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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 PMCID: PMC11182062 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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Zheng YB, Lu S, Chu TB, Pang GF, Yang LY, Zhang Q. Investigate the potential impact of Hemagglutinin from the H1N1 strain on severe pneumonia. Gene 2024; 926:148559. [PMID: 38740352 DOI: 10.1016/j.gene.2024.148559] [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: 01/20/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The most prevalent glycoprotein on the influenza virus envelope is called hemagglutinin (HA), yet little is known about its involvement in the pathophysiology and etiology of severe influenza pneumonia. Here, after stimulating human bronchial epithelial cells (16-HBE) and mice with HA of H1N1 for 12 h, we investigated the proliferation, migration, inflammatory cytokines expression, and apoptosis in 16-HBE and the pathological damage in mouse lung tissue. The expression of inflammatory cytokines plasminogen activator inhibitor 1(PAI-1), urokinase-type (uPA) and tissue-type (tPA) plasminogen activators, and apoptosis were all enhanced by HA, which also prevented the proliferation and migration of bronchial epithelial cells. HA enhanced up-regulated PAI-1, uPA, and tPA protein expression within mouse lung tissue and caused lung injury. In conclusion, HA alone, but not the whole H1N1 virus, induces lung tissue injury by inhibiting cell proliferation and migration, while promoting the expression of inflammatory cytokines and apoptosis.
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Affiliation(s)
- Yu-Bi Zheng
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China.
| | - Song Lu
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Tian-Bao Chu
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Gui-Feng Pang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Lin-Ying Yang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Qing Zhang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China.
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3
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Lei R, Liang W, Ouyang WO, Hernandez Garcia A, Kikuchi C, Wang S, McBride R, Tan TJC, Sun Y, Chen C, Graham CS, Rodriguez LA, Shen IR, Choi D, Bruzzone R, Paulson JC, Nair SK, Mok CKP, Wu NC. Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin. Nat Commun 2024; 15:5175. [PMID: 38890325 PMCID: PMC11189414 DOI: 10.1038/s41467-024-49487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode. Epistasis between G186D and D190N is further demonstrated by glycan binding and thermostability analyses. Immunization and neutralization experiments using mouse and human samples indicate that the evolution of receptor binding mode is accompanied by a change in antigenicity. Besides, combinatorial mutagenesis reveals that G186D and D190N, along with other natural mutations in recent H3N2 strains, alter the compatibility with a common egg-adaptive mutation in seasonal influenza vaccines. Overall, our findings elucidate the role of epistasis in shaping the recent evolution of human H3N2 hemagglutinin and substantiate the high evolvability of its receptor-binding mode.
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MESH Headings
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Epistasis, Genetic
- Animals
- Evolution, Molecular
- Mice
- Binding Sites
- Influenza, Human/virology
- Mutation
- Crystallography, X-Ray
- Influenza Vaccines
- Protein Binding
- Receptors, Virus/metabolism
- Receptors, Virus/genetics
- Receptors, Virus/chemistry
- Female
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Weiwen Liang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Chika Kikuchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Shengyang Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yuanxin Sun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chunke Chen
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire S Graham
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lucia A Rodriguez
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ivana R Shen
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Danbi Choi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Cell Biology and Infection, Institut Pasteur, Paris, Cedex, 75015, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- S.H. Ho Research Centre for Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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Xu L, Ren W, Wang Q, Li J. Advances in Nucleic Acid Universal Influenza Vaccines. Vaccines (Basel) 2024; 12:664. [PMID: 38932393 PMCID: PMC11209422 DOI: 10.3390/vaccines12060664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, vaccination with influenza vaccines is still an effective strategy to prevent infection by seasonal influenza virus in spite of some drawbacks with them. However, due to the rapid evolution of influenza viruses, including seasonal influenza viruses and emerging zoonotic influenza viruses, there is an urgent need to develop broad-spectrum influenza vaccines to cope with the evolution of influenza viruses. Nucleic acid vaccines might meet the requirements well. Nucleic acid vaccines are classified into DNA vaccines and RNA vaccines. Both types induced potent cellular and humoral immune responses, showing great promise for the development of universal influenza vaccines. In this review, the current status of an influenza universal nucleic acid vaccine was summarized.
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Affiliation(s)
- Liang Xu
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China; (L.X.); (W.R.); (Q.W.)
| | - Weigang Ren
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China; (L.X.); (W.R.); (Q.W.)
| | - Qin Wang
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China; (L.X.); (W.R.); (Q.W.)
| | - Junwei Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China; (L.X.); (W.R.); (Q.W.)
- Medical Innovation Center for Infectious Disease of Jiangsu Province, Nanjing 210003, China
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5
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Luczo JM, Spackman E. Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift. FEMS Microbiol Rev 2024; 48:fuae014. [PMID: 38734891 PMCID: PMC11149724 DOI: 10.1093/femsre/fuae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Avian influenza viruses evolve antigenically to evade host immunity. Two influenza A virus surface glycoproteins, the haemagglutinin and neuraminidase, are the major targets of host immunity and undergo antigenic drift in response to host pre-existing humoral and cellular immune responses. Specific sites have been identified as important epitopes in prominent subtypes such as H5 and H7, which are of animal and public health significance due to their panzootic and pandemic potential. The haemagglutinin is the immunodominant immunogen, it has been extensively studied, and the antigenic reactivity is closely monitored to ensure candidate vaccine viruses are protective. More recently, the neuraminidase has received increasing attention for its role as a protective immunogen. The neuraminidase is expressed at a lower abundance than the haemagglutinin on the virus surface but does elicit a robust antibody response. This review aims to compile the current information on haemagglutinin and neuraminidase epitopes and immune escape mutants of H5 and H7 highly pathogenic avian influenza viruses. Understanding the evolution of immune escape mutants and the location of epitopes is critical for identification of vaccine strains and development of broadly reactive vaccines that can be utilized in humans and animals.
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Affiliation(s)
- Jasmina M Luczo
- Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, East Geelong, Victoria 3219, Australia
| | - Erica Spackman
- Exotic & Emerging Avian Viral Diseases Research, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, United States
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6
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Spruit CM, Palme DI, Li T, Ríos Carrasco M, Gabarroca García A, Sweet IR, Kuryshko M, Maliepaard JCL, Reiding KR, Scheibner D, Boons GJ, Abdelwhab EM, de Vries RP. Complex N-glycans are important for interspecies transmission of H7 influenza A viruses. J Virol 2024; 98:e0194123. [PMID: 38470143 PMCID: PMC11019957 DOI: 10.1128/jvi.01941-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Influenza A viruses (IAVs) can overcome species barriers by adaptation of the receptor-binding site of the hemagglutinin (HA). To initiate infection, HAs bind to glycan receptors with terminal sialic acids, which are either N-acetylneuraminic acid (NeuAc) or N-glycolylneuraminic acid (NeuGc); the latter is mainly found in horses and pigs but not in birds and humans. We investigated the influence of previously identified equine NeuGc-adapting mutations (S128T, I130V, A135E, T189A, and K193R) in avian H7 IAVs in vitro and in vivo. We observed that these mutations negatively affected viral replication in chicken cells but not in duck cells and positively affected replication in horse cells. In vivo, the mutations reduced virus virulence and mortality in chickens. Ducks excreted high viral loads longer than chickens, although they appeared clinically healthy. To elucidate why these viruses infected chickens and ducks despite the absence of NeuGc, we re-evaluated the receptor binding of H7 HAs using glycan microarray and flow cytometry studies. This re-evaluation demonstrated that mutated avian H7 HAs also bound to α2,3-linked NeuAc and sialyl-LewisX, which have an additional fucose moiety in their terminal epitope, explaining why infection of ducks and chickens was possible. Interestingly, the α2,3-linked NeuAc and sialyl-LewisX epitopes were only bound when presented on tri-antennary N-glycans, emphasizing the importance of investigating the fine receptor specificities of IAVs. In conclusion, the binding of NeuGc-adapted H7 IAV to tri-antennary N-glycans enables viral replication and shedding by chickens and ducks, potentially facilitating interspecies transmission of equine-adapted H7 IAVs.IMPORTANCEInfluenza A viruses (IAVs) cause millions of deaths and illnesses in birds and mammals each year. The viral surface protein hemagglutinin initiates infection by binding to host cell terminal sialic acids. Hemagglutinin adaptations affect the binding affinity to these sialic acids and the potential host species targeted. While avian and human IAVs tend to bind to N-acetylneuraminic acid (sialic acid), equine H7 viruses prefer binding to N-glycolylneuraminic acid (NeuGc). To better understand the function of NeuGc-specific adaptations in hemagglutinin and to elucidate interspecies transmission potential NeuGc-adapted viruses, we evaluated the effects of NeuGc-specific mutations in avian H7 viruses in chickens and ducks, important economic hosts and reservoir birds, respectively. We also examined the impact on viral replication and found a binding affinity to tri-antennary N-glycans containing different terminal epitopes. These findings are significant as they contribute to the understanding of the role of receptor binding in avian influenza infection.
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Affiliation(s)
- Cindy M. Spruit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana I. Palme
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Tiehai Li
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - María Ríos Carrasco
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Alba Gabarroca García
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Igor R. Sweet
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maryna Kuryshko
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Joshua C. L. Maliepaard
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Karli R. Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - David Scheibner
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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7
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Feoktistova S, Sayganova M, Trutneva K, Glazova O, Blagodatski AS, Shevkova L, Navoikova A, Anisimov Y, Albert E, Mityaeva O, Volchkov P, Deviatkin A. Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses. Viruses 2024; 16:568. [PMID: 38675910 PMCID: PMC11054967 DOI: 10.3390/v16040568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza A viruses (IAVs) pose a serious threat to global health. On the one hand, these viruses cause seasonal flu outbreaks in humans. On the other hand, they are a zoonotic infection that has the potential to cause a pandemic. The most important natural reservoir of IAVs are waterfowl. In this study, we investigated the occurrence of IAV in birds in the Republic of Buryatia (region in Russia). In 2020, a total of 3018 fecal samples were collected from wild migratory birds near Lake Baikal. Of these samples, 11 were found to be positive for the H13N8 subtype and whole-genome sequencing was performed on them. All samples contained the same virus with the designation A/Unknown/Buryatia/Arangatui-1/2020. To our knowledge, virus A/Unknown/Buryatia/Arangatui-1/2020 is the first representative of the H13N8 subtype collected on the territory of Russia, the sequence of which is available in the GenBank database. An analysis of reassortments based on the genome sequences of other known viruses has shown that A/Unknown/Buryatia/Arangatui-1/2020 arose as a result of reassortment. In addition, a reassortment most likely occurred several decades ago between the ancestors of the viruses recently collected in China, the Netherlands, the United States and Chile. The presence of such reassortment emphasizes the ongoing evolution of the H13N8 viruses distributed in Europe, North and East Asia, North and South America and Australia. This study underscores the importance of the continued surveillance and research of less-studied influenza subtypes.
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Affiliation(s)
- Sofia Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Marya Sayganova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Kseniya Trutneva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Glazova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Artem S. Blagodatski
- Federal State Budget Institution of Science Institute of Theoretical and Experimental Biophysics, 142290 Pushchino, Russia;
| | - Liudmila Shevkova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Anna Navoikova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Yuriy Anisimov
- Baikalsky State Nature Biosphere Reserve, 671220 Tankhoi, Russia;
| | - Eugene Albert
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The Moscow Clinical Scientific Center (MCSC) Named after A.S. Loginov, 111123 Moscow, Russia
| | - Andrey Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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8
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Unione L, Ammerlaan ANA, Bosman GP, Uslu E, Liang R, Broszeit F, van der Woude R, Liu Y, Ma S, Liu L, Gómez-Redondo M, Bermejo IA, Valverde P, Diercks T, Ardá A, de Vries RP, Boons GJ. Probing altered receptor specificities of antigenically drifting human H3N2 viruses by chemoenzymatic synthesis, NMR, and modeling. Nat Commun 2024; 15:2979. [PMID: 38582892 PMCID: PMC10998905 DOI: 10.1038/s41467-024-47344-y] [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: 06/08/2023] [Accepted: 03/25/2024] [Indexed: 04/08/2024] Open
Abstract
Prototypic receptors for human influenza viruses are N-glycans carrying α2,6-linked sialosides. Due to immune pressure, A/H3N2 influenza viruses have emerged with altered receptor specificities that bind α2,6-linked sialosides presented on extended N-acetyl-lactosamine (LacNAc) chains. Here, binding modes of such drifted hemagglutinin's (HAs) are examined by chemoenzymatic synthesis of N-glycans having 13C-labeled monosaccharides at strategic positions. The labeled glycans are employed in 2D STD-1H by 13C-HSQC NMR experiments to pinpoint which monosaccharides of the extended LacNAc chain engage with evolutionarily distinct HAs. The NMR data in combination with computation and mutagenesis demonstrate that mutations distal to the receptor binding domain of recent HAs create an extended binding site that accommodates with the extended LacNAc chain. A fluorine containing sialoside is used as NMR probe to derive relative binding affinities and confirms the contribution of the extended LacNAc chain for binding.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands.
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Bizkaia, Spain.
| | - Augustinus N A Ammerlaan
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Gerlof P Bosman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Elif Uslu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Ruonan Liang
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Frederik Broszeit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Yanyan Liu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Shengzhou Ma
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Marcos Gómez-Redondo
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Iris A Bermejo
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Pablo Valverde
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Tammo Diercks
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Bizkaia, Spain
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands.
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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9
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Mader K, Dustin LB. Beyond bNAbs: Uses, Risks, and Opportunities for Therapeutic Application of Non-Neutralising Antibodies in Viral Infection. Antibodies (Basel) 2024; 13:28. [PMID: 38651408 PMCID: PMC11036282 DOI: 10.3390/antib13020028] [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: 03/07/2024] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/25/2024] Open
Abstract
The vast majority of antibodies generated against a virus will be non-neutralising. However, this does not denote an absence of protective capacity. Yet, within the field, there is typically a large focus on antibodies capable of directly blocking infection (neutralising antibodies, NAbs) of either specific viral strains or multiple viral strains (broadly-neutralising antibodies, bNAbs). More recently, a focus on non-neutralising antibodies (nNAbs), or neutralisation-independent effects of NAbs, has emerged. These can have additive effects on protection or, in some cases, be a major correlate of protection. As their name suggests, nNAbs do not directly neutralise infection but instead, through their Fc domains, may mediate interaction with other immune effectors to induce clearance of viral particles or virally infected cells. nNAbs may also interrupt viral replication within infected cells. Developing technologies of antibody modification and functionalisation may lead to innovative biologics that harness the activities of nNAbs for antiviral prophylaxis and therapeutics. In this review, we discuss specific examples of nNAb actions in viral infections where they have known importance. We also discuss the potential detrimental effects of such responses. Finally, we explore new technologies for nNAb functionalisation to increase efficacy or introduce favourable characteristics for their therapeutic applications.
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Affiliation(s)
| | - Lynn B. Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK;
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10
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Tomris I, van der Woude R, de Paiva Froes Rocha R, Torrents de la Peña A, Ward AB, de Vries RP. Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding. Protein Sci 2024; 33:e4974. [PMID: 38533540 DOI: 10.1002/pro.4974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
Enveloped viruses carry one or multiple proteins with receptor-binding functionalities. Functional receptors can be glycans, proteinaceous, or both; therefore, recombinant protein approaches are instrumental in attaining new insights regarding viral envelope protein receptor-binding properties. Visualizing and measuring receptor binding typically entails antibody detection or direct labeling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here, we report a suite of distinct fluorescent fusions, both N- and C-terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained three or six fluorescent protein barrels and were applied directly to cells to assess receptor binding properties.
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Affiliation(s)
- Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Rebeca de Paiva Froes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
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11
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Lim CML, Komarasamy TV, Adnan NAAB, Radhakrishnan AK, Balasubramaniam VRMT. Recent Advances, Approaches and Challenges in the Development of Universal Influenza Vaccines. Influenza Other Respir Viruses 2024; 18:e13276. [PMID: 38513364 PMCID: PMC10957243 DOI: 10.1111/irv.13276] [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: 08/04/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/23/2024] Open
Abstract
Every year, influenza virus infections cause significant morbidity and mortality worldwide. They pose a substantial burden of disease, in terms of not only health but also the economy. Owing to the ability of influenza viruses to continuously evolve, annual seasonal influenza vaccines are necessary as a prophylaxis. However, current influenza vaccines against seasonal strains have limited effectiveness and require yearly reformulation due to the virus undergoing antigenic drift or shift. Vaccine mismatches are common, conferring suboptimal protection against seasonal outbreaks, and the threat of the next pandemic continues to loom. Therefore, there is a great need to develop a universal influenza vaccine (UIV) capable of providing broad and durable protection against all influenza virus strains. In the quest to develop a UIV that would obviate the need for annual vaccination and formulation, a multitude of strategies is currently underway. Promising approaches include targeting the highly conserved epitopes of haemagglutinin (HA), neuraminidase (NA), M2 extracellular domain (M2e) and internal proteins of the influenza virus. The identification and characterization of broadly neutralizing antibodies (bnAbs) targeting conserved regions of the viral HA protein, in particular, have provided important insight into novel vaccine designs and platforms. This review discusses universal vaccine approaches presently under development, with an emphasis on those targeting the highly conserved stalk of the HA protein, recent technological advancements used and the future prospects of a UIV in terms of its advantages, developmental obstacles and potential shortcomings.
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Affiliation(s)
- Caryn Myn Li Lim
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine & Health SciencesMonash University MalaysiaBandar SunwayMalaysia
| | - Thamil Vaani Komarasamy
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine & Health SciencesMonash University MalaysiaBandar SunwayMalaysia
| | - Nur Amelia Azreen Binti Adnan
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine & Health SciencesMonash University MalaysiaBandar SunwayMalaysia
| | - Ammu Kutty Radhakrishnan
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine & Health SciencesMonash University MalaysiaBandar SunwayMalaysia
| | - Vinod R. M. T. Balasubramaniam
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine & Health SciencesMonash University MalaysiaBandar SunwayMalaysia
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12
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Kondratiuk K, Hallmann E, Szymański K, Łuniewska K, Poznańska A, Brydak LB. Prevalence of circulating antibodies against hemagglutinin of influenza viruses in epidemic season 2021/2022 in Poland. Acta Biochim Pol 2024; 71:12289. [PMID: 38721309 PMCID: PMC11077356 DOI: 10.3389/abp.2024.12289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/23/2024] [Indexed: 05/15/2024]
Abstract
The aim of the study was to determine the level of anti-hemagglutinin antibodies in the serum of patients during the 2021/2022 epidemic season in Poland. A total of 700 sera samples were tested, divided according to the age of the patients into 7 age groups: 0-4 years of age, 5-9 years of age, 10-14 years of age, 15-25 years of age, 26-44 years of age, 45-64 years of age and ≥65 years of age, 100 samples were collected from each age group. Anti-hemagglutinin antibody levels was determined using the haemagglutination inhibition assay (OZHA). The results obtained confirm the presence of anti-hemagglutinin antibodies for the antigens A/Victoria/2570/2019 (H1N1) pdm09, A/Cambodia/e0826360/2020 (H3N2), B/Washington/02/2019 and B/Phuket/3073/2013 recommended by World Health Organization (WHO) for the 2021/2022 epidemic season. The analysis of the results shows differences in the levels of individual anti-hemagglutinin antibodies in the considered age groups. In view of very low percentage of the vaccinated population in Poland, which was 6.90% in the 2021/2022 epidemic season, the results obtained in the study would have to be interpreted as the immune system response in patients after a previous influenza virus infection.
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MESH Headings
- Humans
- Poland/epidemiology
- Adult
- Middle Aged
- Adolescent
- Influenza, Human/immunology
- Influenza, Human/epidemiology
- Influenza, Human/blood
- Influenza, Human/virology
- Child
- Aged
- Child, Preschool
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Young Adult
- Infant
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Male
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/immunology
- Female
- Infant, Newborn
- Hemagglutination Inhibition Tests
- Influenza B virus/immunology
- Seasons
- Epidemics
- Prevalence
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Affiliation(s)
- Katarzyna Kondratiuk
- Laboratory of Influenza Viruses and Respiratory Viruses, Department of Virology, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
| | - Ewelina Hallmann
- Laboratory of Influenza Viruses and Respiratory Viruses, Department of Virology, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
| | - Karol Szymański
- Laboratory of Influenza Viruses and Respiratory Viruses, Department of Virology, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
| | - Katarzyna Łuniewska
- Laboratory of Influenza Viruses and Respiratory Viruses, Department of Virology, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
| | - Anna Poznańska
- Department of Population Health Monitoring and Analysis, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
| | - Lidia B. Brydak
- Laboratory of Influenza Viruses and Respiratory Viruses, Department of Virology, National Institute of Public Health NIH—National Research Institute, Warsaw, Poland
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13
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Raju S, Adams LJ, Diamond MS. The many ways in which alphaviruses bind to cells. Trends Immunol 2024; 45:85-93. [PMID: 38135598 PMCID: PMC10997154 DOI: 10.1016/j.it.2023.11.006] [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: 10/22/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023]
Abstract
Only a subset of viruses can productively infect many different host species. Some arthropod-transmitted viruses, such as alphaviruses, can infect invertebrate and vertebrate species including insects, reptiles, birds, and mammals. This broad tropism may be explained by their ability to engage receptors that are conserved across vertebrate and invertebrate classes. Through several genome-wide loss-of-function screens, new alphavirus receptors have been identified, some of which bind to multiple related viruses in different antigenic complexes. Structural analysis has revealed that distinct sites on the alphavirus glycoprotein can mediate receptor binding, which opposes the idea that a single receptor-binding site mediates viral entry. Here, we discuss how different paradigms of receptor engagement on cells might explain the promiscuity of alphaviruses for multiple hosts.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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14
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Uno N, Ross TM. Multivalent next generation influenza virus vaccines protect against seasonal and pre-pandemic viruses. Sci Rep 2024; 14:1440. [PMID: 38228649 PMCID: PMC10792005 DOI: 10.1038/s41598-023-51024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
Each year, new influenza virus vaccine formulations are generated to keep up with continuously circulating and mutating viral variants. A next-generation influenza virus vaccine would provide long-lasting, broadly-reactive immune protection against current and future influenza virus strains for both seasonal and pre-pandemic viruses. Next generation immunogens were designed using computationally optimized broadly reactive antigen (COBRA) methodology to protect against a broad range of strains over numerous seasons. Novel HA and NA amino acid sequences were derived from multilayered consensus sequence alignment for multiple subtypes of influenza. This multivalent formulation was hypothesized to elicit broadly protective immune responses against both seasonal and pre-pandemic influenza viruses. Mice were vaccinated with multivalent mixtures of HA and NA (H1, H2, H3, H5, H7, N1, N2) proteins. Multivalent COBRA vaccinations elicited antibodies that recognized a broad panel of strains and vaccinated mice were protected against viruses representing multiple subtypes. This is a promising candidate for a universal influenza vaccine that elicits protective immune responses against seasonal and pre-pandemic strains over multiple seasons.
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Affiliation(s)
- Naoko Uno
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 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.
- Florida Research and Innovation Center, Cleveland Clinic Florida, 9801 SW Discovery Way, Port Saint Lucie, FL, 34986, USA.
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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15
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Wu NC, Ellebedy AH. Targeting neuraminidase: the next frontier for broadly protective influenza vaccines. Trends Immunol 2024; 45:11-19. [PMID: 38103991 PMCID: PMC10841738 DOI: 10.1016/j.it.2023.11.001] [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: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/19/2023]
Abstract
Current seasonal influenza vaccines, which mainly target hemagglutinin (HA), require annual updates due to the continuous antigenic drift of the influenza virus. Developing an influenza vaccine with increased breadth of protection will have significant public health benefits. The recent discovery of broadly protective antibodies to neuraminidase (NA) has provided important insights into developing a universal influenza vaccine, either by improving seasonal influenza vaccines or designing novel immunogens. However, further in-depth molecular characterizations of NA antibody responses are warranted to fully leverage broadly protective NA antibodies for influenza vaccine designs. Overall, we posit that focusing on NA for influenza vaccine development is synergistic with existing efforts targeting HA, and may represent a cost-effective approach to generating a broadly protective influenza vaccine.
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Affiliation(s)
- Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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16
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Hutchinson GB, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 2023; 42:113552. [PMID: 38096058 PMCID: PMC10801709 DOI: 10.1016/j.celrep.2023.113552] [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: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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17
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Simmons HC, Finney J, Kotaki R, Adachi Y, Moseman AP, Watanabe A, Song S, Robinson-McCarthy LR, Sage VL, Kuraoka M, Moseman EA, Kelsoe G, Takahashi Y, McCarthy KR. A broad antibody class engages the influenza virus hemagglutinin head at its stem interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571543. [PMID: 38168412 PMCID: PMC10760138 DOI: 10.1101/2023.12.13.571543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Influenza infection and vaccination impart strain-specific immunity that fails to protect against both seasonal antigenic variants and the next pandemic. However, antibodies directed to conserved sites can confer broad protection. We identify and characterize a class of human antibodies that engage a previously undescribed, conserved, epitope on the influenza hemagglutinin protein (HA). Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal infection in mice. Their breadth of binding extends across most influenza A serotypes and seasonal human variants. Antibodies to the head-stem interface epitope are present at low frequency in the memory B cell populations of multiple donors. The immunogenicity of the epitope warrants its consideration for inclusion in improved or "universal" influenza vaccines.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joel Finney
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Ryutaro Kotaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Shengli Song
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Lindsey R. Robinson-McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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18
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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19
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Wang X, Liu K, Guo Y, Pei Y, Chen X, Lu X, Gao R, Chen Y, Gu M, Hu J, Liu X, Hu S, Jiao XA, Liu X, Wang X. Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China. Emerg Microbes Infect 2023; 12:2249558. [PMID: 37585307 PMCID: PMC10467529 DOI: 10.1080/22221751.2023.2249558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/30/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
H9N2 avian influenza viruses (AIVs) pose an increasing threat to the poultry industry worldwide and have pandemic potential. Vaccination has been principal prevention strategy to control H9N2 in China since 1998, but vaccine effectiveness is persistently challenged by the emergence of the genetic and/or antigenic variants. Here, we analysed the genetic and antigenic characteristics of H9N2 viruses in China, including 70 HA sequences of H9N2 isolates from poultry, 7358 from online databases during 2010-2020, and 15 from the early reference strains. Bayesian analyses based on hemagglutinin (HA) gene revealed that a new designated clade16 emerged in April 2012, and was prevalent and co-circulated with clade 15 since 2013 in China. Clade 16 viruses exhibited decreased cross-reactivity with those from clade 15. Antigenic Cartography analyses showed represent strains were classified into three antigenic groups named as Group1, Group2 and Group3, and most of the strains in Group 3 (15/17, 88.2%) were from Clade 16 while most of the strains in Group2 (26/29, 89.7%) were from Clade 15. The mean distance between Group 3 and Group 2 was 4.079 (95%CI 3.605-4.554), revealing that major switches to antigenic properties were observed over the emergence of clade 16. Genetic analysis indicated that 11 coevolving amino acid substitutions primarily at antigenic sites were associated with the antigenic differences between clade 15 and clade 16. These data highlight complexities of the genetic evolution and provide a framework for the genetic basis and antigenic characterization of emerging clade 16 of H9N2 subtype avian influenza virus.
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Affiliation(s)
- Xiyue Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Kaituo Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yaqian Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yuru Pei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xia Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xiaolong Lu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Ruyi Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Yu Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Min Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Jiao Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Xiaowen Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Shunlin Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
| | - Xin-an Jiao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Xiaoquan Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou, People’s Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People’s Republic of China
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20
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Zhang J, Wang X, Chen Y, Ye H, Ding S, Zhang T, Liu Y, Li H, Huang L, Qi W, Liao M. Mutational antigenic landscape of prevailing H9N2 influenza virus hemagglutinin spectrum. Cell Rep 2023; 42:113409. [PMID: 37948179 DOI: 10.1016/j.celrep.2023.113409] [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: 07/18/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
H9N2 influenza viruses are globally endemic in birds, and a sharp increase in human infections with H9N2 occurred during 2021 to 2022. In this study, we assess the antigenic and pathogenic impact of 23 hemagglutinin (HA) amino acid mutations. Our study reveals that three specific mutations, labeled R164Q, N166D, and I220T, are responsible for the binding of antibodies with escape mutations. Variants containing R164Q and I220T mutations increase viral replication in avian and mammalian cells. Furthermore, T150A and I220T mutations are found to enhance viral replication in mice, indicating that these mutations may have the potential to adapt mammals. Structure analysis reveals that residues 164 and 220 bearing R164Q and I220T mutations increase interactions with the surrounding residues. Our findings enrich current knowledge about the risk assessment regarding which predominant HA immune-escape mutations of H9N2 viruses may pose the greatest threat to the emergence of pandemics in birds and humans.
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Affiliation(s)
- Jiahao Zhang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Xiaomin Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Yiqun Chen
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Hejia Ye
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Shiping Ding
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Tao Zhang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Yi Liu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Huanan Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Lihong Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
| | - Wenbao Qi
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China.
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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21
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Ogasawara S. Replication-competent influenza virus with a protein-responsive multiplication ability. N Biotechnol 2023; 77:100-110. [PMID: 37586547 DOI: 10.1016/j.nbt.2023.08.001] [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: 02/26/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Applications of influenza A viruses (IAV) for virotherapy and biotechnology have accelerated substantially with the development of reverse genetic technology and advances in the understanding of packaging signals. While the use of a replication-competent IAV is particularly promising, owing to its efficient transmission to organ depths with high infectivity, there is also a risk that its multiplication cannot be controlled in a cell-type-specific manner, causing an infectious disease. Therefore, here a simple and effective replication-competent IAV-based cell-targeting system has been developed. It was demonstrated that the activity of the ribonucleoprotein complex (RNP) of IAV could be regulated by the interaction between the endogenous protein and a nanobody fused to the subunit of RNA-dependent RNA polymerase (RdRp). To validate the feasibility of the method, it was demonstrated that RNP containing RdRp fused with Nb139, a nanobody against p53, is inactive in HEK293T cells expressing endogenous p53, but active in p53-defective Saos-2 cells. Finally, a replication-competent IAV was successfully generated that multiplies only in p53-defective tumor cells and an IAV vector was developed that can deliver a foreign gene in cell type-specific manner. The method is flexible because the nanobody can be easily altered to target a different cell type, offering a valuable platform for virotherapy and biotechnology.
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Affiliation(s)
- Shinzi Ogasawara
- Department of Biology, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
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22
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Al-Shuhaib MBS, Alam S, Khan SA, Al-Shuhaib JMB, Chen YK, M Alshabrmi F. Hemagglutinin 3 and 8 can be the most efficient influenza subtypes for human host invasion; a comparative in silico approach. J Biomol Struct Dyn 2023:1-19. [PMID: 37965722 DOI: 10.1080/07391102.2023.2280674] [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: 06/09/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
The severity of the influenza virus infection is largely determined by its ability to invade the human host receptor. This critical step is conducted by utilizing hemagglutinin (HA) due to its binding with sialic acid 2,6 (SA). Though 18 subtypes (H1-H18) of HA have been identified, the most efficient one for conducting the host entry has not yet been resolved. This study aims to assess the severity of infections for HA variants by conducting a comparative docking of H1-H18 with the human SA receptor. Eighteen viral 3D structures were retrieved, minimized, and optimized for docking with human SA. In all retrieved structures, five conserved amino acid residues were selected for docking with human SA. Special protein grids were prepared by locating these five residues in the 18 selected subtypes. Results showed that H3 and H8 exerted the highest standard precision and extra precision docking scores, and the highest binding affinities with the human SA, respectively. Phylogenetic analyses confirmed the actual positioning of the selected 3D structures and showed these docked structures belonged to their usual classes due to the extremely close distances found in each docked subtype compared with its corresponding non-docked structures. H8-SA showed slightly better RMSD and SASA values than H3-SA, while H3-SIA showed more favourable radius of gyration scores than H8-SIA in the majority of the simulation period. Due to the highest affinity of binding of H3 and H8 with the human receptor, special caution should be exercised regarding any possible outbreak mediated by these subtypes in human populations. However, it is important to acknowledge a limitation inherent to the computational approach; it may hold relative rather than absolute significance. Further research is needed to deepen our understanding of the intricate interplay between HA variants and the host receptor, taking into account the broader context of viral infection dynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sarfaraz Alam
- Tunneling Group Biotechnology Centre, Gliwice, Poland
| | | | | | - Yan-Kun Chen
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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23
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Periferakis A, Periferakis AT, Troumpata L, Periferakis K, Scheau AE, Savulescu-Fiedler I, Caruntu A, Badarau IA, Caruntu C, Scheau C. Kaempferol: A Review of Current Evidence of Its Antiviral Potential. Int J Mol Sci 2023; 24:16299. [PMID: 38003488 PMCID: PMC10671393 DOI: 10.3390/ijms242216299] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Kaempferol and its derivatives are flavonoids found in various plants, and a considerable number of these have been used in various medical applications worldwide. Kaempferol and its compounds have well-known antioxidant, anti-inflammatory and antimicrobial properties among other health benefits. However, the antiviral properties of kaempferol are notable, and there is a significant number of experimental studies on this topic. Kaempferol compounds were effective against DNA viruses such as hepatitis B virus, viruses of the alphaherpesvirinae family, African swine fever virus, and pseudorabies virus; they were also effective against RNA viruses, namely feline SARS coronavirus, dengue fever virus, Japanese encephalitis virus, influenza virus, enterovirus 71, poliovirus, respiratory syncytial virus, human immunodeficiency virus, calicivirus, and chikungunya virus. On the other hand, no effectiveness against murine norovirus and hepatitis A virus could be determined. The antiviral action mechanisms of kaempferol compounds are various, such as the inhibition of viral polymerases and of viral attachment and entry into host cells. Future research should be focused on further elucidating the antiviral properties of kaempferol compounds from different plants and assessing their potential use to complement the action of antiviral drugs.
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Affiliation(s)
- Argyrios Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Aristodemos-Theodoros Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Lamprini Troumpata
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Konstantinos Periferakis
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Pan-Hellenic Organization of Educational Programs (P.O.E.P), 17236 Athens, Greece
| | - Andreea-Elena Scheau
- Department of Radiology and Medical Imaging, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Ilinca Savulescu-Fiedler
- Department of Internal Medicine, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Internal Medicine and Cardiology, Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Ana Caruntu
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
| | - Ioana Anca Badarau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Constantin Caruntu
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, “Prof. N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest, Romania
| | - Cristian Scheau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Radiology and Medical Imaging, “Foisor” Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
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24
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Liu Q, Zeng H, Wu X, Yang X, Wang G. Global Prevalence and Hemagglutinin Evolution of H7N9 Avian Influenza Viruses from 2013 to 2022. Viruses 2023; 15:2214. [PMID: 38005891 PMCID: PMC10674656 DOI: 10.3390/v15112214] [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: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
H7N9 avian influenza viruses have caused severe harm to the global aquaculture industry and human health. For further understanding of the characteristics of prevalence and hemagglutinin evolution of H7N9 avian influenza viruses, we generated the global epidemic map of H7N9 viruses from 2013 to 2022, constructed a phylogenetic tree, predicted the glycosylation sites and compared the selection pressure of the hemagglutinin. The results showed that although H7N9 avian influenza appeared sporadically in other regions worldwide, China had concentrated outbreaks from 2013 to 2017. The hemagglutinin genes were classified into six distinct lineages: A, B, C, D, E and F. After 2019, H7N9 viruses from the lineages B, E and F persisted, with the lineage B being the dominant. The hemagglutinin of highly pathogenic viruses in the B lineage has an additional predicted glycosylation site, which may account for their persistent pandemic, and is under more positive selection pressure. The most recent ancestor of the H7N9 avian influenza viruses originated in September 1991. The continuous evolution of hemagglutinin has led to an increase in virus pathogenicity in both poultry and humans, and sustained human-to-human transmission. This study provides a theoretical basis for better prediction and control of H7N9 avian influenza.
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Affiliation(s)
- Qianshuo Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Haowen Zeng
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Xinghui Wu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Xuelian Yang
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Guiqin Wang
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
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25
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Blake ME, Kleinpeter AB, Jureka AS, Petit CM. Structural Investigations of Interactions between the Influenza a Virus NS1 and Host Cellular Proteins. Viruses 2023; 15:2063. [PMID: 37896840 PMCID: PMC10612106 DOI: 10.3390/v15102063] [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: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The Influenza A virus is a continuous threat to public health that causes yearly epidemics with the ever-present threat of the virus becoming the next pandemic. Due to increasing levels of resistance, several of our previously used antivirals have been rendered useless. There is a strong need for new antivirals that are less likely to be susceptible to mutations. One strategy to achieve this goal is structure-based drug development. By understanding the minute details of protein structure, we can develop antivirals that target the most conserved, crucial regions to yield the highest chances of long-lasting success. One promising IAV target is the virulence protein non-structural protein 1 (NS1). NS1 contributes to pathogenicity through interactions with numerous host proteins, and many of the resulting complexes have been shown to be crucial for virulence. In this review, we cover the NS1-host protein complexes that have been structurally characterized to date. By bringing these structures together in one place, we aim to highlight the strength of this field for drug discovery along with the gaps that remain to be filled.
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Affiliation(s)
| | | | | | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.E.B.)
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Periferakis AT, Periferakis A, Periferakis K, Caruntu A, Badarau IA, Savulescu-Fiedler I, Scheau C, Caruntu C. Antimicrobial Properties of Capsaicin: Available Data and Future Research Perspectives. Nutrients 2023; 15:4097. [PMID: 37836381 PMCID: PMC10574431 DOI: 10.3390/nu15194097] [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: 08/26/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Capsaicin is a phytochemical derived from plants of the genus Capsicum and subject of intensive phytochemical research due to its numerous physiological and therapeutical effects, including its important antimicrobial properties. Depending on the concentration and the strain of the bacterium, capsaicin can exert either bacteriostatic or even bactericidal effects against a wide range of both Gram-positive and Gram-negative bacteria, while in certain cases it can reduce their pathogenicity by a variety of mechanisms such as mitigating the release of toxins or inhibiting biofilm formation. Likewise, capsaicin has been shown to be effective against fungal pathogens, particularly Candida spp., where it once again interferes with biofilm formation. The parasites Toxoplasma gondi and Trypanosoma cruzi have been found to be susceptible to the action of this compound too while there are also viruses whose invasiveness is significantly dampened by it. Among the most encouraging findings are the prospects for future development, especially using new formulations and drug delivery mechanisms. Finally, the influence of capsaicin in somatostatin and substance P secretion and action, offers an interesting array of possibilities given that these physiologically secreted compounds modulate inflammation and immune response to a significant extent.
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Affiliation(s)
- Aristodemos-Theodoros Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Argyrios Periferakis
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
| | - Konstantinos Periferakis
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Pan-Hellenic Organization of Educational Programs (P.O.E.P), 17236 Athens, Greece
| | - Ana Caruntu
- Department of Oral and Maxillofacial Surgery, “Carol Davila” Central Military Emergency Hospital, 010825 Bucharest, Romania
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, “Titu Maiorescu” University, 031593 Bucharest, Romania
| | - Ioana Anca Badarau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Ilinca Savulescu-Fiedler
- Department of Internal Medicine and Cardiology, Coltea Clinical Hospital, 030167 Bucharest, Romania
- Department of Internal Medicine, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Cristian Scheau
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Radiology and Medical Imaging, “Foisor” Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
| | - Constantin Caruntu
- Department of Physiology, The “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, ‘Prof. N.C. Paulescu’ National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest, Romania
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28
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Wang Y, Lv H, Lei R, Yeung YH, Shen IR, Choi D, Teo QW, Tan TJ, Gopal AB, Chen X, Graham CS, Wu NC. An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557288. [PMID: 37745338 PMCID: PMC10515799 DOI: 10.1101/2023.09.11.557288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite decades of antibody research, it remains challenging to predict the specificity of an antibody solely based on its sequence. Two major obstacles are the lack of appropriate models and inaccessibility of datasets for model training. In this study, we curated a dataset of >5,000 influenza hemagglutinin (HA) antibodies by mining research publications and patents, which revealed many distinct sequence features between antibodies to HA head and stem domains. We then leveraged this dataset to develop a lightweight memory B cell language model (mBLM) for sequence-based antibody specificity prediction. Model explainability analysis showed that mBLM captured key sequence motifs of HA stem antibodies. Additionally, by applying mBLM to HA antibodies with unknown epitopes, we discovered and experimentally validated many HA stem antibodies. Overall, this study not only advances our molecular understanding of antibody response to influenza virus, but also provides an invaluable resource for applying deep learning to antibody research.
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Affiliation(s)
- Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuen-Hei Yeung
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ivana R. Shen
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Danbi Choi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Akshita B. Gopal
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire S. Graham
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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29
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Azulay A, Cohen-Lavi L, Friedman LM, McGargill MA, Hertz T. Mapping antibody footprints using binding profiles. CELL REPORTS METHODS 2023; 3:100566. [PMID: 37671022 PMCID: PMC10475849 DOI: 10.1016/j.crmeth.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The increasing use of monoclonal antibodies (mAbs) in biology and medicine necessitates efficient methods for characterizing their binding epitopes. Here, we developed a high-throughput antibody footprinting method based on binding profiles. We used an antigen microarray to profile 23 human anti-influenza hemagglutinin (HA) mAbs using HA proteins of 43 human influenza strains isolated between 1918 and 2018. We showed that the mAb's binding profile can be used to characterize its influenza subtype specificity, binding region, and binding site. We present mAb-Patch-an epitope prediction method that is based on a mAb's binding profile and the 3D structure of its antigen. mAb-Patch was evaluated using four mAbs with known solved mAb-HA structures. mAb-Patch identifies over 67% of the true epitope when considering only 50-60 positions along the antigen. Our work provides proof of concept for utilizing antibody binding profiles to screen large panels of mAbs and to down-select antibodies for further functional studies.
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Affiliation(s)
- Asaf Azulay
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Liel Cohen-Lavi
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tomer Hertz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, USA
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30
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Bugaytsova JA, Moonens K, Piddubnyi A, Schmidt A, Edlund JO, Lisiutin G, Brännström K, Chernov YA, Thorel K, Tkachenko I, Sharova O, Vikhrova I, Butsyk A, Shubin P, Chyzhma R, Johansson DX, Marcotte H, Sjöström R, Shevtsova A, Bylund G, Rakhimova L, Lundquist A, Berhilevych O, Kasianchuk V, Loboda A, Ivanytsia V, Hultenby K, Persson MAA, Gomes J, Matos R, Gartner F, Reis CA, Whitmire JM, Merrell DS, Pan-Hammarström Q, Landström M, Oscarson S, D’Elios MM, Agreus L, Ronkainen J, Aro P, Engstrand L, Graham DY, Kachkovska V, Mukhopadhyay A, Chaudhuri S, Karmakar BC, Paul S, Kravets O, Camorlinga M, Torres J, Berg DE, Moskalenko R, Haas R, Remaut H, Hammarström L, Borén T. Helicobacter pylori attachment-blocking antibodies protect against duodenal ulcer disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542096. [PMID: 37292721 PMCID: PMC10245814 DOI: 10.1101/2023.05.24.542096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The majority of the world population carry the gastric pathogen Helicobacter pylori. Fortunately, most individuals experience only low-grade or no symptoms, but in many cases the chronic inflammatory infection develops into severe gastric disease, including duodenal ulcer disease and gastric cancer. Here we report on a protective mechanism where H. pylori attachment and accompanying chronic mucosal inflammation can be reduced by antibodies that are present in a vast majority of H. pylori carriers. These antibodies block binding of the H. pylori attachment protein BabA by mimicking BabA's binding to the ABO blood group glycans in the gastric mucosa. However, many individuals demonstrate low titers of BabA blocking antibodies, which is associated with an increased risk for duodenal ulceration, suggesting a role for these antibodies in preventing gastric disease.
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Affiliation(s)
- Jeanna A. Bugaytsova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
| | - Kristof Moonens
- Structural and Molecular Microbiology, VIB Department of Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Present address: Ablynx, a Sanofi Company, Technologiepark 21, 9052 Zwijnaarde, Belgium
| | - Artem Piddubnyi
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Alexej Schmidt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
- Present address: Department of Medical Biosciences, Umeå University, SE90185 Umeå, Sweden
| | - Johan Olofsson Edlund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- The Biochemical Imaging Center Umeå (BICU), Umeå University, SE90187 Umeå, Sweden
| | - Gennadii Lisiutin
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Microbiology, Virology and Biotechnology, Odesa Mechnikov National University, 65082 Odesa, Ukraine
| | - Kristoffer Brännström
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- The Biochemical Imaging Center Umeå (BICU), Umeå University, SE90187 Umeå, Sweden
- Present address: Pfizer Worldwide R&D, BioMedicine Design, 10 555 Science Center Drive, San Diego CA, 92121 USA
| | - Yevgen A. Chernov
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Kaisa Thorel
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Iryna Tkachenko
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Oleksandra Sharova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Iryna Vikhrova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Anna Butsyk
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Pavlo Shubin
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Ruslana Chyzhma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Daniel X. Johansson
- Department of Clinical Neuroscience, Karolinska Institutet at Center for Molecular Medicine, Karolinska University Hospital, Solna, SE17176 Stockholm, Sweden
| | - Harold Marcotte
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Rolf Sjöström
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Anna Shevtsova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Göran Bylund
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
| | - Lena Rakhimova
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- Present address: Department of Odontology, Umeå University, SE90187 Umeå, Sweden
| | - Anders Lundquist
- Department of Statistics, USBE, Umeå University, SE90187 Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, SE90187 Umeå, Sweden
| | - Oleksandra Berhilevych
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Victoria Kasianchuk
- Department of Public Health, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Andrii Loboda
- Department of Pediatrics, Medical Institute, Sumy State University, 40018 Sumy, Ukraine
| | - Volodymyr Ivanytsia
- Department of Microbiology, Virology and Biotechnology, Odesa Mechnikov National University, 65082 Odesa, Ukraine
| | - Kjell Hultenby
- Departments of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet at Karolinska University Hospital, SE14186 Huddinge, Sweden
| | - Mats A. A. Persson
- Department of Clinical Neuroscience, Karolinska Institutet at Center for Molecular Medicine, Karolinska University Hospital, Solna, SE17176 Stockholm, Sweden
| | - Joana Gomes
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Rita Matos
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Fátima Gartner
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Celso A. Reis
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | | | - D. Scott Merrell
- Department of Microbiology and Immunology, USUHS, Bethesda, MD 20814, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Maréne Landström
- Present address: Department of Medical Biosciences, Umeå University, SE90185 Umeå, Sweden
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mario M. D’Elios
- Department of Experimental and Clinical Medicine, Largo Brambilla 3, 50134 Firenze, Italy
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Jukka Ronkainen
- University of Oulu, Center for Life Course Health Research and Primary Health Care Center, Tornio Finland
| | - Pertti Aro
- University of Oulu, Center for Life Course Health Research and Primary Health Care Center, Tornio Finland
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE17177 Stockholm, Sweden
- Present address: Science for Life Laboratory, SE17165, Solna, Sweden
| | - David Y. Graham
- Department of Medicine, Molecular Virology and Microbiology, Baylor College of Medicine, Michael E. DeBakey VAMC, 2002 Holcombe Blvd. Houston, TX, 77030 USA
| | - Vladyslava Kachkovska
- Department of Internal Medicine, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Asish Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Sujit Chaudhuri
- Department of Gastroenterology, AMRI Hospital, Salt Lake City. Kolkata, West Bengal 700098, India
| | - Bipul Chandra Karmakar
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Sangita Paul
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases P 33, CIT Road, Scheme XM, Kolkata 700010, India
| | - Oleksandr Kravets
- Department of Surgery, Traumatology, Orthopedics and Physiology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Margarita Camorlinga
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Douglas E. Berg
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Roman Moskalenko
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Department of Pathology, Medical Institute, Sumy State University, 40007 Sumy, Ukraine
| | - Rainer Haas
- German Center for Infection Research (DZIF), Munich Site, 80336 Munich, Germany
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer-Institute, Faculty of Medicine, LMU Munich, Germany
| | - Han Remaut
- Structural and Molecular Microbiology, VIB Department of Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183, Huddinge, Sweden
| | - Thomas Borén
- Department of Medical Biochemistry and Biophysics, Umeå University, SE90187 Umeå, Sweden
- SUMEYA, The Ukrainian-Swedish Research Center, Sumy State University, 40022 Sumy, Ukraine
- Lead contact
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31
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Yang L, Van Beek M, Wang Z, Muecksch F, Canis M, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Chakraborty AK. Antigen presentation dynamics shape the antibody response to variants like SARS-CoV-2 Omicron after multiple vaccinations with the original strain. Cell Rep 2023; 42:112256. [PMID: 36952347 PMCID: PMC9986127 DOI: 10.1016/j.celrep.2023.112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/07/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 is not effectively neutralized by most antibodies elicited by two doses of mRNA vaccines, but a third dose increases anti-Omicron neutralizing antibodies. We reveal mechanisms underlying this observation by combining computational modeling with data from vaccinated humans. After the first dose, limited antigen availability in germinal centers (GCs) results in a response dominated by B cells that target immunodominant epitopes that are mutated in an Omicron-like variant. After the second dose, these memory cells expand and differentiate into plasma cells that secrete antibodies that are thus ineffective for such variants. However, these pre-existing antigen-specific antibodies transport antigen efficiently to secondary GCs. They also partially mask immunodominant epitopes. Enhanced antigen availability and epitope masking in secondary GCs together result in generation of memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
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Affiliation(s)
- Leerang Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew Van Beek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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32
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Sun JY, Guo CY, Wang GR, Yan LT, Feng Q, Li Y, Huo XP, Xie X, Hu J, Sun LJ. Identification of Heterophilic Epitopes of H1N1 Influenza Virus Hemagglutinin. Curr Microbiol 2023; 80:188. [PMID: 37074450 DOI: 10.1007/s00284-023-03294-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/30/2023] [Indexed: 04/20/2023]
Abstract
Our previous studies found that the H1-50 monoclonal antibody (mAb) of influenza A virus hemagglutinin (HA) cross-reacted with pancreatic tissue and islet β-cells, and further studies showed that H1-50 mAb binds to prohibitin (PHB) protein of islet β-cells. These suggest that there are heterophilic epitopes between influenza virus HA and pancreatic tissue, which may be involved in the pathogenesis of type 1 diabetes. To further investigate these heterophilic epitopes, we screened binding epitopes of H1-50 mAb using a phage 12-peptide library. DNA sequencing and comparative analysis were performed on specific positive phage clones, and the sequence of 12-peptide binding to H1-50 mAb was obtained. The binding epitopes of H1-50 mAb in influenza virus HA were determined by sequence analysis and experimental verification, and their distribution within the three-dimensional structure was assessed by PyMOL. The results showed that H1-50 mAb specifically binds to polypeptides (306-SLPFQNIHPITIGK-319) of influenza A virus HA, located in the stem of the HA protein. However, there is no specific binding sequence between H1-50 mAb and the PHB protein of islet β-cells in the primary structure, and we speculate that the binding of H1-50 mAb to islet β-cells may depend on the spatial conformation. The identification of the heterophilic epitopes of H1N1 influenza virus hemagglutinin provides a new perspective on type 1 diabetes that may be caused by influenza virus infection, which may contribute to the prevention and control of influenza.
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Affiliation(s)
- Jing-Ying Sun
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Chun-Yan Guo
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Guo-Rong Wang
- General Surgery Department of Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
| | - Li-Ting Yan
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Qing Feng
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Yan Li
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Xue-Ping Huo
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China
| | - Xin Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Jun Hu
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China.
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China.
| | - Li-Jun Sun
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China.
- Shaanxi Province Research Center of Cell Immunological Engineering and Technology, Xi'an, 710068, Shaanxi, China.
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Einav T, Khoo Y, Singer A. Quantitatively Visualizing Bipartite Datasets. PHYSICAL REVIEW. X 2023; 13:021002. [PMID: 38831998 PMCID: PMC11146982 DOI: 10.1103/physrevx.13.021002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
As experiments continue to increase in size and scope, a fundamental challenge of subsequent analyses is to recast the wealth of information into an intuitive and readily interpretable form. Often, each measurement conveys only the relationship between a pair of entries, and it is difficult to integrate these local interactions across a dataset to form a cohesive global picture. The classic localization problem tackles this question, transforming local measurements into a global map that reveals the underlying structure of a system. Here, we examine the more challenging bipartite localization problem, where pairwise distances are available only for bipartite data comprising two classes of entries (such as antibody-virus interactions, drug-cell potency, or user-rating profiles). We modify previous algorithms to solve bipartite localization and examine how each method behaves in the presence of noise, outliers, and partially observed data. As a proof of concept, we apply these algorithms to antibody-virus neutralization measurements to create a basis set of antibody behaviors, formalize how potently inhibiting some viruses necessitates weakly inhibiting other viruses, and quantify how often combinations of antibodies exhibit degenerate behavior.
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Affiliation(s)
- Tal Einav
- Divisions of Computational Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Yuehaw Khoo
- Department of Statistics, University of Chicago, Chicago, Illinois 60637, USA
| | - Amit Singer
- Department of Mathematics and PACM, Princeton University, Princeton, New Jersey 08540, USA
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Myers ML, Gallagher JR, Kim AJ, Payne WH, Maldonado-Puga S, Assimakopoulos H, Bock KW, Torian U, Moore IN, Harris AK. Commercial influenza vaccines vary in HA-complex structure and in induction of cross-reactive HA antibodies. Nat Commun 2023; 14:1763. [PMID: 36997521 PMCID: PMC10060936 DOI: 10.1038/s41467-023-37162-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 03/03/2023] [Indexed: 04/04/2023] Open
Abstract
Influenza virus infects millions of people annually and can cause global pandemics. Hemagglutinin (HA) is the primary component of commercial influenza vaccines (CIV), and antibody titer to HA is a primary correlate of protection. Continual antigenic variation of HA requires that CIVs are reformulated yearly. Structural organization of HA complexes have not previously been correlated with induction of broadly reactive antibodies, yet CIV formulations vary in how HA is organized. Using electron microscopy to study four current CIVs, we find structures including: individual HAs, starfish structures with up to 12 HA molecules, and novel spiked-nanodisc structures that display over 50 HA molecules along the complex's perimeter. CIV containing these spiked nanodiscs elicit the highest levels of heterosubtypic cross-reactive antibodies in female mice. Here, we report that HA structural organization can be an important CIV parameter and can be associated with the induction of cross-reactive antibodies to conserved HA epitopes.
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Affiliation(s)
- Mallory L Myers
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - John R Gallagher
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - Alexander J Kim
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - Walker H Payne
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - Samantha Maldonado-Puga
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - Haralabos Assimakopoulos
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
| | - Kevin W Bock
- Infectious Disease Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, Room BN25, Bethesda, MD, 20892, USA
| | - Udana Torian
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA
- Laboratory of Human Carcinogenesis, National Cancer Institute, 37 Convent Drive, Room 306C, Bethesda, MD, 20892, USA
| | - Ian N Moore
- Infectious Disease Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, Room BN25, Bethesda, MD, 20892, USA
- Yerkes National Primate Research Center, Emory University, 954 Gatewood Rd NE, Atlanta, GA, 30329 37, USA
| | - Audray K Harris
- Structural Informatics Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD, 20892, USA.
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Einav T, Creanga A, Andrews SF, McDermott AB, Kanekiyo M. Harnessing low dimensionality to visualize the antibody-virus landscape for influenza. NATURE COMPUTATIONAL SCIENCE 2023; 3:164-173. [PMID: 38177625 PMCID: PMC10766546 DOI: 10.1038/s43588-022-00375-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2024]
Abstract
Antibodies constitute a key line of defense against the diverse pathogens we encounter in our lives. Although the interactions between a single antibody and a single virus are routinely characterized in exquisite detail, the inherent tradeoffs between attributes such as potency and breadth remain unclear. Moreover, there is a wide gap between the discrete interactions of single antibodies and the collective behavior of antibody mixtures. Here we develop a form of antigenic cartography called a 'neutralization landscape' that visualizes and quantifies antibody-virus interactions for antibodies targeting the influenza hemagglutinin stem. This landscape transforms the potency-breadth tradeoff into a readily solvable geometry problem. With it, we decompose the collective neutralization from multiple antibodies to characterize the composition and functional properties of the stem antibodies within. Looking forward, this framework can leverage the serological assays routinely performed for influenza surveillance to analyze how an individual's antibody repertoire evolves after vaccination or infection.
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Affiliation(s)
- Tal Einav
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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36
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Agrawal A, Chanana P, Yadav V, Bhutani V, Subbarao N, Srivastava A. Vitamin derivatives as potential drugs for Influenza Hemagglutinin. J Biomol Struct Dyn 2023; 41:11781-11795. [PMID: 36629034 DOI: 10.1080/07391102.2022.2163698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The objective of the study was to identify potential inhibitors of Influenza surface Hemagglutinin (HA), which plays key role in the entry and replication of Influenza virus into the host cell. As ligands, seven vitamins and their derivatives were selected after initial screening based on their metabolizable capacity with no reported side effects, for in silico studies. Docking, and Post docking analysis (X Score and Ligplot+) were performed against nine Influenza HA targets for the vitamins and its derivatives. 'Vitamin Derivatives' with top docking score were further analysed by MD Simulations and free energy was calculated using MMGBSA module. FMNNa and FMNCa displayed high binding free energy with Influenza HA, thereby exhibiting potential as HA inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ananyaa Agrawal
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Pratibha Chanana
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Vikas Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vilakshan Bhutani
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aradhana Srivastava
- University School of Chemical Technology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
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37
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Jiao C, Wang B, Chen P, Jiang Y, Liu J. Analysis of the conserved protective epitopes of hemagglutinin on influenza A viruses. Front Immunol 2023; 14:1086297. [PMID: 36875062 PMCID: PMC9981632 DOI: 10.3389/fimmu.2023.1086297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The conserved protective epitopes of hemagglutinin (HA) are essential to the design of a universal influenza vaccine and new targeted therapeutic agents. Over the last 15 years, numerous broadly neutralizing antibodies (bnAbs) targeting the HA of influenza A viruses have been isolated from B lymphocytes of human donors and mouse models, and their binding epitopes identified. This work has brought new perspectives for identifying conserved protective epitopes of HA. In this review, we succinctly analyzed and summarized the antigenic epitopes and functions of more than 70 kinds of bnAb. The highly conserved protective epitopes are concentrated on five regions of HA: the hydrophobic groove, the receptor-binding site, the occluded epitope region of the HA monomers interface, the fusion peptide region, and the vestigial esterase subdomain. Our analysis clarifies the distribution of the conserved protective epitope regions on HA and provides distinct targets for the design of novel vaccines and therapeutics to combat influenza A virus infection.
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Affiliation(s)
- Chenchen Jiao
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bo Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Pucheng Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongping Jiang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinxiong Liu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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38
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Li J, Zhang Y, Zhang X, Liu L. Influenza and Universal Vaccine Research in China. Viruses 2022; 15:116. [PMID: 36680158 PMCID: PMC9861666 DOI: 10.3390/v15010116] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Influenza viruses usually cause seasonal influenza epidemics and influenza pandemics, resulting in acute respiratory illness and, in severe cases, multiple organ complications and even death, posing a serious global and human health burden. Compared with other countries, China has a large population base and a large number of influenza cases and deaths. Currently, influenza vaccination remains the most cost-effective and efficient way to prevent and control influenza, which can significantly reduce the risk of influenza virus infection and serious complications. The antigenicity of the influenza vaccine exhibits good protective efficacy when matched to the seasonal epidemic strain. However, when influenza viruses undergo rapid and sustained antigenic drift resulting in a mismatch between the vaccine strain and the epidemic strain, the protective effect is greatly reduced. As a result, the flu vaccine must be reformulated and readministered annually, causing a significant drain on human and financial resources. Therefore, the development of a universal influenza vaccine is necessary for the complete fight against the influenza virus. By statistically analyzing cases related to influenza virus infection and death in China in recent years, this paper describes the existing marketed vaccines, vaccine distribution and vaccination in China and summarizes the candidate immunogens designed based on the structure of influenza virus, hoping to provide ideas for the design and development of new influenza vaccines in the future.
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Affiliation(s)
| | | | | | - Longding Liu
- Key Laboratory of Systemic Innovative Research on Virus Vaccine, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
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39
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS CENTRAL SCIENCE 2022; 8:1646-1663. [PMID: 36589893 PMCID: PMC9801513 DOI: 10.1021/acscentsci.2c00981] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 05/28/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from convalescent human donor, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Julia Lederhofer
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Yaroslav Tsybovsky
- Electron
Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
Sponsored by the National Cancer Institute, Frederick, Maryland21702, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California92037, United States
| | - Masaru Kanekiyo
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
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40
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Moin SM, Boyington JC, Boyoglu-Barnum S, Gillespie RA, Cerutti G, Cheung CSF, Cagigi A, Gallagher JR, Brand J, Prabhakaran M, Tsybovsky Y, Stephens T, Fisher BE, Creanga A, Ataca S, Rawi R, Corbett KS, Crank MC, Karlsson Hedestam GB, Gorman J, McDermott AB, Harris AK, Zhou T, Kwong PD, Shapiro L, Mascola JR, Graham BS, Kanekiyo M. Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses. Immunity 2022; 55:2405-2418.e7. [PMID: 36356572 PMCID: PMC9772109 DOI: 10.1016/j.immuni.2022.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/19/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]
Abstract
Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA stem harbors a supersite that is targeted by broadly neutralizing antibodies (bnAbs), representing a prime target for universal vaccines. Here, we showed that the co-immunization of two HA stem immunogens derived from group 1 and 2 influenza A viruses elicits cross-group protective immunity and neutralizing antibody responses in mice, ferrets, and nonhuman primates (NHPs). Immunized mice were protected from multiple group 1 and 2 viruses, and all animal models showed broad serum-neutralizing activity. A bnAb isolated from an immunized NHP broadly neutralized and protected against diverse viruses, including H5N1 and H7N9. Genetic and structural analyses revealed strong homology between macaque and human bnAbs, illustrating common biophysical constraints for acquiring cross-group specificity. Vaccine elicitation of stem-directed cross-group-protective immunity represents a step toward the development of broadly protective influenza vaccines.
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Affiliation(s)
- Syed M Moin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Gallagher
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Brand
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Madhu Prabhakaran
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Brian E Fisher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sila Ataca
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Michelle C Crank
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Audray K Harris
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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41
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Key amino acid position 272 in neuraminidase determines the replication and virulence of H5N6 avian influenza virus in mammals. iScience 2022; 25:105693. [PMID: 36567717 PMCID: PMC9772848 DOI: 10.1016/j.isci.2022.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/14/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Avian influenza H5N6 virus not only wreaks economic havoc in the poultry industry but also threatens human health. Strikingly, as of August 2022, 78 human beings were infected with H5N6, and the spike in the number of human infections with H5N6 occurred during 2021. In the life cycle of influenza virus, neuraminidase (NA) has numerous functions, especially viral budding and replication. Here, we found that NA-D272N mutation became predominant in H5N6 viruses since 2015 and significantly increased the viral replication and virulence in mice. D272N mutation in NA protein increased viral release from erythrocytes, thermostability, early transcription, and accumulation of NA protein. Particularly, the dominant 272 residue switch from N to S has occurred in wild bird-origin H5N6 viruses since late 2016 and N272S mutation induced significantly higher levels of inflammatory cytokines in infected human cells. Therefore, comprehensive surveillance of bird populations needs to be enhanced to monitor mammalian adaptive mutations of H5N6 viruses.
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42
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Kelvin AA, Falzarano D. The influenza universe in an mRNA vaccine. Science 2022; 378:827-828. [DOI: 10.1126/science.adf0900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An mRNA–lipid nanoparticle vaccine protects animals from 20 influenza lineages
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Affiliation(s)
- Alyson A. Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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43
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Zhang M, An Y, Wu X, Cai M, Zhang X, Yang C, Tong J, Cui Z, Li X, Huang W, Zhao C, Wang Y. Retrospective immunogenicity analysis of seasonal flu H3N2 vaccines recommended in the past ten years using immunized animal sera. EBioMedicine 2022; 86:104350. [PMID: 36403423 PMCID: PMC9678686 DOI: 10.1016/j.ebiom.2022.104350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/06/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Influenza A (H3N2) virus (A/H3N2) has complex antigenic evolution, resulting in frequent vaccine strain updates. We aimed to evaluate the protective effect of the vaccine strains on the circulating strains from past ten years and provide a basis for finding a broader and more efficient A/H3N2 vaccine strain. METHODS Eighty-four representative circulating A/H3N2 strains were selected from 65,791 deposited sequences in 2011-2020 and pseudotyped viruses were constructed with the VSV vector. We immunized guinea pigs with DNA vaccine containing the A/H3N2 components of the vaccine strains from 2011 to 2021 and tested neutralizing antibody against the pseudotyped viruses. We used a hierarchical clustering method to classify the eighty-four representative strains into different antigenic clusters. We also immunized animals with monovalent vaccine stock of the vaccine strains for the 2020-2021 and 2021-2022 seasons and tested neutralizing antibody against the pseudotyped viruses. FINDINGS The vaccine strains PE/09, VI/11 and TE/12 induced higher levels of neutralizing antibody against representative strains circulating in recommended year and the year immediately prior whereas vaccine strains HK/14, HK/19 and CA/20 induced poor neutralization against all representative strains. The representative strains were divided into five antigenic clusters (AgV), which were not identical to gene clades. The AgV5 strains were most difficult to be protected among the five clusters. Compared with single-dose immunization, three doses of monovalent vaccine stock (HK/19 or CA/20) could induce stronger and broader neutralizing antibodies against strains in each of the antigenic clusters. INTERPRETATION The protective effect of vaccine strains indicated that the accurate selection of A/H3N2 vaccine strains must remain a top priority. By increasing the frequency of immunization, stronger and broader neutralizing antibodies against strains in all antigenic clusters were induced, which provides direction for a new immunization strategy. FUNDING This work was supported by a grant from National Key R&D Program of China (No. 2021YFC2301700).
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Affiliation(s)
- Mengyi Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Yimeng An
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China,Shanghai Institute of Biological Products Co. LTD, 350 Anshun Road, Changning District, Shanghai, 200051, China
| | - Xi Wu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Meina Cai
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China,Graduate School of Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Xinyu Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Chaoying Yang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Jincheng Tong
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Xueli Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China,Corresponding author.
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China,Corresponding author.
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China,Graduate School of Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China,Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing,Corresponding author. Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), No. 31 Huatuo Street, Daxing District, Beijing, 102629, China.
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44
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Aartse A, Mortier D, Mooij P, Hofman S, van Haaren MM, Corcoran M, Karlsson Hedestam GB, Eggink D, Claireaux M, Bogers WMJM, van Gils MJ, Koopman G. Primary antibody response after influenza virus infection is first dominated by low-mutated HA-stem antibodies followed by higher-mutated HA-head antibodies. Front Immunol 2022; 13:1026951. [PMID: 36405682 PMCID: PMC9670313 DOI: 10.3389/fimmu.2022.1026951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 09/12/2023] Open
Abstract
Several studies have shown that the first encounter with influenza virus shapes the immune response to future infections or vaccinations. However, a detailed analysis of the primary antibody response is lacking as this is difficult to study in humans. It is therefore not known what the frequency and dynamics of the strain-specific hemagglutinin (HA) head- and stem-directed antibody responses are directly after primary influenza virus infection. Here, sera of twelve H1N1pdm2009 influenza virus-infected cynomolgus macaques were evaluated for HA-head and HA-stem domain antibody responses. We observed an early induction of HA-stem antibody responses, which was already decreased by day 56. In contrast, responses against the HA-head domain were low early after infection and increased at later timepoint. The HA-specific B cell repertoires in each animal showed diverse VH-gene usage with preferred VH-gene and JH-gene family usage for HA-head or HA-stem B cells but a highly diverse allelic variation within the VH-usage. HA-head B cells had shorter CDRH3s and higher VH-gene somatic hyper mutation levels relative to HA-stem B cells. In conclusion, our data suggest that HA-stem antibodies are the first to react to the infection while HA-head antibodies show a delayed response, but a greater propensity to enter the germinal center and undergo affinity maturation.
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Affiliation(s)
- Aafke Aartse
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
| | - Daniella Mortier
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Sam Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marlies M. van Haaren
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet (KI), Stockholm, Sweden
| | | | - Dirk Eggink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Mathieu Claireaux
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | | | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
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45
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Shivatare SS, Shivatare VS, Wong CH. Glycoconjugates: Synthesis, Functional Studies, and Therapeutic Developments. Chem Rev 2022; 122:15603-15671. [PMID: 36174107 PMCID: PMC9674437 DOI: 10.1021/acs.chemrev.1c01032] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycoconjugates are major constituents of mammalian cells that are formed via covalent conjugation of carbohydrates to other biomolecules like proteins and lipids and often expressed on the cell surfaces. Among the three major classes of glycoconjugates, proteoglycans and glycoproteins contain glycans linked to the protein backbone via amino acid residues such as Asn for N-linked glycans and Ser/Thr for O-linked glycans. In glycolipids, glycans are linked to a lipid component such as glycerol, polyisoprenyl pyrophosphate, fatty acid ester, or sphingolipid. Recently, glycoconjugates have become better structurally defined and biosynthetically understood, especially those associated with human diseases, and are accessible to new drug, diagnostic, and therapeutic developments. This review describes the status and new advances in the biological study and therapeutic applications of natural and synthetic glycoconjugates, including proteoglycans, glycoproteins, and glycolipids. The scope, limitations, and novel methodologies in the synthesis and clinical development of glycoconjugates including vaccines, glyco-remodeled antibodies, glycan-based adjuvants, glycan-specific receptor-mediated drug delivery platforms, etc., and their future prospectus are discussed.
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Affiliation(s)
- Sachin S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vidya S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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46
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Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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47
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Zhao C, Pu J. Influence of Host Sialic Acid Receptors Structure on the Host Specificity of Influenza Viruses. Viruses 2022; 14:v14102141. [PMID: 36298694 PMCID: PMC9608321 DOI: 10.3390/v14102141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Influenza viruses need to use sialic acid receptors to invade host cells, and the α-2,3 and α-2,6 sialic acids glycosidic bonds linking the terminal sialic acids are generally considered to be the most important factors influencing the cross-species transmission of the influenza viruses. The development of methods to detect the binding of influenza virus HA proteins to sialic acid receptors, as well as the development of glycobiological techniques, has led to a richer understanding of the structure of the sialylated glycan in influenza virus hosts. It was found that, in addition to the sialic acid glycosidic bond, sialic acid variants, length of the sialylated glycan, Gal-GlcNAc-linked glycosidic bond within the sialylated glycan, and sulfation/fucosylation of the GlcNAc within the sialylated glycan all affect the binding properties of influenza viruses to the sialic acid receptors, thus indirectly affecting the host specificity of influenza viruses. This paper will review the sialic acid variants, internal structural differences of sialylated glycan molecules that affect the host specificity of influenza viruses, and distribution characteristics of sialic acid receptors in influenza virus hosts, in order to provide a more reliable theoretical basis for the in-depth investigation of cross-species transmission of influenza viruses and the development of new antiviral drugs.
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48
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Pascha M, Thijssen V, Egido JE, Linthorst MW, van Lanen JH, van Dongen DAA, Hopstaken AJP, van Kuppeveld FJM, Snijder J, de Haan CAM, Jongkees SAK. Inhibition of H1 and H5 Influenza A Virus Entry by Diverse Macrocyclic Peptides Targeting the Hemagglutinin Stem Region. ACS Chem Biol 2022; 17:2425-2436. [PMID: 35926224 PMCID: PMC9486808 DOI: 10.1021/acschembio.2c00040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Influenza A viruses pose a serious pandemic risk, while generation of efficient vaccines against seasonal variants remains challenging. There is thus a pressing need for new treatment options. We report here a set of macrocyclic peptides that inhibit influenza A virus infection at low nanomolar concentrations by binding to hemagglutinin, selected using ultrahigh-throughput screening of a diverse peptide library. The peptides are active against both H1 and H5 variants, with no detectable cytotoxicity. Despite the high sequence diversity across hits, all tested peptides were found to bind to the same region in the hemagglutinin stem by HDX-MS epitope mapping. A mutation in this region identified in an escape variant confirmed the binding site. This stands in contrast to the immunodominance of the head region for antibody binding and suggests that macrocyclic peptides from in vitro display may be well suited for finding new druggable sites not revealed by antibodies. Functional analysis indicates that these peptides stabilize the prefusion conformation of the protein and thereby prevent virus-cell fusion. High-throughput screening of macrocyclic peptides is thus shown here to be a powerful method for the discovery of novel broadly acting viral fusion inhibitors with therapeutic potential.
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Affiliation(s)
- Mirte
N. Pascha
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - Vito Thijssen
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Julia E. Egido
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands,Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Mirte W. Linthorst
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jipke H. van Lanen
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - David A. A. van Dongen
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Antonius J. P. Hopstaken
- Department
of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for
Molecular and Life Sciences, VU Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cornelis A. M. de Haan
- Section
Virology, Division Infectious Diseases and Immunology, Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584
CL Utrecht, The Netherlands,
| | - Seino A. K. Jongkees
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands,Department
of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for
Molecular and Life Sciences, VU Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands,
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49
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.02.502576. [PMID: 35982676 PMCID: PMC9387122 DOI: 10.1101/2022.08.02.502576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States,Corresponding author.
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50
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Abstract
Current influenza vaccines, while being the best method of managing viral outbreaks, have several major drawbacks that prevent them from being wholly-effective. They need to be updated regularly and require extensive resources to develop. When considering alternatives, the recent deployment of mRNA vaccines for SARS-CoV-2 has created a unique opportunity to evaluate a new platform for seasonal and pandemic influenza vaccines. The mRNA format has previously been examined for application to influenza and promising data suggest it may be a viable format for next-generation influenza vaccines. Here, we discuss the prospect of shifting global influenza vaccination efforts to an mRNA-based system that might allow better control over the product and immune responses and could aid in the development of a universal vaccine.
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Affiliation(s)
- Jessica R Shartouny
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), USA
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