structure, Function and Design, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuri Kato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Nishida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriko Karasaki
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kohei Kakino
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takeru Ebihara
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takumi Nagasato
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Hino
- Laboratory of Sanitary Entomology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Ayaka Nakashima
- The Research and Development Department, Euglena Co., Ltd, Tokyo, Japan
| | - Kengo Suzuki
- The Research and Development Department, Euglena Co., Ltd, Tokyo, Japan
| | - Yoshino Tonooka
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Miyu Tanaka
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takato Moriyama
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | | | - Ryosuke Fujita
- Laboratory of Sanitary Entomology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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30
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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31
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Lublin A, Katz C, Gruzdev N, Yadid I, Bloch I, Farnoushi Y, Simanov L, Berkowitz A, Elyahu D, Pitcovski J, Shahar E. Protection against avian coronavirus conferred by oral vaccination with live bacteria secreting LTB-fused viral proteins. Vaccine 2022; 40:726-733. [PMID: 34998606 PMCID: PMC8717763 DOI: 10.1016/j.vaccine.2021.12.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
The devastating impact of infectious bronchitis (IB) triggered by the IB virus (IBV), on poultry farms is generally curbed by livestock vaccination with live attenuated or inactivated vaccines. Yet, this approach is challenged by continuously emerging variants and by time limitations of vaccine preparation techniques. This work describes the design and evaluation of an anti-IBV vaccine comprised of E. coli expressing and secreting viral spike 1 subunit (S1) and nucleocapsid N-terminus and C-terminus polypeptides fused to heat-labile enterotoxin B (LTB) (LS1, LNN, LNC, respectively). Following chicken oral vaccination, anti-IBV IgY levels and cellular-mediated immunity as well as protection against virulent IBV challenge, were evaluated 14 days following the booster dose. Oral vaccination induced IgY levels that exceeded those measured following vaccination with each component separately. Following exposure to inactivated IBV, splenocytes isolated from chicks orally vaccinated with LNN or LNC -expressing bacteria, showed a higher percentage of CD8+ cells as compared to splenocytes isolated from chicks vaccinated with wild type or LTB-secreting E. coli and to chicks subcutaneously vaccinated. Significant reduction in viral load and percent of shedders in the vaccinated chicks was evident starting 3 days following challenge with 107.5 EID50/ml virulent IBV. Taken together, orally delivered LTB-fused IBV polypeptide-expressing bacteria induced virus-specific IgY antibody production and was associated with significantly shorter viral shedding on challenge with a live IBV. The proposed vaccine design and delivery route promise an effective and rapidly adaptable means of protecting poultry farms from devastating IB outbreaks.
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Affiliation(s)
- Avishai Lublin
- The Department of Avian Diseases, Kimron Veterinary Institute,
Israel
| | - Chen Katz
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel
| | - Nady Gruzdev
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel
| | - Itamar Yadid
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel,Tel-Hai Academic College, Upper Galilee, Israel
| | - Itai Bloch
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel
| | - Yigal Farnoushi
- The Department of Avian Diseases, Kimron Veterinary Institute,
Israel
| | - Luba Simanov
- The Department of Avian Diseases, Kimron Veterinary Institute,
Israel
| | - Asaf Berkowitz
- The Department of Avian Diseases, Kimron Veterinary Institute,
Israel
| | - Dalia Elyahu
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel
| | - Jacob Pitcovski
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel,Tel-Hai Academic College, Upper Galilee, Israel
| | - Ehud Shahar
- MIGAL Research Institute in the Galilee, Kiryat Shmona,
Israel,Tel-Hai Academic College, Upper Galilee, Israel,Corresponding author at: MIGAL Research Institute in the Galilee,
Kiryat Shmona, Israel
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32
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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33
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Identification of a novel neutralizing epitope on the N-terminal domain of the HCoV-229E spike protein. J Virol 2021; 96:e0195521. [PMID: 34908442 DOI: 10.1128/jvi.01955-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The receptor binding domain (RBD) of the coronavirus spike protein (S) has been verified to be the main target for potent neutralizing antibodies (nAbs) in most coronaviruses, and the N-terminal domain (NTD) of some betacoronaviruses has also been indicated to induce nAbs. For alphacoronavirus HCoV-229E, its RBD has been shown to have neutralizing epitopes, and these epitopes could change over time. However, whether neutralizing epitopes exist on the NTD and whether these epitopes change like those of the RBD are still unknown. Here, we verified that neutralizing epitopes exist on the NTD of HCoV-229E. Furthermore, we characterized an NTD targeting nAb 5H10, which could neutralize both pseudotyped and authentic HCoV-229E VR740 in vitro. Epitope mapping indicated that 5H10 targeted motif E1 (147-167 aa) and identified F159 as critical for 5H10 binding. More importantly, our results revealed that motif E1 was highly conserved among clinical isolates except for F159. Further data proved that mutations at position 159 gradually appeared over time and could completely abolish the neutralizing ability of 5H10, supporting the notion that position 159 may be under selective pressure during the human epidemic. In addition, we also found that contemporary clinical serum has a stronger binding capacity for the NTD of contemporary strains than historic strains, proving that the epitope on the NTD could change over time. In summary, these findings define a novel neutralizing epitope on the NTD of HCoV-229E S and provide a theoretical basis for the design of vaccines against HCoV-229E or related coronaviruses. Importance Characterization of the neutralizing epitope of the spike (S) protein, the major invasion protein of coronaviruses, can help us better understand the evolutionary characteristics of these viruses and promote vaccine development. To date, the neutralizing epitope distribution of alphacoronaviruses is not well known. Here, we identified a neutralizing antibody that targeted the N-terminal domain (NTD) of the alphacoronavirus HCoV-229E S protein. Epitope mapping revealed a novel epitope that was not previously discovered in HCoV-229E. Further studies identified an important residue, F159. Mutations that gradually appeared over time at this site abolished the neutralizing ability of 5H10, indicating that selective pressure occurred at this position in the spread of HCoV-229E. Furthermore, we found that the epitopes within the NTD also changed over time. Taken together, our findings defined a novel neutralizing epitope and highlighted the role of the NTD in the future prevention and control of HCoV-229E or related coronaviruses.
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34
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Stevenson-Leggett P, Armstrong S, Keep S, Britton P, Bickerton E. Analysis of the avian coronavirus spike protein reveals heterogeneity in the glycans present. J Gen Virol 2021; 102. [PMID: 34424155 PMCID: PMC8513636 DOI: 10.1099/jgv.0.001642] [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] [Indexed: 01/09/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an economically important coronavirus, causing damaging losses to the poultry industry worldwide as the causative agent of infectious bronchitis. The coronavirus spike (S) glycoprotein is a large type I membrane protein protruding from the surface of the virion, which facilitates attachment and entry into host cells. The IBV S protein is cleaved into two subunits, S1 and S2, the latter of which has been identified as a determinant of cellular tropism. Recent studies expressing coronavirus S proteins in mammalian and insect cells have identified a high level of glycosylation on the protein’s surface. Here we used IBV propagated in embryonated hens’ eggs to explore the glycan profile of viruses derived from infection in cells of the natural host, chickens. We identified multiple glycan types on the surface of the protein and found a strain-specific dependence on complex glycans for recognition of the S2 subunit by a monoclonal antibody in vitro, with no effect on viral replication following the chemical inhibition of complex glycosylation. Virus neutralization by monoclonal or polyclonal antibodies was not affected. Following analysis of predicted glycosylation sites for the S protein of four IBV strains, we confirmed glycosylation at 18 sites by mass spectrometry for the pathogenic laboratory strain M41-CK. Further characterization revealed heterogeneity among the glycans present at six of these sites, indicating a difference in the glycan profile of individual S proteins on the IBV virion. These results demonstrate a non-specific role for complex glycans in IBV replication, with an indication of an involvement in antibody recognition but not neutralisation.
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Affiliation(s)
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, UK
| | - Sarah Keep
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
| | - Paul Britton
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
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35
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Stable trimer formation of spike protein from porcine epidemic diarrhea virus improves the efficiency of secretory production in silkworms and induces neutralizing antibodies in mice. Vet Res 2021; 52:102. [PMID: 34233749 PMCID: PMC8261802 DOI: 10.1186/s13567-021-00971-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen of watery diarrhea that causes serious economic loss to the swine industry worldwide. Especially because of the high mortality rate in neonatal piglets, a vaccine with less production cost and high protective effect against PEDV is desired. The intrinsically assembled homotrimer of spike (S) protein on the PEDV viral membrane contributing to the host cell entry is a target of vaccine development. In this study, we designed trimerized PEDV S protein for efficient production in the silkworm-baculovirus expression vector system (silkworm-BEVS) and evaluated its immunogenicity in the mouse. The genetic fusion of the trimeric motif improved the expression of S protein in silkworm-BEVS. A small-scale screening of silkworm strains to further improve the S protein productivity finally achieved the yield of about 2 mg from the 10 mL larval serum. Mouse immunization study demonstrated that the trimerized S protein could elicit strong humoral immunity, including the S protein-specific IgG in the serum. These sera contained neutralizing antibodies that can protect Vero cells from PEDV infection. These results demonstrated that silkworm-BEVS provides a platform for the production of trimeric S proteins, which are promising subunit vaccines against coronaviruses such as PEDV.
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36
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Farooq A, Alam F, Saeed A, Butt F, Khaliq MA, Malik A, Chaudhry M, Abdullah M. Multisystem Inflammatory Syndrome in Children and Adolescents (MIS-C) under the Setting of COVID-19: A Review of Clinical Presentation, Workup and Management. Infect Dis (Lond) 2021; 14:11786337211026642. [PMID: 34220204 PMCID: PMC8221672 DOI: 10.1177/11786337211026642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/30/2021] [Indexed: 12/29/2022] Open
Abstract
Earlier in its course, SARS-CoV-2 was primarily identified to cause an acute respiratory illness in adults, the elderly and immunocompromised, while children were known to be afflicted with milder symptoms. However, since mid-April of 2020, latent effects of the virus have begun emerging in children and adolescents, which is characterised by a multisystem hyperinflammatory state; thus, the term Multisystem Inflammatory Syndrome in Children (MIS-C) was introduced by the WHO and CDC. The syndrome manifests itself approximately 4 weeks after COVID-19 infection, with symptoms mimicking Kawasaki Disease and Kawasaki Disease Shock Syndrome. Demographically, MIS-C peaks in children aged 5 to 14 years, with clusters in Europe, North and Latin America seen, later followed by Asia. Although the exact pathophysiology behind the syndrome is unknown, recent studies have proposed a post-infectious immune aetiology, which explains the increased levels of immunoglobulins seen in affected patients. Patient presentation includes, but is not limited to, persistent fever, rash, gastrointestinal symptoms and cardiac complications including myocarditis. These patients also have raised inflammatory markers including C reactive protein, ferritin and interleukin-6. In poorly controlled patients, the syndrome can lead to multiorgan failure and death. The mainstay of treatment includes the use of intravenous immunoglobulins, steroids, immune modulators and aspirin. Adjunct therapy includes the use of low molecular weight heparin or warfarin for long term anticoagulation. Currently very little is known about the syndrome, highlighting the need for awareness amongst healthcare workers and parents. Moreover, with increased cases of COVID-19 as a result of the second wave, it is essential to keep MIS-C in mind when attending patients with a past history of COVID-19 exposure or infection. Additionally, once these patients have been identified and treated, strict follow-up must be done in order carry out long term studies, and to identify possible sequelae and complications.
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Affiliation(s)
- Ayesha Farooq
- CMH Lahore Medical College and Institute of Dentistry, Lahore, PK-PB, Punjab, Pakistan
| | - Fatima Alam
- CMH Lahore Medical College and Institute of Dentistry, Lahore, PK-PB, Punjab, Pakistan
| | - Asma Saeed
- CMH Lahore Medical College and Institute of Dentistry, Lahore, PK-PB, Punjab, Pakistan
| | - Farooq Butt
- Sialkot Medical College Pvt Ltd, Sialkot, PK-PB Punjab, Pakistan
| | - Muhammad Azeem Khaliq
- CMH Lahore Medical College and Institute of Dentistry, Lahore, PK-PB, Punjab, Pakistan
| | - Ayesha Malik
- Hameed Latif Hospital, Lahore, Lahore, PK-PB Punjab, Pakistan
| | | | - Mohammad Abdullah
- CMH Lahore Medical College and Institute of Dentistry, Lahore, PK-PB, Punjab, Pakistan
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37
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Zhou J, Li J, Li Y, Liu H, Qi Y, Wang A. Identification of a mimotope of an infectious bronchitis virus S1 protein. J Vet Sci 2021; 22:e49. [PMID: 34170090 PMCID: PMC8318793 DOI: 10.4142/jvs.2021.22.e49] [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: 07/16/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 11/20/2022] Open
Abstract
The S1 protein of the infectious bronchitis virus (IBV) is a major structural protein that induces the production of the virus-neutralization antibodies. The monoclonal antibody against the IBV M41 S1 protein was used as a target for biopanning. After three rounds of biopanning, randomly selected phages bound to the monoclonal antibody. Sequence analysis showed that the dominant sequence was SFYDFEMQGFFI. Indirect competitive enzyme-linked immunosorbent assay showed that SFYDFEMQGFFI is a mimotope of the S1 protein that was predicted by PepSurf. The mimotope may provide information for further structural and functional analyses of the S1 protein.
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Affiliation(s)
- Jingming Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jianan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanghui Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanhua Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China.
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38
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González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Viruses 2021; 13:883. [PMID: 34064904 PMCID: PMC8151058 DOI: 10.3390/v13050883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
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Affiliation(s)
- Jorge González-Puelma
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Marco Montes de Oca
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Mónica Pinto
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | | | - Diego Alvarez-Saravia
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Hermy Álvarez
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Gonzalo Encina
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
- Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
| | - Rodrigo Muñoz
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile;
- Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Marcelo A. Navarrete
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
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39
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Millet JK, Jaimes JA, Whittaker GR. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol Rev 2021; 45:fuaa057. [PMID: 33118022 PMCID: PMC7665467 DOI: 10.1093/femsre/fuaa057] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
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Affiliation(s)
- Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
- Cornell Feline Health Center, Ithaca, NY 14853, USA
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40
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Lian J, Wang Z, Xu Z, Chen T, Shao G, Zhang X, Qin J, Xie Q, Lin W. Distribution and molecular characterization of avian infectious bronchitis virus in southern China. Poult Sci 2021; 100:101169. [PMID: 34116347 PMCID: PMC8192861 DOI: 10.1016/j.psj.2021.101169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 11/06/2022] Open
Abstract
Avian infectious bronchitis virus (IBV) is causing considerable economic losses in the world poultry industry. The main difficulty of prevention and control of IB disease is the numerous genotypes and serotypes. The genetic analysis of IBV was mainly based on the S1 gene which played an important role in infectivity. In the study, One hundred and thirty-nine strains of avian infectious bronchitis virus were isolated from chickens showing signs of disease in southern China during the period from April 2019 to March 2020. The nucleotide and amino acid sequences from the isolated field strains were compared to 22 published references. Nucleotide homologies ranged from 64.5% to 100% and amino acid homologies ranging from 70% to 99.8%. Six genotype IBV strains were co-circulating in southern China. QX-type was still the most dominant genotype. Alignment of nucleotide and amino acid sequences of S1 gene revealed that the substitutions, insertions and deletions are widely among isolated strains. Recombination analysis showed that there is a large number of recombinant strains amongst these isolates, forming new sub branches, subtypes and variants. Therefore, long-term continuing surveillance is necessary for IBV prevention and control.
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Affiliation(s)
- Jiamin Lian
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Zhanxin Wang
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, 527400, Guangdong, P.R. China
| | - Zhouyi Xu
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, 527400, Guangdong, P.R. China
| | - Tong Chen
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Guanming Shao
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Xinheng Zhang
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China; Key Laboratory of Healthy Animal Husbandry and Environmental Control of Guangdong Province, Guangzhou, 510642, Guangdong, P.R. China
| | - Jianping Qin
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, 527400, Guangdong, P.R. China
| | - Qingmei Xie
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China; Key Laboratory of Healthy Animal Husbandry and Environmental Control of Guangdong Province, Guangzhou, 510642, Guangdong, P.R. China
| | - Wencheng Lin
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China; Key Laboratory of Healthy Animal Husbandry and Environmental Control of Guangdong Province, Guangzhou, 510642, Guangdong, P.R. China.
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41
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Wang C, van Haperen R, Gutiérrez-Álvarez J, Li W, Okba NMA, Albulescu I, Widjaja I, van Dieren B, Fernandez-Delgado R, Sola I, Hurdiss DL, Daramola O, Grosveld F, van Kuppeveld FJM, Haagmans BL, Enjuanes L, Drabek D, Bosch BJ. A conserved immunogenic and vulnerable site on the coronavirus spike protein delineated by cross-reactive monoclonal antibodies. Nat Commun 2021; 12:1715. [PMID: 33731724 PMCID: PMC7969777 DOI: 10.1038/s41467-021-21968-w] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry and the focus for development of protective antibodies and vaccines. Structural studies show exposed sites on the spike trimer that might be targeted by antibodies with cross-species specificity. Here we isolated two human monoclonal antibodies from immunized humanized mice that display a remarkable cross-reactivity against distinct spike proteins of betacoronaviruses including SARS-CoV, SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both cross-reactive antibodies target the stem helix in the spike S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle. Both antibodies block MERS-CoV infection in cells and provide protection to mice from lethal MERS-CoV challenge in prophylactic and/or therapeutic models. Our work highlights an immunogenic and vulnerable site on the betacoronavirus spike protein enabling elicitation of antibodies with unusual binding breadth.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/immunology
- Betacoronavirus/classification
- Betacoronavirus/immunology
- Camelus
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cross Reactions
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Humans
- Mice
- Protein Conformation
- Protein Subunits
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Chunyan Wang
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Javier Gutiérrez-Álvarez
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Wentao Li
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Irina Albulescu
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Ivy Widjaja
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Merus N.V., Utrecht, the Netherlands
| | - Brenda van Dieren
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raul Fernandez-Delgado
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Daniel L Hurdiss
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Olalekan Daramola
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Frank J M van Kuppeveld
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Harbour BioMed, Rotterdam, the Netherlands
| | - Berend-Jan Bosch
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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42
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Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins. J Virol 2021; 95:JVI.02284-20. [PMID: 33414160 PMCID: PMC8092709 DOI: 10.1128/jvi.02284-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Coronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. The spike (S) homotrimers bind to their receptors via the receptor-binding domain (RBD), which is a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs exist two different conformational states (lying or standing) in the prefusion S-trimer structure. Then, the differences in the immune responses to RBDs from these coronaviruses were analyzed structurally and immunologically. Our results showed that more RBD-specific antibodies (antibody titers: 1.28×105; 2.75×105) were induced by the S-trimer with the RBD in the "standing" state (SARS-CoV and SARS-CoV-2) than the S-trimer with the RBD in the "lying" state (HCoV-229E, antibody titers: <500), and more S-trimer-specific antibodies were induced by the RBD in the SARS-CoV and SARS-CoV-2 (antibody titers: 6.72×105; 5×105) than HCoV-229E (antibody titers:1.125×103). Besides, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was lower than S-trimer, and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus Our findings will provide important implications for future development of coronavirus vaccines.Importance Outbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in "lying" and "standing" states in the prefusion S-trimer structure. Here, we evaluated the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that the S-trimer and RBD are both candidates for subunit vaccines in Beta-coronavirus (SARS-CoV and SARS-CoV-2) with a RBD "standing" state. However, for Alpha-coronavirus (HCoV-229E) with a RBD "lying" state, the S-trimer may be more suitable for subunit vaccines than the RBD. Our results will provide novel ideas for the development of vaccines targeting S protein in the future.
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43
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Song X, Shi Y, Ding W, Niu T, Sun L, Tan Y, Chen Y, Shi J, Xiong Q, Huang X, Xiao S, Zhu Y, Cheng C, Fu ZF, Liu ZJ, Peng G. Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun 2021; 12:141. [PMID: 33420048 PMCID: PMC7794242 DOI: 10.1038/s41467-020-20401-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not been elucidated in Alphacoronavirus. Here, we report the cryo-EM structures of the HCoV-229E S trimer in prefusion state with two conformations. The activated conformation may pose the potential exposure of the S1-RBDs by decreasing of the interaction area between the S1-RBDs and the surrounding S1-NTDs and S1-RBDs compared to the closed conformation. Furthermore, structural comparison of our structures with the previously reported HCoV-229E S structure showed that the S trimers trended to open the S2 subunit from the closed conformation to open conformation, which could promote the transition from pre- to postfusion. Our results provide insights into the mechanisms involved in S glycoprotein-mediated Alphacoronavirus entry and have implications for vaccine and therapeutic antibody design.
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Affiliation(s)
- Xiyong Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Wei Ding
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, P.O.Box 603, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Limeng Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yubei Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiqi Xiong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yanping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Zhi-Jie Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China. .,iHuman Institute, ShanghaiTech University, Shanghai, China.
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. .,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
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44
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Kirchdoerfer RN, Bhandari M, Martini O, Sewall LM, Bangaru S, Yoon KJ, Ward AB. Structure and immune recognition of the porcine epidemic diarrhea virus spike protein. Structure 2020; 29:385-392.e5. [PMID: 33378641 PMCID: PMC7962898 DOI: 10.1016/j.str.2020.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components, including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.
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Affiliation(s)
- Robert N Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mahesh Bhandari
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Olnita Martini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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45
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Noman A, Aqeel M, Khalid N, Hashem M, Alamari S, Zafar S, Qasim M, Irshad MK, Qari SH. Spike glycoproteins: Their significance for corona viruses and receptor binding activities for pathogenesis and viral survival. Microb Pathog 2020; 150:104719. [PMID: 33373693 PMCID: PMC7764473 DOI: 10.1016/j.micpath.2020.104719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
Abstract
The recent outbreak of Covid-19 is posing a severe threat to public health globally. Coronaviruses (CoVs) are the largest known group of positive-sense RNA viruses surviving on an extensive number of natural hosts. CoVs are enveloped and non-segmented viruses with a size between 80 and 120 nm. CoV attachment to the surface receptor and its subsequent entrance into cells is mediated by Spike glycoprotein (S). For enhanced CoV entry and successful pathogenesis of CoV, proteolytic processing and receptor-binding act synergistically for induction of large-scale S conformational changes. The shape, size and orientation of receptor-binding domains in viral attachment proteins are well conserved among viruses of different classes that utilize the same receptor. Therefore, investigations unraveling the distribution of cellular receptors with respect to CoV entry, structural aspects of glycoproteins and related conformational changes are highly significant for understanding virus invasion and infection spread. We present the characteristic features of CoV S-Proteins, their significance for CoVs and related receptor binding activities for pathogenesis and viral survival. We are analyzing the novel role of S-protein of CoVs along with their interactive receptors for improving host immunity and decreasing infection spread. This is hoped that presented information will open new ways in tackling coronavirus, especially for the ongoing epidemic.
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Affiliation(s)
- Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan.
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agroecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Sialkot, Pakistan
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, 71516, Egypt
| | - Saad Alamari
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Prince Sultan Bin Abdulaziz Center for Environmental and Tourism Research and Studies, King Khalid University, Abha, Saudi Arabia
| | - Saad Zafar
- District Headquarters Hospital, Faisalabad Medical University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Ministry of Agricultural and Rural Affairs, Zhejiang University, Hangzhou, 310058, PR China
| | - Muhammad Kashif Irshad
- Department of Environmental Sciences, Government College University, Faisalabad, Pakistan
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al - Qura University, Makkah, Saudi Arabia.
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46
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Sun X, Li L, Pan L, Wang Z, Chen H, Shao C, Yu J, Ren Y, Wang X, Huang X, Zhang R, Li G. Infectious bronchitis virus: Identification of Gallus gallus APN high-affinity ligands with antiviral effects. Antiviral Res 2020; 186:104998. [PMID: 33340637 DOI: 10.1016/j.antiviral.2020.104998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
Infectious bronchitis virus (IBV) is a coronavirus, causes infectious bronchitis (IB) with high morbidity and mortality, and gives rise to huge economic losses for the poultry industry. Aminopeptidase N (APN) may be one of the IBV functional receptors. In this study, Gallus gallus APN (gAPN) protein was screened by phage-displayed 12-mer peptide library. Two high-affinity peptides H (HDYLYYTFTGNP) and T (TKFSPPSFWYLH) to gAPN protein were selected for in depth characterization of their anti-IBV effects. In vitro, indirect ELISA showed that these two high-affinity ligands could bind IBV S1 antibodies. Quantitative real-time PCR (qRT-PCR) assay, virus yield reduction assay and indirect immunofluorescence assay results revealed 3.125-50 μg/ml of peptide H and 6.25-50 μg/ml of peptide T reduced IBV proliferation in chicken embryo kidney cells (CEKs). In vivo, high-affinity phage-vaccinated chickens were able to induce specific IBV S1 antibodies and IBV neutralizing antibodies. QRT-PCR results confirmed that high-affinity phages reduced virus proliferation in chicken tracheas, lungs and kidneys, and alleviated IBV-induced lesions. By multiple sequence alignment, motif 'YxYY' and 'FxPPxxWxLH' of high-affinity peptides were identified in IBV S1-NTD, while another motif 'YxFxGN' located in S2. These results indicated that high affinity peptides of gAPN could present an alternative approach to IB prevention or treatment.
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Affiliation(s)
- Xiaoqi Sun
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lanlan Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Long Pan
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zheng Wang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Huijie Chen
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Changhao Shao
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jia Yu
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yudong Ren
- College of Electrical and Information Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, 150069, China
| | - Xiaodan Huang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ruili Zhang
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Guangxing Li
- College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin, 150030, China.
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47
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Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe 2020; 28:867-879.e5. [PMID: 33271067 PMCID: PMC7670890 DOI: 10.1016/j.chom.2020.11.004] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jared M Sampson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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48
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Wu Y, Zhao S. Furin cleavage sites naturally occur in coronaviruses. Stem Cell Res 2020; 50:102115. [PMID: 33340798 PMCID: PMC7836551 DOI: 10.1016/j.scr.2020.102115] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 01/12/2023] Open
Abstract
The spike protein is a focused target of COVID-19, a pandemic caused by SARS-CoV-2. A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.
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Affiliation(s)
- Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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49
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Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins. J Virol 2020; 94:JVI.01301-20. [PMID: 32817223 DOI: 10.1128/jvi.01301-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/14/2020] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses (CoV) have caused a number of major epidemics in humans and animals, including the current pandemic of coronavirus disease 2019 (COVID-19), which has brought a renewed focus on the evolution and interspecies transmission of coronaviruses. Swine acute diarrhea syndrome coronavirus (SADS-CoV), which was recently identified in piglets in southern China, is an alphacoronavirus that originates from the same genus of horseshoe bats as severe acute respiratory syndrome CoV (SARS-CoV) and that was reported to be capable of infecting cells from a broad range of species, suggesting a considerable potential for interspecies transmission. Given the importance of the coronavirus spike (S) glycoprotein in host range determination and viral entry, we report a cryo-electron microscopy (cryo-EM) structure of the SADS-CoV S trimer in the prefusion conformation at a 3.55-Å resolution. Our structure reveals that the SADS-CoV S trimer assumes an intrasubunit quaternary packing mode in which the S1 subunit N-terminal domain (S1-NTD) and the S1 subunit C-terminal domain (S1-CTD) of the same protomer pack together by facing each other in the lying-down state. SADS-CoV S has several distinctive structural features that may facilitate immune escape, such as a relatively compact architecture of the S trimer and epitope masking by glycan shielding. Comparison of SADS-CoV S with the spike proteins of the other coronavirus genera suggested that the structural features of SADS-CoV S are evolutionarily related to those of the spike proteins of the other genera rather than to the spike protein of a typical alphacoronavirus. These data provide new insights into the evolutionary relationship between spike glycoproteins of SADS-CoV and those of other coronaviruses and extend our understanding of their structural and functional diversity.IMPORTANCE In this article, we report the atomic-resolution prefusion structure of the spike protein from swine acute diarrhea syndrome coronavirus (SADS-CoV). SADS-CoV is a pathogenic alphacoronavirus that was responsible for a large-scale outbreak of fatal disease in pigs and that was reported to be capable of interspecies transmission. We describe the overall structure of the SADS-CoV spike protein and conducted a detailed analysis of its main structural elements. Our results and analyses are consistent with those of previous phylogenetic studies and suggest that the SADS-CoV spike protein is evolutionarily related to the spike proteins of betacoronaviruses, with a strong similarity in S1-NTDs and a marked divergence in S1-CTDs. Moreover, we discuss the possible immune evasion strategies used by the SADS-CoV spike protein. Our study provides insights into the structure and immune evasion strategies of the SADS-CoV spike protein and broadens the understanding of the evolutionary relationships between coronavirus spike proteins of different genera.
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50
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Xiong X, Qu K, Ciazynska KA, Hosmillo M, Carter AP, Ebrahimi S, Ke Z, Scheres SHW, Bergamaschi L, Grice GL, Zhang Y, Nathan JA, Baker S, James LC, Baxendale HE, Goodfellow I, Doffinger R, Briggs JAG. A thermostable, closed SARS-CoV-2 spike protein trimer. Nat Struct Mol Biol 2020; 27:934-941. [PMID: 32737467 PMCID: PMC7116388 DOI: 10.1038/s41594-020-0478-5] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022]
Abstract
The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. It exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor-binding site and, subsequently, from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S-protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S that allow the production of thermostable, disulfide-bonded S-protein trimers that are trapped in the closed, prefusion state. Structures of the disulfide-stabilized and non-disulfide-stabilized proteins reveal distinct closed and locked conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.
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Affiliation(s)
- Xiaoli Xiong
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Kun Qu
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Katarzyna A Ciazynska
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrew P Carter
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | - Zunlong Ke
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sjors H W Scheres
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - Guinevere L Grice
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - Ying Zhang
- Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Francis Crick Institute, London, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - Leo C James
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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