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Sun Y, Zhu Y, Zhang P, Sheng S, Guan Z, Cong Y. Hemagglutinin glycosylation pattern-specific effects: implications for the fitness of H9.4.2.5-branched H9N2 avian influenza viruses. Emerg Microbes Infect 2024; 13:2364736. [PMID: 38847071 DOI: 10.1080/22221751.2024.2364736] [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: 03/27/2024] [Accepted: 06/02/2024] [Indexed: 06/16/2024]
Abstract
Since 2007, h9.4.2.5 has emerged as the most predominant branch of H9N2 avian influenza viruses (AIVs) that affects the majority of the global poultry population. The spread of this viral branch in vaccinated chicken flocks has not been considerably curbed despite numerous efforts. The evolutionary fitness of h9.4.2.5-branched AIVs must consequently be taken into consideration. The glycosylation modifications of hemagglutinin (HA) play a pivotal role in regulating the balance between receptor affinity and immune evasion for influenza viruses. Sequence alignment showed that five major HA glycosylation patterns have evolved over time in h9.4.2.5-branched AIVs. Here, we compared the adaptive phenotypes of five virus mutants with different HA glycosylation patterns. According to the results, the mutant with 6 N-linked glycans displayed the best acid and thermal stability and a better capacity for multiplication, although having a relatively lower receptor affinity than 7 glycans. The antigenic profile between the five mutants revealed a distinct antigenic distance, indicating that variations in glycosylation level have an impact on antigenic drift. These findings suggest that changes in the number of glycans on HA can not only modulate the receptor affinity and antigenicity of H9N2 AIVs, but also affect their stability and multiplication. These adaptive phenotypes may underlie the biological basis for the dominant strain switchover of h9.4.2.5-branched AIVs. Overall, our study provides a systematic insight into how changes in HA glycosylation patterns regulate the evolutionary fitness and epidemiological dominance drift of h9.4.2.5-branched H9N2 AIVs, which will be of great benefit for the glycosylation-dependent vaccine design.
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Affiliation(s)
- Yixue Sun
- Department of Policies and Regulations, Changchun University, Changchun, People's Republic of China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanting Zhu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengju Zhang
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, People's Republic of China
| | - Shouzhi Sheng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhenhong Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanlong Cong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
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2
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Shi K, Feng S, Zhao L, Chen J, Song W, Jia Y, Qu X, Liu Z, Jia W, Du S, Liao M. N-glycosylation on hemagglutinin head reveals inter-branch antigenic variability of avian influenza virus H5-subtypes. Int J Biol Macromol 2024:132901. [PMID: 38848854 DOI: 10.1016/j.ijbiomac.2024.132901] [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: 05/19/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
H5-subtype avian influenza virus (AIV) is globally prevalent and undergoes frequent antigenic drift, necessitating regular updates to vaccines. One of the many influencing elements that cause incompatibility between vaccinations and epidemic strains is the dynamic alteration of glycosylation sites. However, the biological significance of N-glycosylation in the viral evolution and antigenic changes is unclear. Here, we performed a systematic analysis of glycosylation sites on the HA1 subunit of H5N1, providing insights into the changes of primary glycosylation sites, including 140 N, 156 N, and 170 N within the antigenic epitopes of HA1 protein. Multiple recombinant viruses were then generated based on HA genes of historical vaccine strains and deactivated for immunizing SPF chickens. Inactivated recombinant strains showed relatively closer antigenicity compared to which has identical N-glycosylation patterns. The N-glycosylation modification discrepancy highlights the inter-branch antigenic diversity of H5-subtype viruses in avian influenza and serves as a vital foundation for improving vaccination tactics.
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Affiliation(s)
- Keyi Shi
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Saixiang Feng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Zhao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Junhong Chen
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wei Song
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yusheng Jia
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyun Qu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhicheng Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Weixin Jia
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Shouwen Du
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Wuhan 430030, China.
| | - Ming Liao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Zhongkai University of Agricultural and Engineering, Guangzhou 510550, China.
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3
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Su G, Chen Y, Li X, Shao JW. Virus versus host: influenza A virus circumvents the immune responses. Front Microbiol 2024; 15:1394510. [PMID: 38817972 PMCID: PMC11137263 DOI: 10.3389/fmicb.2024.1394510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Influenza A virus (IAV) is a highly contagious pathogen causing dreadful losses to humans and animals around the globe. As is known, immune escape is a strategy that benefits the proliferation of IAVs by antagonizing, blocking, and suppressing immune surveillance. The HA protein binds to the sialic acid (SA) receptor to enter the cytoplasm and initiate viral infection. The conserved components of the viral genome produced during replication, known as the pathogen-associated molecular patterns (PAMPs), are thought to be critical factors for the activation of effective innate immunity by triggering dependent signaling pathways after recognition by pattern recognition receptors (PRRs), followed by a cascade of adaptive immunity. Viral infection-induced immune responses establish an antiviral state in the host to effectively inhibit virus replication and enhance viral clearance. However, IAV has evolved multiple mechanisms that allow it to synthesize and transport viral components by "playing games" with the host. At its heart, this review will describe how host and viral factors interact to facilitate the viral evasion of host immune responses.
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Affiliation(s)
- Guanming Su
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Yiqun Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan, China
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4
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Das T, Luo S, Tang H, Fang J, Mao Y, Yen HH, Dash S, Shajahan A, Pepi L, Huang S, Jones VS, Xie S, Huang GF, Lu J, Anderson B, Zhang B, Azadi P, Huang RP. N-glycosylation of the SARS-CoV-2 spike protein at Asn331 and Asn343 is involved in spike-ACE2 binding, virus entry, and regulation of IL-6. Microbiol Immunol 2024; 68:165-178. [PMID: 38444370 DOI: 10.1111/1348-0421.13121] [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: 07/31/2023] [Revised: 12/06/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health crisis. The causative agent, the SARS-CoV-2 virus, enters host cells via molecular interactions between the viral spike protein and the host cell ACE2 surface protein. The SARS-CoV-2 spike protein is extensively decorated with up to 66 N-linked glycans. Glycosylation of viral proteins is known to function in immune evasion strategies but may also function in the molecular events of viral entry into host cells. Here, we show that N-glycosylation at Asn331 and Asn343 of SARS-CoV-2 spike protein is required for it to bind to ACE2 and for the entry of pseudovirus harboring the SARS-CoV-2 spike protein into cells. Interestingly, high-content glycan binding screening data have shown that N-glycosylation of Asn331 and Asn343 of the RBD is important for binding to the specific glycan molecule G4GN (Galβ-1,4 GlcNAc), which is critical for spike-RBD-ACE2 binding. Furthermore, IL-6 was identified through antibody array analysis of conditioned media of the corresponding pseudovirus assay. Mutation of N-glycosylation of Asn331 and Asn343 sites of the spike receptor-binding domain (RBD) significantly reduced the transcriptional upregulation of pro-inflammatory signaling molecule IL-6. In addition, IL-6 levels correlated with spike protein levels in COVID-19 patients' serum. These findings establish the importance of RBD glycosylation in SARS-CoV-2 pathogenesis, which can be exploited for the development of novel therapeutics for COVID-19.
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Affiliation(s)
- Tuhin Das
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Shuhong Luo
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Hao Tang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Jianmin Fang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Yinging Mao
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Haw-Han Yen
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Sabyasachi Dash
- Department of Pathology, Center for Vascular Biology, Weill Cornell Medicine, New York, New York, USA
| | - Asif Shajahan
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Lauren Pepi
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Steven Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Shehuo Xie
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | | | - Jinqiao Lu
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Benyue Zhang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Ruo-Pan Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
- South China Biochip Research Center, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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5
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Stiving AQ, Foreman DJ, VanAernum ZL, Durr E, Wang S, Vlasak J, Galli J, Kafader JO, Tsukidate T, Li X, Schuessler HA, Richardson DD. Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:62-73. [PMID: 38032172 DOI: 10.1021/jasms.3c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.
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Affiliation(s)
- Alyssa Q Stiving
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - David J Foreman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary L VanAernum
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eberhard Durr
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shiyi Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Josef Vlasak
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer Galli
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Taku Tsukidate
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hillary A Schuessler
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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6
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Sun W, Zhang Q, Zhang X, Tran NH, Ziaur Rahman M, Chen Z, Peng C, Ma J, Li M, Xin L, Shan B. Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics. Nat Commun 2023; 14:4046. [PMID: 37422459 PMCID: PMC10329677 DOI: 10.1038/s41467-023-39699-5] [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: 09/26/2022] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based and glycan-based search strategies to address the challenge of complex fragmentation of glycopeptides. A deep learning model is designed to capture glycan tree structures and their fragment ions for de novo sequencing of glycans that do not exist in the database. We performed extensive analyses to validate the false discovery rates (FDRs) at both peptide and glycan levels and to evaluate GlycanFinder based on comprehensive benchmarks from previous community-based studies. Our results show that GlycanFinder achieved comparable performance to other leading glycoproteomics softwares in terms of both FDR control and the number of identifications. Moreover, GlycanFinder was also able to identify glycopeptides not found in existing databases. Finally, we conducted a mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses, which had been a challenging problem to previous studies.
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Affiliation(s)
- Weiping Sun
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Qianqiu Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Xiyue Zhang
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Ngoc Hieu Tran
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - M Ziaur Rahman
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Zheng Chen
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Chao Peng
- BaizhenBio Inc., Wuhan, China
- Wuhan BioBank, Wuhan, China
| | - Jun Ma
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Ming Li
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada.
- Henan Academy of Sciences, Zhengzhou, Henan, China.
| | - Lei Xin
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada.
| | - Baozhen Shan
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada.
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7
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Cia G, Pucci F, Rooman M. Critical review of conformational B-cell epitope prediction methods. Brief Bioinform 2023; 24:6972295. [PMID: 36611255 DOI: 10.1093/bib/bbac567] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 01/09/2023] Open
Abstract
Accurate in silico prediction of conformational B-cell epitopes would lead to major improvements in disease diagnostics, drug design and vaccine development. A variety of computational methods, mainly based on machine learning approaches, have been developed in the last decades to tackle this challenging problem. Here, we rigorously benchmarked nine state-of-the-art conformational B-cell epitope prediction webservers, including generic and antibody-specific methods, on a dataset of over 250 antibody-antigen structures. The results of our assessment and statistical analyses show that all the methods achieve very low performances, and some do not perform better than randomly generated patches of surface residues. In addition, we also found that commonly used consensus strategies that combine the results from multiple webservers are at best only marginally better than random. Finally, we applied all the predictors to the SARS-CoV-2 spike protein as an independent case study, and showed that they perform poorly in general, which largely recapitulates our benchmarking conclusions. We hope that these results will lead to greater caution when using these tools until the biases and issues that limit current methods have been addressed, promote the use of state-of-the-art evaluation methodologies in future publications and suggest new strategies to improve the performance of conformational B-cell epitope prediction methods.
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Affiliation(s)
- Gabriel Cia
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, F. Roosevelt Avenue, 1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Triumph Boulevard, 1050, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, F. Roosevelt Avenue, 1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Triumph Boulevard, 1050, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, F. Roosevelt Avenue, 1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Triumph Boulevard, 1050, Brussels, Belgium
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8
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Rockman S, Laurie K, Ong C, Rajaram S, McGovern I, Tran V, Youhanna J. Cell-Based Manufacturing Technology Increases Antigenic Match of Influenza Vaccine and Results in Improved Effectiveness. Vaccines (Basel) 2022; 11:52. [PMID: 36679895 PMCID: PMC9861528 DOI: 10.3390/vaccines11010052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
To ensure that vaccination offers the best protection against an infectious disease, sequence identity between the vaccine and the circulating strain is paramount. During replication of nucleic acid, random mutations occur due to the level of polymerase fidelity. In traditional influenza vaccine manufacture, vaccine viruses are propagated in fertilized chicken eggs, which can result in egg-adaptive mutations in the antigen-encoding genes. Whilst this improves infection and replication in eggs, mutations may reduce the effectiveness of egg-based influenza vaccines against circulating human viruses. In contrast, egg-adaptive mutations are avoided when vaccine viruses are propagated in Madin-Darby canine kidney (MDCK) cell lines during manufacture of cell-based inactivated influenza vaccines. The first mammalian cell-only strain was included in Flucelvax® Quadrivalent in 2017. A sequence analysis of the viruses selected for inclusion in this vaccine (n = 15 vaccine strains, containing both hemagglutinin and neuraminidase) demonstrated that no mutations occur in the antigenic sites of either hemagglutinin or neuraminidase, indicating that cell adaptation does not occur during production of this cell-based vaccine. The development of this now entirely mammalian-based vaccine system, which incorporates both hemagglutinin and neuraminidase, ensures that the significant protective antigens are equivalent to the strains recommended by the World Health Organization (WHO) in both amino acid sequence and glycosylation pattern. The inclusion of both proteins in a vaccine may provide an advantage over recombinant vaccines containing hemagglutinin alone. Findings from real world effectiveness studies support the use of cell-based influenza vaccines.
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Affiliation(s)
- Steven Rockman
- CSL Seqirus Ltd., Parkville, VIC 3050, Australia
- Department of Immunology and Microbiology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Karen Laurie
- CSL Seqirus Ltd., Parkville, VIC 3050, Australia
| | - Chi Ong
- CSL Seqirus Ltd., Parkville, VIC 3050, Australia
| | | | | | - Vy Tran
- CSL Seqirus Ltd., Kirkland, QC H9H 4M7, Canada
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9
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Masoomi Nomandan SZ, Azimzadeh Irani M, Hosseini SM. In silico design of refined ferritin-SARS-CoV-2 glyco-RBD nanoparticle vaccine. Front Mol Biosci 2022; 9:976490. [PMID: 36148012 PMCID: PMC9486171 DOI: 10.3389/fmolb.2022.976490] [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: 06/23/2022] [Accepted: 08/11/2022] [Indexed: 12/04/2022] Open
Abstract
With the onset of Coronavirus disease 2019 (COVID-19) pandemic, all attention was drawn to finding solutions to cure the coronavirus disease. Among all vaccination strategies, the nanoparticle vaccine has been shown to stimulate the immune system and provide optimal immunity to the virus in a single dose. Ferritin is a reliable self-assembled nanoparticle platform for vaccine production that has already been used in experimental studies. Furthermore, glycosylation plays a crucial role in the design of antibodies and vaccines and is an essential element in developing effective subunit vaccines. In this computational study, ferritin nanoparticles and glycosylation, which are two unique facets of vaccine design, were used to model improved nanoparticle vaccines for the first time. In this regard, molecular modeling and molecular dynamics simulation were carried out to construct three atomistic models of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD)-ferritin nanoparticle vaccine, including unglycosylated, glycosylated, and modified with additional O-glycans at the ferritin–RBD interface. It was shown that the ferritin–RBD complex becomes more stable when glycans are added to the ferritin–RBD interface and optimal performance of this nanoparticle can be achieved. If validated experimentally, these findings could improve the design of nanoparticles against all microbial infections.
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10
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Youk S, Leyson CM, Parris DJ, Kariithi HM, Suarez DL, Pantin-Jackwood MJ. Phylogenetic analysis, molecular changes, and adaptation to chickens of Mexican lineage H5N2 low-pathogenic avian influenza viruses from 1994 to 2019. Transbound Emerg Dis 2022; 69:e1445-e1459. [PMID: 35150205 PMCID: PMC9365891 DOI: 10.1111/tbed.14476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
The Mexican lineage H5N2 low pathogenic avian influenza viruses (LPAIVs) were first detected in 1994 and mutated to highly pathogenic avian influenza viruses (HPAIVs) in 1994-1995 causing widespread outbreaks in poultry. By using vaccination and other control measures, the HPAIVs were eradicated but the LPAIVs continued circulating in Mexico and spread to several other countries. To get better resolution of the phylogenetics of this virus, the full genome sequences of 44 H5N2 LPAIVs isolated from 1994 to 2011, and 6 detected in 2017 and 2019, were analysed. Phylogenetic incongruence demonstrated genetic reassortment between two separate groups of the Mexican lineage H5N2 viruses between 2005 and 2010. Moreover, the recent H5N2 viruses reassorted with previously unidentified avian influenza viruses. Bayesian phylogeographic results suggested that mechanical transmission involving human activity is the most probable cause of the virus spillover to Central American, Caribbean, and East Asian countries. Increased infectivity and transmission of a 2011 H5N2 LPAIV in chickens compared to a 1994 virus demonstrates improved adaptation to chickens, while low virus shedding, and limited contact transmission was observed in mallards with the same 2011 virus. The sporadic increase in basic amino acids in the HA cleavage site, changes in potential N-glycosylation sites in the HA, and truncations of PB1-F2 should be further examined in relation to the increased infectivity and transmission in poultry. The genetic changes that occur as this lineage of H5N2 LPAIVs continues circulating in poultry is concerning not only because of the effect of these changes on vaccination efficacy, but also because of the potential of the viruses to mutate to the highly pathogenic form. Continued vigilance and surveillance efforts, and the pathogenic and genetic characterization of circulating viruses, are required for the effective control of this virus.
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Affiliation(s)
- Sungsu Youk
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
| | - Christina M. Leyson
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
| | - Darren J. Parris
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
| | - Henry M. Kariithi
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
- Biotechnology Research Centre, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - David L. Suarez
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
| | - Mary J. Pantin-Jackwood
- Exotic and Emerging Avian Diseases Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture
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11
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Baker AN, Hawker-Bond GW, Georgiou PG, Dedola S, Field RA, Gibson MI. Glycosylated gold nanoparticles in point of care diagnostics: from aggregation to lateral flow. Chem Soc Rev 2022; 51:7238-7259. [PMID: 35894819 PMCID: PMC9377422 DOI: 10.1039/d2cs00267a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Current point-of-care lateral flow immunoassays, such as the home pregnancy test, rely on proteins as detection units (e.g. antibodies) to sense for analytes. Glycans play a fundamental role in biological signalling and recognition events such as pathogen adhesion and hence they are promising future alternatives to antibody-based biosensing and diagnostics. Here we introduce the potential of glycans coupled to gold nanoparticles as recognition agents for lateral flow diagnostics. We first introduce the concept of lateral flow, including a case study of lateral flow use in the field compared to other diagnostic tools. We then introduce glycosylated materials, the affinity gains achieved by the cluster glycoside effect and the current use of these in aggregation based assays. Finally, the potential role of glycans in lateral flow are explained, and examples of their successful use given. Antibody-based lateral flow (immune) assays are well established, but here the emerging concept and potential of using glycans as the detection agents is reviewed.![]()
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Affiliation(s)
- Alexander N Baker
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
| | - George W Hawker-Bond
- Oxford University Clinical Academic Graduate School, John Radcliffe Hospital Oxford, Oxford, OX3 9DU, UK
| | - Panagiotis G Georgiou
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
| | | | - Robert A Field
- Iceni Glycoscience Ltd, Norwich, NR4 7GJ, UK.,Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK. .,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
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12
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Nagashima K, Dzimianski JV, Han J, Abbadi N, Gingerich AD, Royer F, O'Rourke S, Sautto GA, Ross TM, Ward AB, DuBois RM, Mousa JJ. The Pre-Existing Human Antibody Repertoire to Computationally Optimized Influenza H1 Hemagglutinin Vaccines. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:5-15. [PMID: 35697384 PMCID: PMC9246865 DOI: 10.4049/jimmunol.2101171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/04/2022] [Indexed: 05/28/2023]
Abstract
Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA Ags. Cross-reactivity between wild-type HA and H1 COBRA HA proteins P1, X6, and Y2 were observed for isolated mAbs. The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 HA head and stem domains, and most mAbs had hemagglutination inhibition and neutralizing activity against 2009 pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had hemagglutination inhibition and neutralizing activity against a prepandemic H1 strain. One mAb, P1-05, targeted the stem region of H1 HA, but did not compete with a known stem-targeting H1 mAb. We determined that mAb P1-05 recognizes a recently discovered HA epitope, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by mAb P1-05, suggesting the importance of protein design for vaccine formulations. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA-reactive B cells that target head, central stalk, and anchor epitopes, and they demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.
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Affiliation(s)
- Kaito Nagashima
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - John V Dzimianski
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA; and
| | - Nada Abbadi
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Aaron D Gingerich
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Fredejah Royer
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Sara O'Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Giuseppe A Sautto
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Ted M Ross
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA; and
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Jarrod J Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA;
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA
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13
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In-Silico Design of a Multi‑epitope Construct Against Influenza A Based on Nucleoprotein Gene. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10418-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Ruiz-May E, Álvarez-Sánchez ME, Aguilar-Tipacamú G, Elizalde-Contreras JM, Bojórquez-Velázquez E, Zamora-Briseño JA, Vázquez-Carrillo LI, López-Esparza A. Comparative proteome analysis of the midgut of Rhipicephalus microplus (Acari: Ixodidae) strains with contrasting resistance to ivermectin reveals the activation of proteins involved in the detoxification metabolism. J Proteomics 2022; 263:104618. [DOI: 10.1016/j.jprot.2022.104618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/09/2022] [Accepted: 05/14/2022] [Indexed: 11/15/2022]
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15
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Escobar EE, Wang S, Goswami R, Lanzillotti MB, Li L, McLellan JS, Brodbelt JS. Analysis of Viral Spike Protein N-Glycosylation Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2022; 94:5776-5784. [PMID: 35388686 PMCID: PMC9272412 DOI: 10.1021/acs.analchem.1c04874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Characterization of protein glycosylation by tandem mass spectrometry remains challenging owing to the vast diversity of oligosaccharides bound to proteins, the variation in monosaccharide linkage patterns, and the lability of the linkage between the glycan and protein. Here, we have adapted an HCD-triggered-ultraviolet photodissociation (UVPD) approach for the simultaneous localization of glycosites and full characterization of both glycan compositions and intersaccharide linkages, the latter provided by extensive cross-ring cleavages enabled by UVPD. The method is applied to study glycan compositions based on analysis of glycopeptides from proteolytic digestion of recombinant human coronaviruse spike proteins from SARS-CoV-2 and HKU1. UVPD reveals unique intersaccharide linkage information and is leveraged to localize N-linked glycoforms with confidence.
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Affiliation(s)
- Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Shuaishuai Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Michael B Lanzillotti
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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16
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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17
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Keresztes G, Baer M, Alfenito MR, Verwoerd TC, Kovalchuk A, Wiebe MG, Andersen TK, Saloheimo M, Tchelet R, Kensinger R, Grødeland G, Emalfarb M. The Highly Productive Thermothelomyces heterothallica C1 Expression System as a Host for Rapid Development of Influenza Vaccines. Vaccines (Basel) 2022; 10:vaccines10020148. [PMID: 35214607 PMCID: PMC8877961 DOI: 10.3390/vaccines10020148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Influenza viruses constantly change and evade prior immune responses, forcing seasonal re-vaccinations with updated vaccines. Current FDA-approved vaccine manufacturing technologies are too slow and/or expensive to quickly adapt to mid-season changes in the virus or to the emergence of pandemic strains. Therefore, cost-effective vaccine technologies that can quickly adapt to newly emerged strains are desirable. (2) The filamentous fungal host Thermothelomyces heterothallica C1 (C1, formerly Myceliophthora thermophila) offers a highly efficient and cost-effective alternative to reliably produce immunogens of vaccine quality at large scale. (3) We showed the utility of the C1 system expressing hemagglutinin (HA) and a HA fusion protein from different H1N1 influenza A virus strains. Mice vaccinated with the C1-derived HA proteins elicited anti-HA immune responses similar, or stronger than mice vaccinated with HA products derived from prototypical expression systems. A challenge study demonstrated that vaccinated mice were protected against the aggressive homologous viral challenge. (4) The C1 expression system is proposed as part of a set of protein expression systems for plug-and-play vaccine manufacturing platforms. Upon the emergence of pathogens of concern these platforms could serve as a quick solution for producing enough vaccines for immunizing the world population in a much shorter time and more affordably than is possible with current platforms.
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Affiliation(s)
- Gabor Keresztes
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Mark Baer
- EnGen Bio LLC, 61 Avondale Ave., Redwood City, CA 94062, USA; (M.B.); (M.R.A.)
| | - Mark R. Alfenito
- EnGen Bio LLC, 61 Avondale Ave., Redwood City, CA 94062, USA; (M.B.); (M.R.A.)
| | - Theo C. Verwoerd
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Andriy Kovalchuk
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Marilyn G. Wiebe
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Tor Kristian Andersen
- Institute of Clinical Medicine, University of Oslo, 0027 Oslo, Norway; (T.K.A.); (G.G.)
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 Espoo, Finland; (A.K.); (M.G.W.); (M.S.)
| | - Ronen Tchelet
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
| | - Richard Kensinger
- Sanofi Pasteur, 1541 Ave. Marcel Mérieux, 69280 Marcy l’Etoile, France;
| | - Gunnveig Grødeland
- Institute of Clinical Medicine, University of Oslo, 0027 Oslo, Norway; (T.K.A.); (G.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0027 Oslo, Norway
| | - Mark Emalfarb
- Dyadic International Inc., 140 Intracoastal Pointe Drive, Suite 404, Jupiter, FL 33477, USA; (G.K.); (T.C.V.); (R.T.)
- Correspondence:
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18
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Qiu J, Tian X, Liu Y, Lu T, Wang H, Shi Z, Lu S, Xu D, Qiu T. Univ-flu: A structure-based model of influenza A virus hemagglutinin for universal antigenic prediction. Comput Struct Biotechnol J 2022; 20:4656-4666. [PMID: 36090813 PMCID: PMC9436755 DOI: 10.1016/j.csbj.2022.08.052] [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: 05/24/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
The rapid mutations on hemagglutinin (HA) of influenza A virus (IAV) can lead to significant antigenic variance and consequent immune mismatch of vaccine strains. Thus, rapid antigenicity evaluation is highly desired. The subtype-specific antigenicity models have been widely used for common subtypes such as H1 and H3. However, the continuous emerging of new IAV subtypes requires the construction of universal antigenic prediction model which could be applied on multiple IAV subtypes, including the emerging or re-emerging ones. In this study, we presented Univ-Flu, series structure-based universal models for HA antigenicity prediction. Initially, the universal antigenic regions were derived on multiple subtypes. Then, a radial shell structure combined with amino acid indexes were introduced to generate the new three-dimensional structure based descriptors, which could characterize the comprehensive physical–chemical property changes between two HA variants within or across different subtypes. Further, by combining with Random Forest classifier and different training datasets, Univ-Flu could achieve high prediction performances on intra-subtype (average AUC of 0.939), inter-subtype (average AUC of 0.771), and universal-subtype (AUC of 0.978) prediction, through independent test. Results illustrated that the designed descriptor could provide accurate universal antigenic description. Finally, the application on high-throughput antigenic coverage prediction for circulating strains showed that the Univ-Flu could screen out virus strains with high cross-protective spectrum, which could provide in-silico reference for vaccine recommendation.
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Abstract
Antibody immunodominance refers to the preferential and asymmetric elicitation of antibodies against specific epitopes on a complex protein antigen. Traditional vaccination approaches for rapidly evolving pathogens have had limited success in part because of this phenomenon, as elicited antibodies preferentially target highly variable regions of antigens, and thus do not confer long lasting protection. While antibodies targeting functionally conserved epitopes have the potential to be broadly protective, they often make up a minority of the overall repertoire. Here, we discuss recent protein engineering strategies used to favorably alter patterns of immunodominance, and selectively focus antibody responses toward broadly protective epitopes in the pursuit of next-generation vaccines for rapidly evolving pathogens.
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20
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Warnke S, Ben Faleh A, Rizzo TR. Toward High-Throughput Cryogenic IR Fingerprinting of Mobility-Separated Glycan Isomers. ACS MEASUREMENT SCIENCE AU 2021; 1:157-164. [PMID: 34939078 PMCID: PMC8679095 DOI: 10.1021/acsmeasuresciau.1c00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/10/2023]
Abstract
Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be used for biomolecular identification. This is particularly important in the analysis of isomeric biopolymers, which are difficult to distinguish using mass spectrometry. However, IR spectroscopy typically requires laser systems that need substantial user attention and measurement times of tens of minutes, which limits its analytical utility. We report here the development of a new high-throughput instrument that combines ultrahigh-resolution ion-mobility spectrometry with cryogenic IR spectroscopy and mass spectrometry, and we apply it to the analysis of isomeric glycans. The ion mobility step, which is based on structures for lossless ion manipulations (SLIM), separates glycan isomers, and an IR fingerprint spectrum identifies them. An innovative cryogenic ion trap allows multiplexing the acquisition of analyte IR fingerprints following mobility separation, and using a turn-key IR laser, we can obtain spectra and identify isomeric species in less than a minute. This work demonstrates the potential of IR fingerprinting methods to impact the analysis of isomeric biomolecules and more specifically glycans.
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21
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Influenza A and D Viruses in Non-Human Mammalian Hosts in Africa: A Systematic Review and Meta-Analysis. Viruses 2021; 13:v13122411. [PMID: 34960680 PMCID: PMC8706448 DOI: 10.3390/v13122411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
We conducted a systematic review and meta-analysis to investigate the prevalence and current knowledge of influenza A virus (IAV) and influenza D virus (IDV) in non-human mammalian hosts in Africa. PubMed, Google Scholar, Wiley Online Library and World Organisation for Animal Health (OIE-WAHIS) were searched for studies on IAV and IDV from 2000 to 2020. Pooled prevalence and seroprevalences were estimated using the quality effects meta-analysis model. The estimated pooled prevalence and seroprevalence of IAV in pigs in Africa was 1.6% (95% CI: 0-5%) and 14.9% (95% CI: 5-28%), respectively. The seroprevalence of IDV was 87.2% (95% CI: 24-100%) in camels, 9.3% (95% CI: 0-24%) in cattle, 2.2% (95% CI: 0-4%) in small ruminants and 0.0% (95% CI: 0-2%) in pigs. In pigs, H1N1 and H1N1pdm09 IAVs were commonly detected. Notably, the highly pathogenic H5N1 virus was also detected in pigs. Other subtypes detected serologically and/or virologically included H3N8 and H7N7 in equids, H1N1, and H3N8 and H5N1 in dogs and cats. Furthermore, various wildlife animals were exposed to different IAV subtypes. For prudent mitigation of influenza epizootics and possible human infections, influenza surveillance efforts in Africa should not neglect non-human mammalian hosts. The impact of IAV and IDV in non-human mammalian hosts in Africa deserves further investigation.
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22
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Zhang Y, Zheng S, Zhao W, Mao Y, Cao W, Zeng W, Liu Y, Hu L, Gong M, Cheng J, Chen Y, Yang H. Sequential Analysis of the N/O-Glycosylation of Heavily Glycosylated HIV-1 gp120 Using EThcD-sceHCD-MS/MS. Front Immunol 2021; 12:755568. [PMID: 34745128 PMCID: PMC8567067 DOI: 10.3389/fimmu.2021.755568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/06/2021] [Indexed: 02/05/2023] Open
Abstract
Deciphering the glycosylation of the viral envelope (Env) glycoprotein is critical for evaluating viral escape from the host’s immune response and developing vaccines and antiviral drugs. However, it is still challenging to precisely decode the site-specific glycosylation characteristics of the highly glycosylated Env proteins, although glycoproteomics have made significant advances in mass spectrometry techniques and data analysis tools. Here, we present a hybrid dissociation technique, EThcD-sceHCD, by combining electron transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) into a sequential glycoproteomic workflow. Following this scheme, we characterized site-specific N/O-glycosylation of the human immunodeficiency virus type 1 (HIV-1) Env protein gp120. The EThcD-sceHCD method increased the number of identified glycopeptides when compared with EThcD, while producing more comprehensive fragment ions than sceHCD for site-specific glycosylation analysis, especially for accurate O-glycosite assignment. Finally, eighteen N-glycosites and five O-glycosites with attached glycans were assigned unambiguously from heavily glycosylated gp120. These results indicate that our workflow can achieve improved performance for analysis of the N/O-glycosylation of a highly glycosylated protein containing numerous potential glycosites in one process. Knowledge of the glycosylation landscape of the Env glycoprotein will be useful for understanding of HIV-1 infection and development of vaccines and drugs.
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Affiliation(s)
- Yong Zhang
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Cao
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wenjuan Zeng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yueqiu Liu
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Younan Chen
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu, China
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23
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Yang Y, Yan G, Kong S, Wu M, Yang P, Cao W, Qiao L. GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control. Nat Commun 2021; 12:6073. [PMID: 34663801 PMCID: PMC8523693 DOI: 10.1038/s41467-021-26246-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.
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Affiliation(s)
- Yi Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Siyuan Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Mengxi Wu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China
| | - Weiqian Cao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
- The Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, 200000, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai, 200000, China.
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200000, China.
| | - Liang Qiao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200000, China.
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Sun Z, Ren K, Zhang X, Chen J, Jiang Z, Jiang J, Ji F, Ouyang X, Li L. Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications. ENGINEERING 2021; 7:1441-1451. [PMID: 32904601 PMCID: PMC7456593 DOI: 10.1016/j.eng.2020.07.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/22/2020] [Accepted: 07/05/2020] [Indexed: 05/18/2023]
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25
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Nuwarda RF, Alharbi AA, Kayser V. An Overview of Influenza Viruses and Vaccines. Vaccines (Basel) 2021; 9:1032. [PMID: 34579269 PMCID: PMC8473132 DOI: 10.3390/vaccines9091032] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/12/2023] Open
Abstract
Influenza remains one of the major public health concerns because it causes annual epidemics and can potentially instigate a global pandemic. Numerous countermeasures, including vaccines and antiviral treatments, are in use against seasonal influenza infection; however, their effectiveness has always been discussed due to the ongoing resistance to antivirals and relatively low and unpredictable efficiency of influenza vaccines compared to other vaccines. The growing interest in vaccines as a promising approach to prevent and control influenza may provide alternative vaccine development options with potentially increased efficiency. In addition to currently available inactivated, live-attenuated, and recombinant influenza vaccines on the market, novel platforms such as virus-like particles (VLPs) and nanoparticles, and new vaccine formulations are presently being explored. These platforms provide the opportunity to design influenza vaccines with improved properties to maximize quality, efficacy, and safety. The influenza vaccine manufacturing process is also moving forward with advancements relating to egg- and cell-based production, purification processes, and studies into the physicochemical attributes and vaccine degradation pathways. These will contribute to the design of more stable, optimized vaccine formulations guided by contemporary analytical testing methods and via the implementation of the latest advances in the field.
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Affiliation(s)
| | | | - Veysel Kayser
- Faculty of Medicine and Health, Sydney Pharmacy School, The University of Sydney, Sydney, NSW 2006, Australia; (R.F.N.); (A.A.A.)
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26
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Sun Z, Zheng X, Ji F, Zhou M, Su X, Ren K, Li L. Mass Spectrometry Analysis of SARS-CoV-2 Nucleocapsid Protein Reveals Camouflaging Glycans and Unique Post-Translational Modifications. INFECTIOUS MICROBES & DISEASES 2021; 3:149-157. [PMID: 38630108 PMCID: PMC8454284 DOI: 10.1097/im9.0000000000000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 01/08/2023]
Abstract
The devastating coronavirus disease 2019 (COVID-19) pandemic has prompted worldwide efforts to study structural biological traits of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its viral components. Compared to the Spike protein, which is the primary target for currently available vaccines or antibodies, knowledge about other virion structural components is incomplete. Using high-resolution mass spectrometry, we report a comprehensive post-translational modification (PTM) analysis of nucleocapsid phosphoprotein (NCP), the most abundant structural component of the SARS-CoV-2 virion. In addition to phosphoryl groups, we show that the SARS-CoV-2 NCP is decorated with a variety of PTMs, including N-glycans and ubiquitin. Based on newly identified PTMs, refined protein structural models of SARS-CoV-2 NCP were proposed and potential immune recognition epitopes of NCP were aligned with PTMs. These data can facilitate the design of novel vaccines or therapeutics targeting NCP, as valuable alternatives to the current vaccination and treatment paradigm that is under threat of the ever-mutating SARS-CoV-2 Spike protein.
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Affiliation(s)
- Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoqin Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiyang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Menghao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Keyi Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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27
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Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Genome-informed characterisation of antigenic drift in the haemagglutinin gene of equine influenza strains circulating in the United States from 2012 to 2017. Transbound Emerg Dis 2021; 69:e52-e63. [PMID: 34331828 DOI: 10.1111/tbed.14262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/14/2021] [Accepted: 07/24/2021] [Indexed: 01/14/2023]
Abstract
Equine influenza virus (EIV) is a major infectious pathogen causing significant respiratory signs in equids worldwide. Voluntary surveillances in the United States recently reported EIV detection in horses with respiratory signs even with adequate vaccine protocols and biosecurity programs and posed a concern about suboptimal effectiveness of EIV vaccine in the United States. This study aims to determine the genetic characteristics of 58 field EIV H3N8 strains in the United States from 2012 to 2017 using the phylogenetic analysis based on the haemagglutinin (HA) gene. Amino acid substitution and acquisition of N-glycosylation of the HA gene were also evaluated. Phylogenetic analysis identified that almost all US field strains belonged to the Florida clade 1 (FC1) except one Florida clade 2 strain from a horse imported in 2014. US EIV strains in 2017 shared 11 fixed amino acid substitutions in the HA gene, compared to the vaccine strain (A/equine/Ohio/2003), and two additional amino acid substitutions were detected in 2019. The introduction of foreign EIV strains into the United States was not detected, but antigenic drift without acquisition of N-glycosylation in the HA gene was observed in US field strains until 2017. Considering the global dominance of FC1 strains, subsequent antigenic drift of US EIV strains should be monitored for better effectiveness of the EIV vaccine in the United States and global equine industries.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, the University of Connecticut, Storrs, Connecticut, USA
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
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28
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Schön K, Lepenies B, Goyette-Desjardins G. Impact of Protein Glycosylation on the Design of Viral Vaccines. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 175:319-354. [PMID: 32935143 DOI: 10.1007/10_2020_132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycans play crucial roles in various biological processes such as cell proliferation, cell-cell interactions, and immune responses. Since viruses co-opt cellular biosynthetic pathways, viral glycosylation mainly depends on the host cell glycosylation machinery. Consequently, several viruses exploit the cellular glycosylation pathway to their advantage. It was shown that viral glycosylation is strongly dependent on the host system selected for virus propagation and/or protein expression. Therefore, the use of different expression systems results in various glycoforms of viral glycoproteins that may differ in functional properties. These differences clearly illustrate that the choice of the expression system can be important, as the resulting glycosylation may influence immunological properties. In this review, we will first detail protein N- and O-glycosylation pathways and the resulting glycosylation patterns; we will then discuss different aspects of viral glycosylation in pathogenesis and in vaccine development; and finally, we will elaborate on how to harness viral glycosylation in order to optimize the design of viral vaccines. To this end, we will highlight specific examples to demonstrate how glycoengineering approaches and exploitation of different expression systems could pave the way towards better self-adjuvanted glycan-based viral vaccines.
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Affiliation(s)
- Kathleen Schön
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Bernd Lepenies
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany.
| | - Guillaume Goyette-Desjardins
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany.
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29
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Wang W, Li Q, Wu J, Hu Y, Wu G, Yu C, Xu K, Liu X, Wang Q, Huang W, Wang L, Wang Y. Lentil lectin derived from Lens culinaris exhibit broad antiviral activities against SARS-CoV-2 variants. Emerg Microbes Infect 2021; 10:1519-1529. [PMID: 34278967 PMCID: PMC8330776 DOI: 10.1080/22221751.2021.1957720] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutated continuously and newly emerging variants escape from antibody-mediated neutralization raised great concern. S protein is heavily glycosylated and the glycosylation sites are relatively conserved, thus glycans on S protein surface could be a target for the development of anti-SARS-CoV-2 strategies against variants. Here, we collected 12 plant-derived lectins with different carbohydrate specificity and evaluated their anti-SARS-CoV-2 activity against mutant strains and epidemic variants using a pseudovirus-based neutralization assay. The Lens culinaris-derived lentil lectin which specifically bind to oligomannose-type glycans and GlcNAc at the non-reducing end terminus showed most potent and broad antiviral activity against a panel of mutant strains and variants, including the artificial mutants at N-/O-linked glycosylation site, natural existed amino acid mutants, as well as the epidemic variants B.1.1.7, B.1.351, and P.1. Lentil lectin also showed antiviral activity against SARS-CoV and MERS-CoV. We found lentil lectin could block the binding of ACE2 to S trimer and inhibit SARS-CoV-2 at the early steps of infection. Using structural information and determined N-glycan profile of S trimer, taking together with the carbohydrate specificity of lentil lectin, we provide a basis for the observed broad spectrum anti-SARS-CoV-2 activity. Lentil lectin showed weak haemagglutination activity at 1 mg/mL and no cytotoxicity activity, and no weight loss was found in single injection mouse experiment. This report provides the first evidence that lentil lectin strongly inhibit infection of SARS-COV-2 variants, which should provide valuable insights for developing future anti-SARS-CoV-2 strategies.
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Affiliation(s)
- Wenbo Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Jiajing Wu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Wuhan Institute of Biological Products, Hubei, People's Republic of China
| | - Yu Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People's Republic of China.,School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
| | - Gang Wu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Chuanfei Yu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Kangwei Xu
- Division of Respiratory Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Xumei Liu
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,School of Pharmacy, Yantai University, Yantai, People's Republic of China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Lan Wang
- Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
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30
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Krishnan S, Krishnan GP. N-Glycosylation Network Construction and Analysis to Modify Glycans on the Spike (S) Glycoprotein of SARS-CoV-2. FRONTIERS IN BIOINFORMATICS 2021; 1:667012. [PMID: 36303733 PMCID: PMC9581045 DOI: 10.3389/fbinf.2021.667012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022] Open
Abstract
Background: The N-glycan structure and composition of the spike (S) protein of SARS-CoV-2 are pertinent to vaccine development and efficacy. Methods: We reconstructed the glycosylation network based on previously published mass spectrometry data using GNAT, a glycosylation network analysis tool. Our compilation of the network tool had 26 glycosyltransferase and glucosidase enzymes and could infer the pathway of glycosylation machinery based on glycans in the virus spike protein. Once the glycan biosynthesis pathway was generated, we simulated the effect of blocking specific enzymes—swainsonine or deoxynojirimycin for blocking mannosidase-II and indolizidine for blocking alpha-1,6-fucosyltransferase—to see how they would affect the biosynthesis network and the glycans that were synthesized. Results: The N-glycan biosynthesis network of SARS-CoV-2 spike protein shows an elaborate enzymatic pathway with several intermediate glycans, along with the ones identified by mass spectrometric studies. Of the 26 enzymes, the following were involved—Man-Ia, MGAT1, MGAT2, MGAT4, MGAT5, B3GalT, B4GalT, Man-II, SiaT, ST3GalI, ST3GalVI, and FucT8. Blocking specific enzymes resulted in a substantially modified glycan profile of SARS-CoV-2. Conclusion: Variations in the final N-glycan profile of the virus, given its site-specific microheterogeneity, are factors in the host response to the infection, vaccines, and antibodies. Heterogeneity in the N-glycan profile of the spike (S) protein and its potential effect on vaccine efficacy or adverse reactions to the vaccines remain unexplored. Here, we provide all the resources we generated—the glycans in the glycoCT xml format and the biosynthesis network for future work.
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31
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Abstract
Introduction: As the pathogen that caused the first influenza virus pandemic in this century, the swine-origin A(H1N1) pdm09 influenza virus has caused continuous harm to human public health. The evolution of hemagglutinin protein glycosylation sites, including the increase in number and positional changes, is an important way for influenza viruses to escape host immune pressure. Based on the traditional influenza virus molecular monitoring, special attention should be paid to the influence of glycosylation evolution on the biological characteristics of virus antigenicity, transmission and pathogenicity. The epidemiological significance of glycosylation mutants should be analyzed as a predictive tool for early warning of new outbreaks and pandemics, as well as the design of vaccines and drug targets.Areas covered: We review on the evolutionary characteristics of glycosylation on the HA protein of the A(H1N1)pdm09 influenza virus in the last ten years.Expert opinion: We discuss the crucial impact of evolutionary glycosylation on the biological characteristics of the virus and the host immune responses, summarize studies revealing different roles of glycosylation play during host adaptation. Although these studies show the significance of glycosylation evolution in host-virus interaction, much remains to be discovered about the mechanism.
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Affiliation(s)
- Pan Ge
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, University of Georgia, Athens, GA USA
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32
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Li Y, Liu D, Wang Y, Su W, Liu G, Dong W. The Importance of Glycans of Viral and Host Proteins in Enveloped Virus Infection. Front Immunol 2021; 12:638573. [PMID: 33995356 PMCID: PMC8116741 DOI: 10.3389/fimmu.2021.638573] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Animal viruses are parasites of animal cells that have characteristics such as heredity and replication. Viruses can be divided into non-enveloped and enveloped viruses if a lipid bilayer membrane surrounds them or not. All the membrane proteins of enveloped viruses that function in attachment to target cells or membrane fusion are modified by glycosylation. Glycosylation is one of the most common post-translational modifications of proteins and plays an important role in many biological behaviors, such as protein folding and stabilization, virus attachment to target cell receptors and inhibition of antibody neutralization. Glycans of the host receptors can also regulate the attachment of the viruses and then influence the virus entry. With the development of glycosylation research technology, the research and development of novel virus vaccines and antiviral drugs based on glycan have received increasing attention. Here, we review the effects of host glycans and viral proteins on biological behaviors of viruses, and the opportunities for prevention and treatment of viral infectious diseases.
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Affiliation(s)
- Yuqing Li
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Dongqi Liu
- The Queen's University of Belfast Joint College, China Medical University, Shenyang, China
| | - Yating Wang
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Wenquan Su
- Dalian Medical University, Dalian, China
| | - Gang Liu
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Weijie Dong
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
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33
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Nagashima KA, Mousa JJ. Next-Generation Influenza HA Immunogens and Adjuvants in Pursuit of a Broadly Protective Vaccine. Viruses 2021; 13:v13040546. [PMID: 33805245 PMCID: PMC8064354 DOI: 10.3390/v13040546] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
Influenza virus, a highly mutable respiratory pathogen, causes significant disease nearly every year. Current vaccines are designed to protect against circulating influenza strains of a given season. However, mismatches between vaccine strains and circulating strains, as well as inferior vaccine effectiveness in immunodeficient populations, represent major obstacles. In an effort to expand the breadth of protection elicited by influenza vaccination, one of the major surface glycoproteins, hemagglutinin (HA), has been modified to develop immunogens that display conserved regions from multiple viruses or elicit a highly polyclonal antibody response to broaden protection. These approaches, which target either the head or the stalk domain of HA, or both domains, have shown promise in recent preclinical and clinical studies. Furthermore, the role of adjuvants in bolstering the robustness of the humoral response has been studied, and their effects on the vaccine-elicited antibody repertoire are currently being investigated. This review will discuss the progress made in the universal influenza vaccine field with respect to influenza A viruses from the perspectives of both antigen and adjuvant, with a focus on the elicitation of broadly neutralizing antibodies.
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Affiliation(s)
- Kaito A. Nagashima
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA;
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jarrod J. Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA;
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Correspondence:
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34
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Gautam S, Banazadeh A, Cho BG, Goli M, Zhong J, Mechref Y. Mesoporous Graphitized Carbon Column for Efficient Isomeric Separation of Permethylated Glycans. Anal Chem 2021; 93:5061-5070. [DOI: 10.1021/acs.analchem.0c04395] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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35
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Zhang Y, Zhao W, Mao Y, Chen Y, Wang S, Zhong Y, Su T, Gong M, Du D, Lu X, Cheng J, Yang H. Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins. Mol Cell Proteomics 2021; 20:100058. [PMID: 33077685 DOI: 10.1101/2020.03.28.013276] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
The glycoprotein spike (S) on the surface of severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a determinant for viral invasion and host immune response. Herein, we characterized the site-specific N-glycosylation of S protein at the level of intact glycopeptides. All 22 potential N-glycosites were identified in the S-protein protomer and were found to be preserved among the 753 SARS-CoV-2 genome sequences. The glycosites exhibited glycoform heterogeneity as expected for a human cell-expressed protein subunit. We identified masses that correspond to 157 N-glycans, primarily of the complex type. In contrast, the insect cell-expressed S protein contained 38 N-glycans, completely of the high-mannose type. Our results revealed that the glycan types were highly determined by the differential processing of N-glycans among human and insect cells, regardless of the glycosites' location. Moreover, the N-glycan compositions were conserved among different sizes of subunits. Our study indicates that the S protein N-glycosylation occurs regularly at each site, albeit the occupied N-glycans were diverse and heterogenous. This N-glycosylation landscape and the differential N-glycan patterns among distinct host cells are expected to shed light on the infection mechanism and present a positive view for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shisheng Wang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Du
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaofeng Lu
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
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36
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Zhang Y, Zhao W, Mao Y, Chen Y, Wang S, Zhong Y, Su T, Gong M, Du D, Lu X, Cheng J, Yang H. Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins. Mol Cell Proteomics 2021; 20:100058. [PMID: 33077685 PMCID: PMC7876485 DOI: 10.1074/mcp.ra120.002295] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The glycoprotein spike (S) on the surface of severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a determinant for viral invasion and host immune response. Herein, we characterized the site-specific N-glycosylation of S protein at the level of intact glycopeptides. All 22 potential N-glycosites were identified in the S-protein protomer and were found to be preserved among the 753 SARS-CoV-2 genome sequences. The glycosites exhibited glycoform heterogeneity as expected for a human cell-expressed protein subunit. We identified masses that correspond to 157 N-glycans, primarily of the complex type. In contrast, the insect cell-expressed S protein contained 38 N-glycans, completely of the high-mannose type. Our results revealed that the glycan types were highly determined by the differential processing of N-glycans among human and insect cells, regardless of the glycosites' location. Moreover, the N-glycan compositions were conserved among different sizes of subunits. Our study indicates that the S protein N-glycosylation occurs regularly at each site, albeit the occupied N-glycans were diverse and heterogenous. This N-glycosylation landscape and the differential N-glycan patterns among distinct host cells are expected to shed light on the infection mechanism and present a positive view for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shisheng Wang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Du
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaofeng Lu
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
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37
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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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38
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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39
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Zhang J, Peng Q, Zhao W, Sun W, Yang J, Liu N. Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications. J Proteome Res 2020; 20:110-121. [PMID: 33348980 DOI: 10.1021/acs.jproteome.0c00778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.
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Affiliation(s)
- Jinming Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Qisheng Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Weizheng Zhao
- Clinical Medical College, Jilin University, Changchun 130021, PR China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Jingbo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
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40
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Shajahan A, Supekar NT, Gleinich AS, Azadi P. Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2. Glycobiology 2020; 30:981-988. [PMID: 32363391 PMCID: PMC7239183 DOI: 10.1093/glycob/cwaa042] [Citation(s) in RCA: 348] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022] Open
Abstract
The current emergence of the novel coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands the development of new therapeutic strategies to prevent rapid progress of mortalities. The coronavirus spike (S) protein, which facilitates viral attachment, entry and membrane fusion is heavily glycosylated and plays a critical role in the elicitation of the host immune response. The spike protein is comprised of two protein subunits (S1 and S2), which together possess 22 potential N-glycosylation sites. Herein, we report the glycosylation mapping on spike protein subunits S1 and S2 expressed on human cells through high-resolution mass spectrometry. We have characterized the quantitative N-glycosylation profile on spike protein and interestingly, observed unexpected O-glycosylation modifications on the receptor-binding domain of spike protein subunit S1. Even though O-glycosylation has been predicted on the spike protein of SARS-CoV-2, this is the first report of experimental data for both the site of O-glycosylation and identity of the O-glycans attached on the subunit S1. Our data on the N- and O-glycosylation are strengthened by extensive manual interpretation of each glycopeptide spectra in addition to using bioinformatics tools to confirm the complexity of glycosylation in the spike protein. The elucidation of the glycan repertoire on the spike protein provides insights into the viral binding studies and more importantly, propels research toward the development of a suitable vaccine candidate.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Nitin T Supekar
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Anne S Gleinich
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
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41
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Wang D, Baudys J, Bundy JL, Solano M, Keppel T, Barr JR. Comprehensive Analysis of the Glycan Complement of SARS-CoV-2 Spike Proteins Using Signature Ions-Triggered Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. Anal Chem 2020; 92:14730-14739. [PMID: 33064451 PMCID: PMC7586457 DOI: 10.1021/acs.analchem.0c03301] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic of coronavirus disease 2019 (COVID-19). The spike protein expressed on the surface of this virus is highly glycosylated and plays an essential role during the process of infection. We conducted a comprehensive mass spectrometric analysis of the N-glycosylation profiles of the SARS-CoV-2 spike proteins using signature ions-triggered electron-transfer/higher-energy collision dissociation (EThcD) mass spectrometry. The patterns of N-glycosylation within the recombinant ectodomain and S1 subunit of the SARS-CoV-2 spike protein were characterized using this approach. Significant variations were observed in the distribution of glycan types as well as the specific individual glycans on the modification sites of the ectodomain and subunit proteins. The relative abundance of sialylated glycans in the S1 subunit compared to the full-length protein could indicate differences in the global structure and function of these two species. In addition, we compared N-glycan profiles of the recombinant spike proteins produced from different expression systems, including human embryonic kidney (HEK 293) cells and Spodoptera frugiperda (SF9) insect cells. These results provide useful information for the study of the interactions of SARS-CoV-2 viral proteins and for the development of effective vaccines and therapeutics.
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Affiliation(s)
- Dongxia Wang
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Jakub Baudys
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Jonathan L. Bundy
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Maria Solano
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Theodore Keppel
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - John R. Barr
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
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42
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Polasky DA, Yu F, Teo GC, Nesvizhskii AI. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 2020. [PMID: 33020657 DOI: 10.1101/2020.05.18.102665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale glycoproteomics datasets, but interpreting these data remains challenging. We present MSFragger-Glyco, a glycoproteomics mode of the MSFragger search engine, for fast and sensitive identification of N- and O-linked glycopeptides and open glycan searches. Reanalysis of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide spectrum matches (glycoPSMs) than previously reported. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same glycans as the original search, and yielded 4- to 6-fold increases when expanding searches to include additional glycan compositions and other modifications. Expanded searches also revealed many sulfated and complex glycans that remained hidden to the original search. With greatly improved spectral annotation, coupled with the speed of index-based scoring, MSFragger-Glyco makes it possible to comprehensively interrogate glycoproteomics data and illuminate the many roles of glycosylation.
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Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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43
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Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 2020; 17:1125-1132. [PMID: 33020657 PMCID: PMC7606558 DOI: 10.1038/s41592-020-0967-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022]
Abstract
Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale glycoproteomics datasets, but interpreting this data remains challenging. We present MSFragger-Glyco, a glycoproteomics mode of the MSFragger search engine, for fast and sensitive identification of N- and O-linked glycopeptides and open glycan searches. Reanalysis of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide-spectrum matches (glycoPSMs) than previously reported. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same glycans as the original search and yielded 4–6-fold increases when expanding searches to include additional glycan compositions and other modifications. Expanded searches also revealed many sulfated and complex glycans that remained hidden to the original search. With greatly improved spectral annotation, coupled with the speed of index-based scoring, MSFragger-Glyco makes it possible to comprehensively interrogate glycoproteomics data and illuminate the many roles of glycosylation.
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44
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Using the Past to Maximize the Success Probability of Future Anti-Viral Vaccines. Vaccines (Basel) 2020; 8:vaccines8040566. [PMID: 33019507 PMCID: PMC7712378 DOI: 10.3390/vaccines8040566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022] Open
Abstract
Rapid obtaining of safe, effective, anti-viral vaccines has recently risen to the top of the international agenda. To maximize the success probability of future anti-viral vaccines, the anti-viral vaccines successful in the past are summarized here by virus type and vaccine type. The primary focus is on viruses with both single-stranded RNA genomes and a membrane envelope, given the pandemic past of influenza viruses and coronaviruses. The following conclusion is reached, assuming that success of future strategies is positively correlated with strategies successful in the past. The primary strategy, especially for emerging pandemic viruses, should be development of vaccine antigens that are live-attenuated viruses; the secondary strategy should be development of vaccine antigens that are inactivated virus particles. Support for this conclusion comes from the complexity of immune systems. These conclusions imply the need for a revision in current strategic planning.
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45
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Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Sci Rep 2020; 10:14991. [PMID: 32929138 PMCID: PMC7490396 DOI: 10.1038/s41598-020-71748-7] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the innate and adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight of the S trimer (17% for the HEK293 glycoform) they shield approximately 40% of the protein surface.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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46
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Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction. Molecules 2020; 25:molecules25184133. [PMID: 32927621 PMCID: PMC7571139 DOI: 10.3390/molecules25184133] [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: 08/01/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.
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47
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Kalonda A, Saasa N, Nkhoma P, Kajihara M, Sawa H, Takada A, Simulundu E. Avian Influenza Viruses Detected in Birds in Sub-Saharan Africa: A Systematic Review. Viruses 2020; 12:v12090993. [PMID: 32906666 PMCID: PMC7552061 DOI: 10.3390/v12090993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
In the recent past, sub-Saharan Africa has not escaped the devastating effects of avian influenza virus (AIV) in poultry and wild birds. This systematic review describes the prevalence, spatiotemporal distribution, and virus subtypes detected in domestic and wild birds for the past two decades (2000–2019). We collected data from three electronic databases, PubMed, SpringerLink electronic journals and African Journals Online, using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol. A total of 1656 articles were reviewed, from which 68 were selected. An overall prevalence of 3.0% AIV in birds was observed. The prevalence varied between regions and ranged from 1.1% to 7.1%. The Kruskal–Wallis and Wilcoxon signed-rank sum test showed no significant difference in the prevalence of AIV across regions, χ2(3) = 5.237, p = 0.1553 and seasons, T = 820, z = −1.244, p = 0.2136. Nineteen hemagglutinin/neuraminidase subtype combinations were detected during the reviewed period, with southern Africa recording more diverse AIV subtypes than other regions. The most detected subtype was H5N1, followed by H9N2, H5N2, H5N8 and H6N2. Whilst these predominant subtypes were mostly detected in domestic poultry, H1N6, H3N6, H4N6, H4N8, H9N1 and H11N9 were exclusively detected in wild birds. Meanwhile, H5N1, H5N2 and H5N8 were detected in both wild and domestic birds suggesting circulation of these subtypes among wild and domestic birds. Our findings provide critical information on the eco-epidemiology of AIVs that can be used to improve surveillance strategies for the prevention and control of avian influenza in sub-Saharan Africa.
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Affiliation(s)
- Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Disease of Humans and Animals, School of Veterinary Medicine, Lusaka 10101, Zambia
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
| | - Masahiro Kajihara
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Macha Research Trust, Choma 20100, Zambia
- Correspondence: ; Tel.: +260-977469479
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Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.07.030445. [PMID: 32511307 PMCID: PMC7217288 DOI: 10.1101/2020.04.07.030445] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight (17% for the HEK293 glycoform) the level of surface shielding is disproportionately high at 42%.
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Affiliation(s)
- Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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