Viruses: From Understanding to Investigation

Front Cover
Viruses
Copyright Page
Contents
About the author
Preface
Acknowledgments
1 Introduction to animal viruses
What is a virus?
Diversity in the world of viruses
Are viruses alive?
Basic steps in the virus replication-cycle
Propagating viruses
Categorizing viruses (taxonomy)
Outcomes of viral infection
Introduction to viral pathogenesis
Introduction to viral transmission
References
2 Virus structure
Anatomy of a virus
Capsid structure and function
Capsids are built using many copies of one or a few types of protein
Simple icosahedral capsids
Larger icosahedral capsids
Polyomavirus and papillomavirus capsids
Adenovirus capsids
Reoviruses
Herpesvirus capsids
Surface structures of capsids
Viral envelopes
Glycosylation
Other membrane proteins
Matrix proteins
Nucleocapsid structure
References
3 Virus interactions with the cell
Virion attachment
The extracellular space
The plasma membrane
Attachment
Virus penetration and uncoating
Virus penetration and uncoating of unenveloped viruses
Virus penetration and uncoating of enveloped viruses
Movement through the cell, interactions with the cytoskeleton
Amplification of viral proteins and nucleic acids in the context of the infected cell
A short review of transcription in the eukaryotic cell
Transcription of viral mRNAs
A short review of translation in the eukaryotic host cell
Translation of viral proteins
Synthesis of viral genomes
The endgame: virus assembly, release, and maturation
Assembly
Virion release
Virion maturation
4 Methods to study viruses
Growing viruses
Generating cell cultures
Purifying viruses
Visualizing viruses
Optical microscopy
Electron microscopy
Counting viruses
Infectivity assays
Chemical/physical methods of virus quantitation
Direct visualization by electron microscopy
Hemagglutination assay
Serological assays
Enzyme-linked immunosorbent assays
Western blots
Genome detection and quantitation by PCR
Basic principles of diagnostic virology
Deep sequencing for virus discovery and characterization
References
5 Virus transmission and epidemiology
Modes of transmission
Respiratory routes
Food and water
Exchange of body fluids
Insect vectors
Role of the host specificity in virus transmission
Transmissibility
Describing viral infection and disease
Infection versus disease
Pathogenicity and virulence
Acute versus persistent infection
Incubation, latent, and infectious periods
Incidence versus prevalence
6 Immunity and resistance to viruses
What is immunity?
Innate immunity
Pattern recognition receptors
Toll-like receptors
Retinoic acid-inducible gene-like receptors
Nucleotide-binding oligomerization domain (NOD)-like receptors
Pyrin and HIN200 domain-containing proteins
Cyclic GMP-AMP synthase
Adapter proteins: next level players in innate immunity
Inflammasomes
Other proinflammatory molecules
Interferons
Type-I interferons
Type-II interferon
Type-III interferons
JAK-STAT signaling
Interferon-stimulated genes and the antiviral state
Protein kinase RNA-activated pathway
2′-5′ Oligo A synthase pathway
Other interferon-stimulated genes
Intrinsic immunity
Restriction factors
Autophagy
Natural killer cell responses to viral infection
Specific immunity
Antibody responses
Cell-mediated responses
Antigen presentation
Viruses fight back
Antigenic variation
Suppression of antigen presentation
Suppression of interferon responses
Immunosuppression
Poxviruses encode molecules that mimic cytokines, interferons, and their receptors
Hiding from the immune system
Micro-RNAs
7 Viral vaccines
Vaccines provide a source of antigen
Antigen recognition
Classical versus engineered vaccines
Replicating versus inactivated vaccines
Viral vaccines that contain infectious agents
Killed, inactivated, and subunit vaccines
Correlates of protection
Vaccine development and assessment of efficacy
COVID-19 vaccines
A final word about safety
References
8 Antiviral agents
Inhibitors of attachment, entry, or uncoating
Inhibitors of viral nucleic acid synthesis
Protease inhibitors
Neuraminidase inhibitors
Interferons
The future of antivirals
9 Virus evolution and genetics
Virus evolution
Measuring virus evolution
Point mutation
Recombination
Reassortment
Genotypes and phenotypes
Essential and nonessential genes
Coevolution of virus and host
Genetic manipulation of viruses
Reverse genetics of positive-strand RNA viruses
Reverse genetics of negative-strand RNA viruses
Reverse genetics of retroviruses
Reverse genetics of small DNA viruses
Reverse genetics of large DNA viruses
10 Viral pathogenesis
Natural barriers to infection
Primary replication
Movement to secondary replication sites
Genesis of disease
Immunopathogenesis
Virulence
Approaches to study viral pathogenesis
Virally induced cancers
11 Introduction to RNA viruses
Definition and basic properties of RNA viruses
Positive-strand RNA viruses
Negative-sense RNA, ambisense, and double-stranded RNA viruses
Negative-sense RNA viruses
Ambisense RNA viruses
dsRNA viruses
Hepatitis delta virus uses host DNA-dependent RNA polymerase for replication
Structural features of RNA virus genomes
Priming viral RNA synthesis
Mechanisms to generate capped mRNAs
Mechanisms to generate polyadenylated mRNAs
Mechanisms to regulate synthesis of genomes and transcripts
RNA viruses and quasispecies
References
12 Family Picornaviridae
Genome organization
Virion structure
Picornavirus replication (poliovirus model)
Binding and penetration
Translation
Genome replication
Assembly and maturation
Diseases caused by picornaviruses
Genus enterovirus
Genus hepatovirus
Genus kobuvirus
Genus parechovirus
Genus apthovirus
13 Family Caliciviridae
Genome organization
Virion structure
General replication cycle
Attachment/penetration
Genome replication
Translation
Assembly/release
Diseases
Acute gastrointestinal disease
Feline calicivirus
Rabbit calicivirus
14 Family Hepeviridae
Genome organization
Virion morphology
General replication cycle of HEV
Disease
References
15 Family Astroviridae
Genome organization
Virion morphology
General replication strategy
Diseases caused by astroviruses
16 Family Flaviviridae
Genome structure/organization
Virion structure
General overview of replication
Protein products
Diseases
Hepatitis C
Diseases caused by members of the genus Flavivirus
Yellow fever virus
Dengue fever virus
Zika virus
West Nile virus
Genus Pestivirus
Diseases caused by members of the genus Pegivirus
References
17 Families Togaviridae and Matonaviridae
Family Togaviridae
Genome structure
Virion structure
Togavirus replication
Attachment and penetration
Translation
Genome replication
Assembly and release
Transmission
Togaviruses associated with rash and arthritis
Chikungunya virus
Other togaviruses of human concern
Alphaviruses of veterinary importance
Family Matonaviridae
Rubella virus
Features and general replication cycle
Disease
Reference
18 Family Coronaviridae
Coronavirus genome organization
Virion structure
Coronavirus structural proteins
Coronavirus replication cycle
Attachment
Penetration
Amplification
RNA synthesis
Assembly and release
Diseases caused by coronaviruses
Severe acute respiratory syndrome
Middle East respiratory syndrome
Feline coronavirus and feline infectious peritonitis
Porcine coronaviruses
Reference
19 SARS-CoV-2/COVID-19
Genome organization
Virion and structural proteins
Nonstructural and accessory proteins
Overview of replication
Binding and entry
Amplification
Assembly and release
Origins and pathogenesis of SARS-CoV-2
Origins of SARS-CoV-2
Route of transmission and target cells
Disease
Vaccines
Treatments
Viral variation
Reference
20 Family Arteriviridae
Genome organization
Virion structure
Replication cycle
Diseases caused by arteriviruses
Equine viral arteritis
Porcine reproductive and respiratory syndrome
Simian hemorrhagic fever virus and related viruses
References
21 Family Rhabdoviridae
Genome organization
Virus structure
Overview of replication
Attachment and penetration
Transcription and translation
The switch from mRNA synthesis to genome replication
Assembly/release
Diseases
Rabies and rabies-related viruses
Chandipura virus
Vesicular stomatitis virus
Other rhabdoviruses associated with disease
22 Family Paramyxoviridae
Genome structure/organization
Virion structure
Overview of replication
Attachment and penetration
Transcription
Protein synthesis
Genome replication
Assembly, release, and maturation
Diseases
Measles
Mumps
Respiratory tract diseases
Canine distemper
Henipaviruses
23 Family Pneumoviridae
Genome organization
Virion structure
Overview of replication
Attachment and penetration
Transcription
HRSV proteins
Genome replication, assembly, and release
Diseases
Human respiratory syncytial virus disease
Human metapneumovirus disease
24 Family Filoviridae
Genome organization
Virion structure
Overview of replication
Attachment/Penetration
Transcription, translation, genome replication
Assembly
Disease
Transmission
Pathogenesis
Ebolavirus and Marburg virus antagonize innate immune responses
Therapeutics and vaccines
25 Family Bornaviridae
Genome organization
Virion structure
Overview of replication
Genome replication
Diseases
Borna disease
Birds and bornaviruses
26 Family Orthomyxoviridae
Genome structure/organization
Virion structure
Classification and nomenclature of orthomyxoviruses
Influenza virus A proteins
Hemagglutinin
Neuraminidase
Matrix protein (M1)
M2 ion channel protein
Nucleoprotein
RNA polymerase complex
Nonstructural protein 1
Nuclear export protein
Overview of replication
Attachment/penetration
Transcription
Translation
Genome replication
Assembly, budding, and maturation
Antigenic drift and antigenic shift
Disease
Human influenza
Avian influenza
Antiviral drugs
Vaccines
Reference
27 Family Hantaviridae
Virion structure
Genome organization
General replication strategy
Diseases
Hantavirus pulmonary syndrome
Hemorrhagic fever with renal syndrome
References
28 Order Bunyavirales: Families Peribunyaviridae, Phenuiviridae, and Nairoviridae
Genome organization
Virion structure
General replication strategy
Diseases
Crimean Congo hemorrhagic fever
Oropouche fever
La Crosse encephalitis
Schmallenberg and Cache Valley viruses
Rift Valley fever virus
References
29 Family Arenaviridae
Genome organization
Virion structure
Overview of replication
Diseases caused by arenaviruses
Lassa fever
Lymphocytic choriomeningitis
New World arenaviruses
30 Family Reoviridae
Genome organization
Virus structure
Overview of replication
Attachment/entry
Amplification
Genome replication
Assembly, maturation, and release
Diseases
Genus rotavirus
Genus orbivirus
Genus orthoreovirus
Genus coltivirus
31 Family Birnaviridae
Genome structure
Virion structure
General replication cycle
Disease
Infectious bursal disease (Gumboro)
References
32 Hepatitis delta virus
Virion Structure
Genome organization
Hepatitis delta antigens
General replication cycle
Disease
33 Introduction to DNA viruses
Taxonomy of DNA viruses
Viral DNA replication
DNA viruses and cell cycle
Oncogenesis
34 Family Parvoviridae
Genome organization
Virion structure
Overview of replication
Diseases
Human B19 parvovirus
Feline panleukopenia virus
Canine parvovirus
Aleutian mink disease
35 Other small DNA viruses
Family Circoviridae
Diseases
Beak and feather disease
Porcine circoviruses
Family Anelloviridae
References
36 Family Polyomaviridae
Genome structure
Virion structure
Tumor antigens
Replication
Attachment and penetration
Early transcription
Genome replication
Late transcription
Assembly and release
Transformation
Human polyomavirus and disease
37 Family Papillomaviridae
Genome structure
Virion structure
Replication cycle
Attachment/penetration
Early transcription and genome replication
Late transcription and vegetative DNA replication
Disease
Human papillomaviruses
Epidermodysplasia verruciformis
Animal papillomaviruses
Reference
38 Family Adenoviridae
Genome organization
Virion structure
Adenovirus replication cycle
Attachment/penetration
Early transcription
E1A
E1B
E2
E3
Viral DNA replication
Late transcription
VA RNAs
Assembly and release
Adenoviruses and human disease
Adenoviruses and transformation
Oncolytic adenoviruses
Adenoviral vectors
39 Family Herpesviridae
Genome organization
Virus structure
Replication cycle
Attachment/penetration
Transcription/DNA replication
Assembly/release
Latency
Diseases caused by human herpesviruses
HHV-1 and -2 disease
HHV-3 (varicella zoster virus)
HHV-4 (Epstein–Barr virus)
HHV-4 and Burkitt lymphoma
HHV-4 and nasopharyngeal carcinoma
HHV-5 (cytomegalovirus)
HHV-6 and -7
HHV-8 (Kaposi sarcoma herpesvirus)
Monkey B herpesvirus
Antiherpesviral drugs
References
40 Family Poxviridae
Genome organization
Virion structure
Replication
Attachment/penetration
Transcription and genome replication
Assembly/release
Immune avoidance
Diseases
Smallpox
Molluscum contagiosum
Monkeypox
Rabbit myxoma
References
41 Other large DNA viruses
Family Asfarviridae
Genome organization
Virion structure
Overview of replication
Epidemiology and disease
Family Iridoviridae
The giant viruses of acanthameoba
References
42 Family Retroviridae
Virion structure
Genome organization
Overview of the retroviral replication cycle
The process of reverse transcription
Integration
Transcription of retroviral mRNA
Structural proteins
Assembly, release, and maturation
Unique aspects of spumaretrovirus replication
Mechanisms of retroviral oncogenesis
References
43 Replication and pathogenesis of human immunodeficiency virus
History of HIV and acquired immunodeficiency syndrome
HIV is a lentivirus
HIV Structural proteins
GAG precursor (Pr55Gag)
GAG–POL polyprotein precursor (Pr160Gag-pol)
ENV precursor
TAT
REV
Other HIV-1 proteins
Virus infectivity factor
Viral protein U
Viral protein R
Viral protein X is unique to HIV-2
NEF
Summary of HIV replication
Binding/entry
Reverse transcription, nuclear entry, and integration
Transcription and translation
Assembly/release/maturation
Overview of HIV pathogenesis
HIV-1 infection of CD4+ T-lymphocytes
HIV-1 infection of monocytes and macrophages
HIV-1 infection of dendritic cells
Disruption of immune function
Immune activation
HIV transmission
Disease course
Antiretroviral drugs
Entry/fusion inhibitors
Nucleoside/nucleotide reverse transcriptase inhibitors
Nonnucleoside reverse transcriptase inhibitors
Integrase inhibitors
Protease inhibitors
Combination drugs
Prophylaxis
Vaccines
44 Family Hepadnaviridae
Genome organization
Virion structure
Replication cycle
Attachment/penetration
Transcription
Protein products
Genome replication
Assembly/release of infectious particles
Hepatitis B virus and disease
Index
Back Cover