1. Medical Virology Dept. of Medical Microbiology and Parasitology
Shanghai Second Medical University
Shanghai, China.
E.mail: ( )

2. General Virology Conception Viruses Virion Size and Shape Structure
Replication
Viral Variation
Classification

3. Conception
Virology is the bioscience for study of viral nature,and the relationship between viruses and hosts. Viruses often cause serious diseases, relate to some cancers and congenital deformities, also can be used as tool for genetic engineering.

4. 3000BC

5. History
Smallpox was endemic in China by 1000BC. In response, the practice of variolation was developed. Recognizing that survivors of smallpox outbreaks were protected from subsequent infection, variolation involved inhalation of the dried crusts from smallpox lesions like snuff, or in later modifications, inoculation of the pus from a lesion into a scratch on the forearm of a child.

6. Definition of Virus
Viruses may be defined as acellular organisms whose genomes consist of nucleic acid, and which obligately replicate inside host cells using host metabolic machinery and ribosomes to form a pool of components which assemble into particles called VIRIONS, which serve to protect the genome and to transfer it to other cells

7. Viral Properties Viruses are inert (nucleoprotein ) filterable Agents
Viruses are obligate intracellular parasites
Viruses cannot make energy or proteins independent of a host cell
Viral genome are RNA or DNA but not both.
Viruses have a naked capsid or envelope with attached proteins
Viruses do not have the genetic capability to multiply by division.
Viruses are non-living entities

8. Consequences of Viral Properties
Viruses are not living
Viruses must be infectious to endure in nature
Viruses must be able to use host cell processes to produce their components (viral messenger RNA, protein, and identical copies of the genome)
Viruses must encode any required processes not provided by the cell
Viral components must self-assemble

9. Challenges the way we define life
viruses do not respire,
nor do they display irritability应急性;
they do not move
they do not grow
they do most certainly reproduce, and may adapt to new hosts.

10. Size and Shape
Methods
Size of Viruses
Shapes of Viruses

11. Methods of Analysis Electron microscopy :
The resolution is 5nm (1nm = 10-9 m)
X-ray crystallography

12. Size of Viruses A small virus has a diameter of about 20nm. Parvovirus
A large virus have a diameter of up to 400nm.
Poxviruses

15. Shape of Viruses Spherical Rod-shaped Brick-shaped Tadpole-shaped
Bullet-shaped
Filament

16. Shapes of Viruses:Spherical

17. Shapes of Viruses :Rod-shaped

18. Shapes of Viruses :Brick-shaped.
                                                                           

19. Tadpole-shaped

20. Shapes of Viruses :Bullet-shaped

21. Shapes of Viruses :Filament

22. Structure of Viruses

23. Virion the complete infectious unit of virus particle
Structurally mature, extracellular virus particles.

24. Virion
envelope
Capsid
Viral core

25. Viral core
Viral core
The viral nucleic acid genome, In the center of the virion, : Control the viral heredity and variation, responsible for the infectivity.

26. Genome The genome of a virus can be either DNA or RNA
DNA-double stranded (ds): linear or circular
Single stranded (ss) : linear or circular
RNA- ss:segmented or non-segmented
ss:polarity+(sense) or polarity –(non-sense)
ds: linear (only reovirus family)

27. DNA
RNA
double-stranded
single-stranded
linear
circular
linear (circular)*
single
multiple
(+)sense
(-)sense

29. Viral Capsid
The protein shell, or coat, that encloses the nucleic acid genome.
Functions: a. Protect the viral nucleic acid. b. Participate in the viral infection. c. Share the antigenicity

30. Nucleocapsid
The core of a virus particle consisting of the genome plus a complex of proteins.
complex of proteins = Structural proteins +Non- Structural proteins (Enzymes &Nucleic acid binding proteins)

31. Symmetry of Nucleocapsid
Helical
Cubic /Icosahedral
Complex

32. Helical symmetry

33. Helical symmetry
How to assemble

34. Helical
California Encephalitis Virus Coronavirus Hantavirus Influenza Virus (Flu Virus) Measles Virus ( Rubeola) Mumps Virus Parainfluenza Virus Rabies Virus Respiratory Syncytial Virus(RSV)

35. Cubic or icosahedral symmetry

38. Icosahedral
Herpes Simplex Virus 1 (HHV1) Herpes Simplex Virus 2 (HHV2) Human Immunodeficiency Virus (HIV) Human T-lymphotrophic Virus (HTLV) Norwalk Virus Papilloma Virus (HPV) Polio virus Rhinovirus Rubella Virus Saint Louis Encephalitis Virus Varicella-Zoster Virus (HHV3) Western Equine Encephalitis Virus (WEEV) Yellow Fever Virus
Adeno-associated Virus (AAV) Adenovirus B19 Coxsackievirus - A Coxsackievirus - B Cytomegalovirus (CMV) Eastern Equine Encephalitis Virus (EEEV) Echovirus Epstein-Barr Virus (EBV) Hepatitis A Virus (HAV) Hepatitis B Virus (HBV) Hepatitis C Virus (HCV) Hepatitis Delta Virus (HDV) Hepatitis E Virus (HEV)

39. Complex Virus Structures
A well known example is the tailed bacteriophages such as T4.
The head of these viruses is cubic with a triangulation number of 7. This is attached by a collar to a contractile tail with helical symmetry.

40. T4 Bacteriophage

41. Properties of naked viruses
Stable in hostile environment
Not damaged by drying, acid, detergent, and heat
Released by lysis of host cells
Can sustain in dry environment
Can infect the GI tract and survive the acid and bile
Can spread easily via hands, dust, fomites, etc
Can stay dry and still retain infectivity
Neutralizing mucosal and systemic antibodies are needed to control the establishment of infection

42. Naked viruses( Non Enveloped )
Adeno-associated Virus (AAV) Adenovirus B19 Coxsackievirus - A Coxsackievirus - B Echovirus Hepatitis A Virus (HAV) Hepatitis E Virus (HEV) Norwalk Virus

43. Envelope
A lipid-containing membrane that surrounds some viral particles.
It is acquired during viral maturation by a budding process through a cellular membrane, Viruses-encoded glycoproteins are exposed on the surface of the envelope.
Not all viruses have the envelope, and viruses can be divided into 2 kinds: enveloped virus and naked virus.

44. Functions of envelope Antigenicity some viruses possess neuraminidase
Infectivity
Resistance

46. Envelope

47. Properties of enveloped viruses
Labile in dry , arid environment
Damaged by drying, acid, detergent, and heat
Pick up new cell membrane during multiplication
Insert new virus-specific proteins after assembly
Virus is released by budding

48. Consequences of Properties for enveloped viruses
Must stay moist
Must not infect the GI tract for survival
Must be transmitted in the protective, droplets, secretions, blood and body fluids
Must reinfect another host cell to sustain
Humoral and cell-mediated immunity are needed to control the infection

50. Enveloped
Herpes Simplex Virus 2 (HHV2) Human Immunodeficiency Virus (HIV) Human T-lymphotrophic Virus (HTLV) Influenza Virus (Flu Virus) Molluscum contagiosum Papilloma Virus (HPV) Polio virus Rhinovirus Varicella-Zoster Virus (HHV3) Venezuelan Equine Encephal. Vir. (VEEV) Western Equine Encephalitis Virus (WEEV) Yellow Fever Virus
California Encephalitis Virus
Coronavirus
Cytomegalovirus (CMV)
Eastern Equine Encephalitis Virus (EEEV)
Epstein-Barr Virus (EBV)
Hantavirus Hepatitis B Virus (HBV) Hepatitis C Virus (HCV) Hepatitis Delta Virus (HDV) Herpes Simplex Virus 1 (HHV1)
Rotavirus
Rubella Virus
Saint Louis Encephalitis Virus Smallpox Virus (Variola) Vaccinia Virus

51. Spike or Peplomere

53. summarize

54. Virion structure
Nucleocapsid(Naked Virus) = DNA or RNA +Structural proteins +Enzymes &Nucleic acid binding proteins
Enveloped Virus =Nucleocapsid+ Viral specific glycoproteins and Host Membrane

55. Helical
Cubic
Naked Virus
Enveloped Virus

56. CHEMICAL COMPOSITION OF VIRUSES
Viral Protein
Viral Nucleic Acid
Viral Lipids
Viral carbohydrate

57. Viral Nucleic Acid DNA-double stranded (ds): linear or circular
Single stranded (ss) : linear or circular
RNA- ss:segmented or non-segmented
ss:polarity+(sense) or polarity –(non-sense)
ds: linear (only reovirus family)

58. Viral Protein Structural protein (Capsomere) Enzyme
glycoproteins (spike/viral attachment protein, VAP)

59. Culture of Viruses

60. System for the propagation of viruses
People
Animals : cows;chickens; mice; rats; suckling mice
Embryonated eggs
Organ and tissue culture
Organ culture
primary tissue culture
cell lines: diploid
Tumor or immortalized cell line

64. Cytopathic effect, CPE
Inclusion Bodies

65. CPE:Viral Cytopathological Effects
Cell death
Cell rounding/Degeneration/Aggregation
Lass of attachments to substrate
Inclusion bodies in the nucleus or cytoplasm, margination of chromatin
Syncytia: multinucleated giant cells caused by virus-induced cell-cell fusion
Cell surface changes
Viral antigen expression
Hemadsorption (hemagglutinin expression)

66. Normal cell and CPE

67. Inclusions
Negri body

68. TCD50,LD50,ID50
PFU: plaque forming units

69. Replication of Viruses

70. Replicative cycle
As obligate intracellular parasites, Virus must enter and replicate in living cells in order to “reproduce” themselves. This “growth cycle” involves specific attachment of virus, penetration and uncoating, nucleic acid transcription, protein synthesis, matureation and assembly of the virions and their subsequent release from the cell by budding or lysis

74. Initiation Phase
Attachment
Penetration
Uncoating

75. Attachment/Adsorption
Virus attaches to the cell surface. Attachment is via ionic interactions which are temperature-independent.
Viral attachment protein recognizes specific receptors on the cell surface (These may be protein or carbohydrate or lipid components of the cell surface).
Cells without the appropriate receptors are not susceptible to the virus.

76. PENETRATION (Virus enters the cell)
Virions are either engulfed into vacuoles by “endocytosis” or the virus envelope fuses with the plasma membrane to facilitate entry
Enveloped viruses
Non-enveloped viruses

77. Fusing
(A) Entry by fusing with the plasma membrane. Some enveloped viruses fuse directly with the plasma membrane. Thus, the internal components of the virion are immediately delivered to the cytoplasm of the cell.

78. HIV

79. Endocytosis
(B) Entry via endosomes at the cell surface

80. influenza virus

81. Enveloped viruses
Some enveloped viruses require an acid pH for fusion to occur and are unable to fuse directly with the plasma membrane. These viruses are taken up by invagination of clathrin coated pits into endosomes. As the endosomes become acidified, the latent fusion activity of the virus proteins becomes activated by the fall in pH and the virion membrane fuses with the endosome membrane. This results in delivery of the internal components of the virus to the cytoplasm of the cell

82. Non-enveloped viruses
Non-enveloped viruses may cross the plasma membrane directly
may be taken up via clathrin-coated pits into endosomes. They then cross (or destroy) the endosomal membrane.

83. unenveloped viruses

84. UNCOATING
Nucleic acid has to be sufficiently uncoated that virus replication can begin at this stage. When the nucleic acid is uncoated, infectious virus particles cannot  be recovered  from the cell - this is the start of the ECLIPSE phase - which lasts until new infectious virions are made
Uncoating is usually achieved by cellular proteases “opening up” the capsid

85. genome synthesis mRNA production protein synthesis
BIOSYNTHESIS
genome synthesis
mRNA production
protein synthesis

86. Flow of events during the replication of Hepadna viruses

87. Flow of events during the replication of herpesviruses

88. Flow of events during the replication of reoviruses.

89. Flow of events during the replication of togaviruses

90. Flow of events during the replication of orthomyxoviruses and paramyxoviruses.

91. Flow of events during the replication of retroviruses

92. Maturation assembly release

93. Maturation
The stage of viral replication at which a virus particle becomes infectious; nucleic acids and capsids are assembled together.

94. ASSEMBLY
The stage of replication during which all the structural components come together at one site in the cell and the basic structure of the virus particle is formed.

95. RELEASE Disintegration : naked virus cause the host cell lysis
Budding: enveloped viruses
Budding viruses do not necessarily kill the cell. Thus, some budding viruses may be able to set up persistence

96. Assembly

98. Products of viral replication
Virion
DEFECTIVE VIRUS
ABORTIVE INFECTION
integration

99. DEFECTIVE VIRUS
deficiency in some aspects of replication, but interfering the replication of normal viruses 
ABORTIVE INFECTION
When a virus infects a cell (or host), but cannot complete the full replication cycle ( not biosynthesize their components or not assemble virions.), i.e. a non-productive infection.

100. INTERFERENCE
Interferon, IFN
Defective interfering particle, DIP

101. Viral Genetics

102. Genome The genome of a virus can be either DNA or RNA
DNA-double stranded (ds): linear or circular
Single stranded (ss) : linear or circular
RNA- ss:segmented or non-segmented
ss:polarity+(sense) or polarity –(non-sense)
ds: linear (only reovirus family)

103. Virus Genomes

104. The Structure & Complexity of Virus Genomes
The nucleic acid comprising the genome may be single-stranded or double-stranded, & in a linear, circular or segmented configuration. Single-stranded virus genomes may be:
positive (+)sense, i.e. of the same polarity (nucleotide sequence) as mRNA
negative (-)sense
ambisense - a mixture of the two.

105. The Structure & Complexity of Virus Genomes
any virus genome will usually include the following:
Composition - DNA or RNA, single-stranded or double-stranded, linear or circular.
Size & number of segments.
Terminal structures.
Nucleotide sequence.
Coding capacity - open reading frames.
Regulatory signals - transcription enhancers, promoters & terminators.

106. The Structure & Complexity of Virus Genomes

107. Transfection
Infection of cells caused by nucleic acid alone

108. Variation
There are two important variation which relate well with medical practices
Antigenicity variation: In most viruse the antigenicity is stable but in some viruses such as influenze virus the antigenicity may vary and cause the disease to epidemic.
Virulence variation(Virulent viruses): Less virulent viruses always used in prevention.

109. Mutation
Mutant
Variant
temperature sensitive(ts) mutant

110. Interactions when two genetically distinct viruses infect a cell 3 different phenomena can ensue
Recombination /Reassortment
Complementation
Phenotypic mixing

111. Recombination
dsDNA viruses
Reassortment ( segmented genomes)
RNA viruses: influenza virus

112. Complementation

113. Phenotypic mixing
The genome of virus A can be coated with the surface protein of virus type B

114. Classification of Viruses

116. CLASSIFICATION OF VIRUSES -------basis of classification
Virion morphology
Physicochemical properties of the virion
Virus genome properties
Virus protein proteries
Genome organization and replication
Antigenic properties
Biologic properties

117. CLASSIFICATION OF VIRUSES
By 1995
--71 families, 11 subfamilies
--164 genera
For humans and animals
--24 families,
--DNA: 7; RNA: 17 for humans

118. Survey of DNA-containing Viruses
Parvoviruses: human parvovirus B19
Papovaviruses: papillomaviruses
Adenoviruses: 47 types infect humans
Herpesviruses: human herpesvirus 1-8
Poxviruses: smallpox; vaccinia
Hepadnaviruses: HBV

122. Survey of RNA-containing Viruses
Retroviruses
Bunyaviruses
Othomyxoviruses
Paramyxoviruses:
Rhabdoviruses:rabies virus
Bornaviruses: BDV
Filoviruses
Other viruses
Viroids
Picornaviruses
Astroviruses
Caliciviruses
Reoviruses
Arboviruses
Togaviruses
Flaviviruses
Arenaviruses
Coronaviruses: SARS

128. DNA and RNA Viruses
嗜肝病毒科（Headnasviridae）
逆转录病毒（ Retroviridae ）

129. Viroids(类病毒)
Viroids are small ( nt), circular RNA molecules with a rod-like secondary structure which possess no capsid or envelope which are associated with certain plant diseases. Their replication strategy like that of viruses - they are obligate intracellular parasites.

130. Dependovirus /Virusoids卫星病毒
Viroids are small ( nt), circular RNA molecules with a rod-like secondary structure which possess no capsid or envelope which are associated with certain plant diseases. Their replication strategy like that of viruses - they are obligate intracellular parasites.

131. 朊粒 (Prions)
Prions are rather ill-defined infectious agents believed to consist of a single type of protein molecule with no nucleic acid component. Confusion arises from the fact that the prion protein & the gene which encodes it are also found in normal 'uninfected' cells. These agents are associated with diseases such as Creutzfeldt-Jakob disease in humans, scrapie in sheep & bovine spongiform encephalopathy (BSE) in cattle.