Pseudotyped Viruses

This book intends to report the new progress of pseudotyped viruses, including the construction of pseudotyped viruses with different strategies or vectors for most important viruses. Especially for emerging viruses, optimization of the condition and parameters for assay development based on the pseudotyped viruses and widely application as surrogate of authentic virus to study the biological functions of virus, detection of neutralizing antibody, screening viral entry inhibiters, and others. It includes most pseudotyped viruses that have the protein of the target virus on the surface of the parent virus with incomplete genome. The book is likely to be of interest to all researchers in the field of virology, vaccine, and anti-viral drug development and evaluation. Preface Contents Editor and Contributors Chapter 1: Pseudotyped Viruses 1.1 Introduction 1.2 The Vectors for Enveloped Viruses 1.2.1 Lentiviral Vectors for Enveloped Viruses 1.2.1.1 HIV Vector 1.2.1.2 Murine Leukemia Virus Vector 1.2.1.3 FIV Vector 1.2.2 The Vesicular Stomatitis Virus Vector 1.2.2.1 VSV Reverse Genetics 1.2.2.2 Recombinant VSV Vectors 1.3 Self-Assembled Constructed Pseudotyped Viruses 1.3.1 Self-Assembled Pseudotyped Virus for Enveloped Viruses 1.3.2 Self-Assembled Pseudotyped Virus for Non-enveloped Viruses 1.4 The Parameters and Conditions for Construction and Package of Pseudotyped Viruses 1.4.1 Viral Biological Characteristic Affects Pseudotyped Virus Formation and Titer 1.4.2 The Effects of Envelope Protein Expression 1.4.3 The Effects of Packaging System 1.4.4 Effects of Proteases 1.4.5 Selection of Cell Lines for Pseudovirus Packaging and Detection 1.4.6 The Effect of Packaging Conditions References Chapter 2: Assays Based on Pseudotyped Viruses 2.1 Introduction 2.2 Development of In Vitro Assays Based on Pseudotyped Viruses 2.2.1 Establishment and Optimization of In Vitro Assays Based on Pseudotyped Viruses 2.2.1.1 Selection of Target Cells 2.2.1.2 Optimization of Cell Inoculation 2.2.1.3 Optimization of the Amount of Pseudotyped Virus 2.2.1.4 Optimization of Infection Conditions 2.2.1.5 Optimization of Culture Time 2.2.1.6 Validation of In Vitro Assays Based on Pseudotyped Viruses 2.2.1.7 Specificity 2.2.1.8 Accuracy 2.2.1.9 Linear Range 2.2.1.10 Precision 2.3 Development of In Vivo Assays Based on Pseudotyped Viruses 2.3.1 Selection of Model Animals 2.3.2 Optimization of Infection Pathway 2.3.3 Determination of Infection Dose of Pseudotyped Virus 2.3.4 Comparison of Pseudotyped and Live Virus Infection Model 2.4 Conclusion References Chapter 3: Application of Pseudotyped Viruses 3.1 Analysis of Viral Infectivity 3.1.1 Receptor Usage 3.1.2 Cellular Tropism 3.2 In Vitro Pseudovirion-Based Neutralization Assay (PBNA) 3.2.1 Development and Evaluation of Vaccines 3.2.2 Screening and Validation of Monoclonal Neutralizing Antibodies 3.3 Screening and Validation of Viral Entry Inhibitors 3.4 Animal Model of Pseudotyped Virus Infection In Vivo 3.5 Analysis of Variations in Viral Infectivity and Antigenicity 3.5.1 Viral Variants 3.5.2 Variations in Viral Glycosylation 3.6 Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC) 3.7 Conclusion References Chapter 4: Pseudotyped Viruses for Retroviruses 4.1 Introduction to Retroviruses 4.2 The Retrovirus Genome and Replication Cycle: Important Regions for Retroviral Vectors 4.2.1 Genome Structure 4.2.2 Retroviral Proteins 4.2.3 Viral RNA Replication 4.3 Retroviral Pseudotyping Systems 4.3.1 Overview of Retroviral Pseudotyping Plasmid Systems 4.3.2 Commonly Used Retrovirus-Derived Transgene Vectors 4.3.2.1 MLV 4.3.2.2 HIV-1 and SIV 4.3.2.3 PFV 4.4 Applications of Pseudotyped Retroviruses 4.4.1 Functions of Viral Glycoproteins and Cell Entry 4.4.2 Identification and Characterization of Host Restriction 4.4.3 Discovery of Antivirals and Characterization of Drug Resistance 4.4.4 CRISPR-Cas9 Delivery and Gene Editing 4.4.5 Gene Therapy 4.4.5.1 Monogenic Blood Disorders 4.4.5.2 Cancer Immunotherapy 4.4.6 Insertional Mutagenesis: Lessons Learned 4.5 Conclusions References Chapter 5: Pseudotyped Virus for Papillomavirus 5.1 Introduction 5.2 Construction of Pseudotyped Papillomavirus 5.2.1 Pseudotyped Virus Packaging System Based on Virus Vector 5.2.2 Pseudotyped Virus Packaging System Based on Plasmid Transfection 5.3 Application of Pseudotyped Papillomavirus 5.3.1 The In Vitro L1 Pseudotyped Virus Based Neutralization Assay (PBNA) 5.3.1.1 PBNA Based on Green Fluorescent Protein (GFP) and Secretory Alkaline Phosphatase (SEAP) 5.3.1.2 PBNA Based on Secretory Membrane-Anchored Luciferase (Gaussia Luciferase, Gluc) 5.3.1.3 Multiple-Color PBNA Based on Fluorescent Protein 5.3.2 In Vitro L2 Pseudotyped Virus Neutralization Test 5.3.2.1 L2-Based PBNA Mimicking In Vivo Infection 5.3.2.2 Detection of L2 Pseudotyped Virus Neutralizing Antibody Based on Furin Cleavage Intermediates 5.3.3 Animal Model of HPV Pseudotyped Virus Infection 5.3.3.1 Mouse Model of HPV Pseudotyped Virus Infection 5.3.3.2 Chimeric Pseudotyped Virus Animal Model 5.3.4 Other Applications of Pseudotyped Papillomavirus 5.4 Conclusion References Chapter 6: Pseudotyped Viruses for Marburgvirus and Ebolavirus 6.1 Introduction 6.2 The Biological Characteristics of Marburgvirus and Ebolavirus 6.2.1 Morphology and Genome Structure 6.2.2 Virus Entry 6.3 Drugs and Vaccines for Marburgvirus and Ebolavirus 6.4 Construction of Pseudotyped Marburgvirus and Ebolavirus 6.4.1 VSV-Based Pseudotyped Marburgvirus and Ebolavirus 6.4.2 Lentiviral-Based Pseudotyped Marburgvirus and Ebolavirus 6.4.3 Influenza-Based Pseudotyped Marburgvirus and Ebolavirus 6.4.4 Comparison of Different Types of Pseudotyped Filoviruses and Authentic Filoviruses 6.5 Application of the Pseudotyped Viruses 6.5.1 Neutralization Antibody Detection 6.5.1.1 Vaccine Efficacy Evaluation 6.5.1.2 Therapeutic Antibody Analysis 6.5.1.3 Investigation of the Kinetics of Convalescent Sera 6.5.2 Antibody-Dependent Enhancement (ADE) Evaluation 6.5.3 Study of the Mechanisms of Filovirus Infection 6.5.3.1 Mapping the Key Domains and Amino Acids on the GP 6.5.3.2 Cell Tropism Examination 6.5.3.3 Proteolytic Enzyme Analysis 6.5.3.4 Discovery and Analysis of Receptor NPC1 6.5.3.5 Receptor Tyrosine Kinase (RTK)-Related Studies 6.5.3.6 Glycosylation and Acylation Analysis 6.5.3.7 Studies of Other Host Factors 6.5.3.8 Comparisons Between Filoviruses 6.5.4 Virus Entry Inhibitor Screening 6.5.4.1 In Vitro Screening 6.5.4.2 In Vivo Verification 6.5.5 Analysis of Mutations Within the GP 6.6 Summary References Chapter 7: Pseudotyped Viruses for Coronaviruses 7.1 Biological Characteristics of Coronavirus 7.1.1 Structure of Coronaviruses 7.1.2 Infection of Coronaviruses 7.1.3 Diversity for Each Coronavirus 7.2 Construction of Pseudotyped Viruses for Coronaviruses 7.2.1 CoV Pseudotyped Virus Based on Vesicular Stomatitis Virus (VSV) 7.2.2 CoV Pseudotyped Virus Based on Human Immunodeficiency Virus (HIV) 7.2.3 Construction of CoV Pseudotyped Virus Based on Other Packaging Systems 7.2.4 Construction of CoV Pseudotyped Virus Based on Protein-Autonomous Packaging Systems for Virus like Particles 7.3 Application of the HCoV Pseudotyped Viruses 7.3.1 Infectivity of Highly Pathogenic hCoV and the Possibility of Cross-Species Transmission 7.3.2 Study of Highly Pathogenic hCoV Mutant Strains 7.3.3 Pseudotyped Virus for Quantifying hCoV Neutralizing Antibodies 7.3.3.1 Natural Infection 7.3.3.2 Pseudotyped Virus for CoV Vaccine Development and Clinical Evaluation 7.4 Summary References Chapter 8: Pseudotyped Viruses for Influenza 8.1 Introduction 8.2 Production of Pseudotyped Viruses and Developing Assays Based on Pseudotyped Viruses 8.2.1 Materials 8.2.2 Protocols for Production of Pseudotyped Viruses and Developing Assays 8.2.2.1 Production of Influenza Hemagglutinin (HA) and Neuraminidase (NA) Pseudotypes (PV) 8.2.2.2 Titration of Influenza Hemagglutinin (HA) PV 8.2.2.3 Titration of H11_Neuraminidase (H11_NA) PV via Enzyme Linked Lectin Assay (pELLA) 8.2.2.4 Pseudotype Microneutralization (pMN) Assay Using HA PV (Fig. 8.5) 8.2.2.5 Inhibition of H11_NA(X) PV by Antisera and Monoclonal Antibodies via Enzyme-Linked Lectin Assay (pELLA) (Fig. 8.6) 8.2.2.6 AutoPlate Analysis 8.3 Commentary 8.3.1 Background 8.3.2 Critical Parameters and Troubleshooting 8.3.3 Understanding Results 8.3.4 Time Considerations References Chapter 9: Pseudotyped Virus for Henipavirus 9.1 General Information About Henipaviruses 9.1.1 Transmission of HNV Viruses 9.1.2 Structure of HNV 9.1.3 Diversity of HNV 9.2 Construction of Pseudotyped Viruses 9.2.1 Pseudotyped Viruses Using the Moloney Murine Leukemia Virus (MuLV) Packaging System 9.2.2 Pseudotyped Viruses Using the Human Immunodeficiency Virus Type 1 (HIV-1) Packaging System 9.2.3 Pseudotyped Viruses Using the Vesicular Stomatitis Virus (VSV) Packaging System 9.2.4 Pseudotyped Viruses Using the VSV-NiV-SEAP Novel Packaging System 9.2.5 Pseudotyped Viruses Using the Self-Assembling NiV-M-VLP Packaging System 9.3 Applications of HNV Pseudotyped Viruses 9.3.1 Studies of Potential Virus Receptors 9.3.2 Viral Infectivity Studies 9.3.3 Evaluation of Neutralization Detection Systems and Potential Antibody Candidates 9.3.4 Screening Studies of Inhibitory Drugs 9.4 Conclusions References Chapter 10: Pseudotyped Viruses for Lyssavirus 10.1 General Information About Lyssavirus 10.2 General Information About RABV 10.2.1 Glycoprotein Structure and Its Biological Role 10.2.2 Variation and Mutation on RABV G Protein 10.3 Construction of RABV G Protein Pseudotyped Virus 10.4 Application of Pseudotyped RABV 10.4.1 Application of Pseudotyped RABV in Neutralizing Antibody Detection 10.4.2 Application of Pseudotyped RABV in mAb Screening and Epitope Mapping 10.4.3 Application of Pseudotyped RABV in Evaluation of Viral Infection, Cell Tropism, and Antigenicity 10.4.4 Application of Pseudotyped RABV in Screening of Antiviral Drugs 10.5 Summary References Chapter 11: Pseudotyped Viruses for Enterovirus 11.1 Introduction of Enterovirus 11.2 Biological Characteristics of Enterovirus 11.2.1 Classification of Enterovirus 11.2.2 Genome and Life Cycle of the Enterovirus 11.3 Construction of Pseudotyped Enterovirus 11.3.1 Plasmid Construction 11.3.2 Preparation of Pseudotyped Enterovirus 11.3.3 Pseudotyped Enterovirus Shows High Physical, Chemical, and Antigenic Similarities with Wild-Type Virus 11.3.4 Investigation of Encapsidation Efficiency of Pseudotyped Enterovirus 11.3.4.1 Sequence Accuracy Is the Key to the Successful Package of Pseudotyped Enterovirus 11.3.4.2 Compatibility of Trans-packaging 11.4 The Application of Pseudotyped Enterovirus 11.4.1 An Useful Tool of Studying Molecular Virology of Enterovirus 11.4.2 An Useful Tool for Detection of NtAb 11.4.2.1 The Advantage of the NtAb Detection Based on Pseudotyped Enterovirus 11.4.2.2 The Principle of pvNA 11.4.2.3 Clinical Application of pvNA for Measurement of NtAb in Human Samples 11.4.3 A Safe, Sensitive, and Visualizing Model with Pseudotyped Enterovirus 11.4.4 Screening and Evaluation of Anti-enterovirus Drugs 11.5 Summary References Chapter 12: Pseudotyped Viruses for Orthohantavirus 12.1 Introduction 12.2 General Property of Orthohantavirus 12.2.1 Orthohantavirus Particle and Genome 12.2.2 Orthohantavirus Entry Pathway 12.2.3 Structure and Function of Orthohantavirus Glycoproteins 12.3 Construction of Pseudotyped Orthohantaviruses 12.3.1 Construction of Replication-Deficient Pseudotyped Orthohantaviruses 12.3.1.1 The VSV-Based Packaging System 12.3.1.2 The LV-Based Packaging System 12.3.1.3 The MLV-Based Packaging System 12.3.2 Construction of Replication-Competent Pseudotyped Orthohantaviruses 12.4 Applications of Pseudotyped Orthohantaviruses 12.4.1 Mechanistic Study for Viral Entry and Infection 12.4.1.1 Identification of Cellular Receptors and Factors 12.4.1.2 Identification of Key Amino Acid in Gn/Gc 12.4.1.3 Cell Tropism 12.4.2 Quantification of Neutralizing Antibodies 12.4.3 Antigenic Property Study 12.4.4 Identification of Viral Entry Inhibitors 12.4.5 Vaccine Approach 12.5 Conclusions References Chapter 13: Pseudotyped Viruses for Phlebovirus 13.1 Biological Characteristics of Phlebovirus 13.1.1 Structure of Rift Valley Fever Virus (RVFV) 13.1.2 Molecular Evolution 13.2 Construction of Pseudotyped RVFV 13.2.1 Construction of Pseudotyped RVFV Using Lentiviral Vectors 13.2.2 Construction of Pseudotyped RVFV Using VSV-Based Vectors 13.2.3 Construction of Pseudotyped RVFV Using the Self-Assembly System 13.3 Application of Pseudotyped RVFV 13.3.1 Neutralizing Assay Based on Pseudotyped RVFV 13.3.2 Visual In Vivo Neutralizing Antibody Evaluation Model 13.3.3 The Mechanism of Viral Infection 13.3.4 Pseudotyped RVFV as a Candidate Vaccine 13.3.5 Neutralization Sensitivity Analysis of Natural and Artificial RVFV Variants 13.4 Conclusion References Chapter 14: Pseudotyped Virus for Bandavirus 14.1 Introduction 14.2 General Property of Dabie Bandavirus 14.2.1 Virion Structure and Genome Characteristics 14.2.2 Infection Mechanisms of Dabie Bandavirus 14.2.3 Genetic Diversity 14.2.4 Characteristics of the Glycoprotein 14.3 Construction of Pseudotyped Dabie Bandavirus 14.3.1 VSV-Based System 14.3.2 Lentiviral-Based System 14.4 Application of the Pseudotyped Dabie Bandavirus 14.4.1 Pseudotyped Dabie Bandavirus as Vaccine 14.4.2 Analysis of Neutralizing Antibody 14.4.3 Analysis of Viral Tropism and Entry 14.4.4 Infectivity and Neutralization Analysis of Pseudotyped Dabie Bandavirus Mutants 14.5 General Conclusions References Chapter 15: Pseudotyped Viruses for Mammarenavirus 15.1 Introduction 15.2 Biological Characteristics of Mammarenavirus 15.2.1 Morphology and Genome Structure 15.2.2 Replication of the Viral Genome 15.2.3 Pathogenicity 15.2.4 Diversity of LASV and LCMV 15.3 Construction of Pseudotyped Mammarenaviruses 15.3.1 The Lentiviral Vectors 15.3.2 VSV-Based Vector 15.3.3 MLV-Based Vectors 15.3.4 Recombinant Mammarenaviruses 15.3.5 The Genus of Successful Constructed Pseudotyped Mammarenaviruses 15.4 Application of the Pseudotyped Mammarenaviruses 15.4.1 The Analysis of Virus-Receptor Interactions and Host Range 15.4.2 The Mechanism of Viral Infection, Endocytosis, and Fusion 15.4.3 Detection of Neutralizing Antibodies and Evaluation of Candidate Vaccines 15.4.4 High-Throughput Screening of Viral Inhibitors 15.4.5 Analysis on the Virulence Mechanisms of Viral Mutants 15.4.6 Functional Analysis of N-linked Glycans of GPC 15.5 Conclusion References Chapter 16: Pseudotyped Viruses for the Alphavirus Chikungunya Virus 16.1 Biological Characteristics of Chikungunya Virus 16.1.1 Molecular Structure 16.1.2 Genotypes and Variants 16.1.3 Pathogenic Mechanisms and Biosafety Risk 16.2 Construction of Pseudotyped CHIKV 16.2.1 Construction of Pseudotyped CHIKV Using Different Vectors 16.2.1.1 Lentiviral Vectors 16.2.1.2 VSV-Based Vectors 16.2.1.3 MLV-Based Vectors 16.2.2 CHIKV Infectious Clones and Virus-like Particles 16.3 Application of Pseudotyped CHIKV 16.3.1 Neutralizing Assay Based on Pseudotyped CHIKV 16.3.1.1 Correlation of PBNA and PRNT 16.3.1.2 Factors Closely Related to CHIKV PBNA 16.3.2 Establishment of an in Vivo Imaging Model of Small Animals 16.3.3 Use of a Capture Antigen in CHIKV IgM Detection 16.3.4 Drug Screening 16.3.5 The Mechanism of Viral Infection 16.4 Conclusion References Chapter 17: Pseudotyped Virus for Flaviviridae 17.1 Introduction 17.2 Construction Strategies of Pseudotyped Flaviviridae 17.2.1 Construction Strategies of HCV Pseudotyped Virus 17.2.2 Construction Strategies of JEV Pseudotyped Virus 17.2.3 Construction Strategies of DENV Pseudotyped Virus 17.2.4 Construction Strategies of ZIKV Pseudotyped Virus 17.3 Application of Pseudotyped Flaviviridae 17.3.1 Study the Interaction between Virus and Host Cell 17.3.2 Neutralizing Antibody Detection and Vaccine Effect Evaluation 17.3.3 Screening of Antiviral Drugs 17.3.4 Research on Antitumor Therapy 17.4 Summary and Prospect References Chapter 18: Replicating-Competent VSV-Vectored Pseudotyped Viruses 18.1 Construction of Replicating-Competent VSV Viruses 18.1.1 History of Replicating-Competent VSV Viruses 18.1.2 Rescue Method of Replicating-Competent VSV Viruses 18.2 Application of Replicating-Competent VSV 18.2.1 Screening of Viral Host Factors/Receptors 18.2.2 Screening of Mutations that Escape Therapeutic mAbs 18.2.3 Vaccine Development 18.2.3.1 VSV-Based EBOV Vaccine 18.2.3.2 VSV-Based SARS-CoV-2 Vaccine References