Chapter 4 Viruses
The concept of viruses
Viruses are a unique group of tiny infectious
particles that are obligate parasites of cells,are
not cells but resemble complex molecules
composed of DNA or RNA,Most of them are so
small (0.02-0.3μm) that an electron microscope
is necessary to detect them,
Classification of the viruses,
Viruses
Subviral
agents
Viroids
Prions
Satellites and Deltavirus
Non-cell organism
Characteristics of virions (virus particles),
1） are tiny particles that are ultramicroscopic size,can go through the bacteria filter,
2） are not cell but composed of protein and nucleic acid
3） Nucleic acid can be either DNA or RNA but not both,
4） use themselves nucleic acid to replicate and apply the assembling of viral protein
and nucleic acid to multiply massively,
5） are obligate intracellular parasites and lack enzymes for most metabolic processes
and synthesizing protein,multiply by taking control of host cell’s metabolism and
synthetic machinery,
6） are abiotic macromolecular and contain the infectivity for a long time outside of
the host cell,
7） are not sensitive to antibiotic but sensitive to interferon,
8） Some of them can be integrated into the host cell’s genome in provirus,
Significance of virus research,
1) Control and eliminate the aversive viruses,which do harm to the
human health and the domestic animals,The national economy is
severely affected by the virus diseases,In fermentation
industry,contamination of phages will have bad influence in the
fermentation production,
2) By study of the virus,we can upgrade the species,cultivate live
virus vaccine strain,protect the ecological environment,apply
virus as insecticida and use them as vectors for gene engineering,
Section 1.The General structure and
Chemical Composition of Viruses
1.Size of the virus particle
Most of them are so small and vary widely （ 0.02-0.3μm） that an electron
microscope is necessary to detect them,their size relegates them to the realm
of the ultramicroscopic,
The tiniest circoviridae,17nm in diameter,is a little bigger than ribosome,
while the maximum Poxviruses,200nm in diameter,is as big as the minimum
bacteria,even to be detected by light microscope,
2,Structure of viruses
The mode of naked nucleocapsid virus 有囊膜病毒模式结构
Capsid
capsomere
Nucleic
acid
ca
ps
id
Spike
Virus
particle
Nucleocapsid
(Basic Unit)
Envelopewith
Spike
(nonbasic Unit）
Centrel
core
Capsid
DNA/RNA
Genome:Double/single strand
sectile/unsectile
多肽
（ 结构亚单位 ）
Capsomer
Component of virus
particle
3,Morphology and symmetry of viruses
3.1 Morphology of Virus
3.2 Architecture type of Virus
helical symmetry
icosahedral symmetry
complex symmetry
Naked
envelope
habditiform,TMV etc
silkiness,Bacterium coli M13phage etc
coiling,Influenza virus etc
bullet,Wut virus etc
Envelope
Naked
envelope
Envelope,herper virus
small,Poliovirus
big,adenovirus
Envelope, poxvirus（ Brick shape）
Naked envelope,Bacterium coli T phage (tadpole shape)
Architecture
type of Virus
1,Helical symmetry
A typical virus helical symmetry is the
tobacco mosaic virus( TMV),This is a RNA
virus in which the 2130 protein subunits (each
158 amino acids in length) are arranged in
helix,In TMV,the helix has 16 ? subunits
per turn and the overall dimensions of the
virus particles are 18*300 nm,The lengths of
helical viruses are determined by the lengths
of the nucleic acid,but the width of the
helical viruses particles is determined by the
size and packing of the protein subunits,
2,Icosahedral symmetry
Take adenovirus for example,The icosahedral capsid (70 to 100 nm) is made up of 252
capsomeres,240 hexons forming the faces and 12 pentons at the vertices,Each penton bears
a slender fiber and is composed of a pentamer(Ⅲ ) and a trimer fibrin(Ⅳ ) but each hexamere
is not hexamer but trimer constituted by three 110K polypeptide Ⅱ,
Sense and antisense single strand,
sense（ +）,identical to the mRNA base sequence,
antisense（ -）,complementary to the mRNA base sequence,
Sense/antisence（ ± ）,complementary double strands,
+RNA,as mRNA template for translation to protein,
-RNA,complementary to +RNA,can not as mRNA template for translation to
protein,
+DNA,complementary to-DNA,not as template for transcription to mRNA,
-DNA,as template for transcription to mRNA。
Segmentation and amerism,
Some RNA viruses are not strictly ?antisense' but ambisense,since they are
part (-)sense & part (+)sense,
4,Proteins of viruses
1.Constitutive protein,constitute the morphological maturity
and infectious virus particle,including capsid,peplos and
enzymes accounting for 30-70% per particle,
（ 1） capsid protein,the protein covering of a virus?s
nucleic acid core,exhibit symmetry due to the subunits called
capsomers,
Functions of capsid protein,constitutes the virus capsid
to shield the nucleic acid; naked virus?s capsid participates
the absorption,penetration,determination the host tropsim
and surface antigen,
(2） peplomere protein,are composed of peplos glycoprotein
and matrix protein,located in peplos surface,
Peplos glycoprotein,are the chief surface antigen (SA) of virus;
most of them are virus attachment protein by interaction with cell
receptor to switch to the infection,
Some of them may mediate the penetration of virus,agglutinate
vertebrate animal akaryocyte,cell fusion and enzyme activity,
Matrix protein,is the submembrane structure between lipid bilayer
and nucleocapsid for supporting the peplos and virus structure,It can
also mediate the recognition between nucleocapsid and peplos
glycoprotein and is very important in virus budding off,
(3) Virion enzyme,exist in virocapsomer,categorized as follow by
function,
One kind is mediate penetration and release of virus,such as T4
phage lysozyme,flu virus neuramidinase,
Another is involved in virus macromolecule synthesis,such as
retrovirus,hepadnavirus,the dsRNA virus,antisense RNA virus,As
for some complicate viruses,for instance the poxvirus duplicated in
cytoplasm have many enzymes involved in DNA duplication and
RNA transcript fabrication,
2,Non-structure protein (NS protein),it means proteins encoded
by virus genome have function but do not bind the virus particles in
duplicate process,
The quantities and quality of them are dependent on the virus
species,complex of virus genome and the periods of virus
duplication,Mostly NS proteins have enzyme activities and
involved in regulating virus replication and transcription,Recently
data show that part of viruses have the ability to antiapoptosis and
inhibition antigen presentation,For example,the 3ABC protein in
foot and mouth disease virus is used to classify the wild virus and
attentuated vaccine immune,
3,Virus lipoid,virus lipoid is formed from the host cell during the release
of virus,mainly resides in virus peplos,The lipoid accounts for 20-35%
in the structural composition,the poxvirus lipoid is 5% and the rabies
virus is up to 50%,
4.Viral carbohydrate Some of viruses contain a few carbohydrate,It is
present in virus carbohydrate and glucolipide by oligosacharide lateral
chain or mucopolysaccharides,Except for the enveloped viruses ’
glucoprotein ecphyma,some of complex virus particles have internal
glucoprotein or glycosylated capsid protein,Glucoprotein is significant
immunigen,for instance,anti - influenza virus hemagglutinin serum
have conspicuous virus neutralization,
5.Other composition There are some positive ionic compounds(such as
tetramethylenediamine,apermidine,spermine) in some animal viruses,
plant viruses and phage viruses,It is reported that there is metal
positive ion in several plant viruses,These minimal organic positive ion
or inorganic positive ion bind randomly with virus nucleic acid and
affect the conformation of nucleic acid,The combining weight of them
is relevant to the correlated ion concentration in environment and
acquire the unconstant ingredient from environment when virus
assembly,
Section 3 Reproduction and taxnomy
of viruses
1,Principle groups and classification system
Number character
1 Nature of host（ animal,plant,bacteria,insect,mycetes）
2 Nature of nucleic acid（ DNA or RNA； single or double strands；
molecular mass； segmentation or not,how many
segments(RNA virus)； sense or antisense genome
3 Capsid symmetry——icosahedron,helical,complex symmetry
4 With or without envelope,sensitive to ether
5 Diameter of virus particle of nucleocapsid
6 Numbers of icosahedron
7 Immune character
8 Number of genome and genetic map
9 Location of virus in cell duplication
10 DNA replicative intermediate(ssRNA virus)； reverse
11 Mode of release
12 Specific clinical symptom,propagative pathway
International Committee on the Taxonomy of Viruses( ICTV) is the "international court"
of experts that rules on names and relationships of all viruses,but only to the level of
species,,The ICTV virus classification system apply order,family,subfamily,genus and
species as categorization units,Below this level,the nomenclature of serovar,genotype,
toxicity,variant,isolation are determined by received international experts,It is reported
that all the recoganized viruses are categorized into 233 families,1550 species and 204
families are belonged to 64 orders,Since the sixth report,the viruses are categorized into
DNA viruses,DNA and RNA retroviruses and RNA viruses,On the basis of virus evolution
genetics,ICTV set up 3 orders based on part families in the 7th report,which are
Caudovirales,Mononegavirales,Nidovirales, The classification of different genera in a
subfamily is based on the virus’s immunology properties and host specificity,But the
viral specie is a kind of uncertain taxonomical unit,In 1990,ICTV make a definition
that the species is a group of viruses with generation relation and occupancy of
some niche,It also means that,under the preconditions having same family and
genus features,the virus having some similar secondory features but not same are
classified into the same kind if viruses,
Virus Nomenclature,
The principal style changes are that the virus family,subfamily,and genus names
should be capitalized and printed in italics,When such a name is used formally,the
term for the taxon should precede the term for the taxonomic unit,for example,“the
family Bunyaviridae” and,the genus Tospovirus”,When used formally,a virus
species name should also be printed in italics,with the first word of any subsequent
proper noun capitalized,for example,Avian leukosis virus,Lucerne Australian
latent virus,Queensland Kashmir bee virus,Generally,the designation of the
taxonomic unit,species” need not precede the species name,for example,Rous
sarcoma virus need not be written as,the species Rous sarcoma virus”,The first
use of a virus species name in a paper should usually be treated formally and
therefore should appear in italics with the first word capitalized,Subsequent
reference to the same virus should be an accepted acronym,which is not
italicized,for example,AMV for Alfalfa mosaic virus.Virus names presented in tables
should be written formally,The name of a tentative species whose taxonomic status
is uncertain should not be written in italics,but its first word (and any proper nouns)
should be capitalized,
2,Bacteriophage
Phages are a kind of virus that infect protocaryon
microorganism (bacteria,ray fungus and cyanobacteria et al) and
distributes widespread,They are divided into dsRNA virus,ssDNA
virus,dsRNA virus and ssRNA virus without envelope,They are in
the shape of tadpole,microballoons and silk(Fig 4-19),The
quantities and qualities of fermentation badly contaminated by
phages will result in heavy loss,It is extensively used in molecular
biology research,such as the colibacillary λ phage as gene
engineering vector; colibacillary M13 phage as phage display
technique for expression of polypeptide and protein as well as
protein-protein interaction,
Bateriaphage pantomorphia（ source from Richard ）
1.Virulent bacteriaphage and reproductive mode
This kind of phages makes cell release virion by lysis cell
when they penetrate host cell,Therefor they are called virulent
phage,such as T4 phage,
The cycle of virus mutiplication,
The cycle is separated into adsorption,penetration,duplication,assembly
,maturation and release,This process iscalled lytic cycle,
1,Adsorption
2,Penetration
Nucleic acid Type
Nucleic Acid Structure
Virus Examples
Single-Stranded
Double-stranded
Linear,single stranded,positive
strand
Linear,single stranded,negative strand
Linear,single
stranded,segmented,positive strand
Linear,single
stranded,segmented,diploid (two
identical single strands),positive
strand
Linear,single stranded,segmented,
negative strand
Linear,double stranded,segmented
Picornaviruses(polio,rhinoviruses)
,togaviruses,RNAbacteriophage
s,TMV,and most plant viruses
Rhabdoviruses(rabies),paramyxov
-iruses(mumps,measles)
Brome mosaic virus(individual
segments in separate virions)
Retroviruses(Rous sarcoma virus,
human immunodeficiency
virus)
Paramyxoviruses,orthomyxovirus
es(influenza)
Retroviruses,wound-tumor virus
of plants,cytoplasmic
polyhdrosis virus of
insects,phage Ф 6,many
mycoviruses
Types of Viral Nucleic Acids(RNA)
3,Biosynthesis
± DNA +mRNA Translation Proteins
New virions
Transcription
Replication
（ a） The Reproduction of Double-Stranded DNA
（ T4 Bacteriophages）
+DNA
Bacterial
DNA
polymerase ± DNA
(Replicative form)
+DNA
+mRNA
Translation
Transcription
Replication
New virions
Proteins
（ b） The Reproduction of ФX174,a +Strand DNA
＋ RNA ± RNA
(replicative form)
RNA replicase
＋ RNA genomes
Replication Translation
＋ RNA
New virions Virus Proteins
mRNA
activity
（ c） The Reproduction of Single-Stranded RNA
Bacteriophages
Viral replicase
New virions
+RNA Proteins(after processing by host and
virus-coded proteinases
± RNA
Replicative
form
+RNA
（ a） positive single-stranded RNA viruses(picornaviruses)
RNA Animal virus Reproductive Strategies,
RNA-dependent RNA polymerases*
(Transcriptases)
＋ mRNA
New virions
± RNA Proteins
RNA-dependent
RNA polymerase
(Replicase)
± RNA
(b) Double-stranded RNA viruses (reoviruses)
－ RNA ＋ mRNA proteins
RNN-dependent
RNA polymerase
(viral replicase) ± RNA
Replicative
form
－ RNA
RNA-dependent RNA polymerase+
(Transcriptase)
New
virions
（ c） Negative single-stranded RNA viruses (paramyxoviruses-
mumps and measles;orthomyxoviruses-influenza
＋ mRNA
New virions
RNA-dependent DNA polymerase
Reverse transcriptase+
Proteins
+RNA
Ribonuclease H
Component of
RT
Reverse
transcriptase+
+RNA/-DNA Proviral DNA ± DNA -DNA
+RNA（ virion）
Transcription
(d )Retroviruses (Rous sarcoma virus,HIV)
4,Assembly and
maturation
5.Release(lysis)
（ 1 ） Eclipse period, it is the period from the virus
penetrating host cell to the releasing of virion,
Latent prophase or called as eclipse phase means the
period during which virus nucleic acid penetrates host cell and
assembly the first virion,At that time there are not complete,
infectious mature virion,
Latency anaphase,During this period,the titer of active
virus particles inside cell rises dramatically,but are not release
from host cell,which marks the end of latency,
（ 2） Burst phase,During this period,the number of virion
increases rapidly with lysis of host cell,
（ 3） Platform phage,It is the period that all of the host
cells are lysated and the valence of virus reaches the apogee,
Two characteristic data
Eclipse period:,it is the minimum course from the
penetration of virus to virion release,It is different from
different viruses,such as phage’s eclipse period is counted by
minute,animal and plant viruses are by hour or day,
Burst size,it is the average number of released virion,which is
equal to the number of all the released virion divided by
infected cell numbers in eclipse period and is also equal to the
ratio between viral valence in stable phage and viral valence in
eclipse period,Determined by one step growth curve,the
phage’s burst size is generously from a few to a few hundred
and plant and animal viruses’ burst size are up to a few
hundred even to ten thousand,
3.Template phage and lysogeny
Some of phages integrate their genome into the host
genome and duplicate along with host material at the time
of cell division but do not induce host cell lysis after they
penetrating the host cell,Therefore, they are called
temperate phage,The concurrent state is called lysogeny,
the infected cells called lysogen,the virus integrated into
cell genome called as prophage,
细胞反复分裂
溶原途径
裂解途径
The mode of λphage lysis
and lysogenic pathway
诱导
The characters of of lysogeny,
（ 1） lysogenic conversion,The prophage will result in
the phenotypic alternation of host cell,which is not directly
related to the completion of life cycle and are known as
lysogenic conversion,
（ 2） Immunity,Although a lysogenic bacterium may be
susceptible to other viruses,it can not be infected by virus
particles of the type for which it is lysogenic,The λ repressor
protein expressed by prophage gene can inhibits the
duplication of virus in host cell,
3.Pathogenicity conversion,Some of prophages result
in pathogenicity conversion,For instance,Corynebecterium
diphtheriae and Clostridium botulinum are not toxic to
human,Once infected by template phages,they are converted
into toxogenic strains,resulting in damage to infected tissue
and diphtherea and botulism toxic symtom,
4.Lysogeny is reversible, The prophages can be
reactivated spontaneously of under outside stimulus,and
enter lytic cycle with lysis of host cells,The probability of
this process is very low(1/10000-1/100000 or so）,
3.Vertebrate animal virus
There many virus parasitize in all kind s of vertebrate
animals,but only those associated with human healthy
and domestice livestock poultry are investigated much
more,There are more than 300 kind of viruses associated
with human health and more than 900 with other
vertebrate animals,70-80% of human contagious diseases
are caused by viruses,The vertebrate animals viruses are
categorized into dsRNA,ssDNA,daDNA,dsRNA and
ssRNA,Some of them have envelope or not; Some of
them have spike protein outside envelope or not,
1.Vertebrate animal
Viruses multiplication 1.Adsorption.The virus
attaches to its host cell by
specific binding of its
spikes to cell receptors,2.Penetration,The virus is engulfed into a vesicle and
its envelope is uncoated,
thereby freeing the viral
RNA into cell cytoplasm,
Duplication,Under the control of
viral genes,the cell synthesizes
the basic components of new
viruses,RNA molecule,
capsomers,spikes,
4.Assembly,Viral
spike proteins are
inserted into the
cell membrane for
viral envelope;
nucleocapsid id
formed form RNA
and capsomers,
5,Release,Enveloped viruses
bud off of the membrane,
carrying away an envelope
with spikes,This complete
virus of virion id ready to
infect another cell,
The mode by which animal
viruses adsorb to the host
cell membrane,
1） Naked virus direct
penetration,
2） Virus with envelope
penetrates by endocytosis,
3） Virus with envelope penetrate by fusion of cell membrane
The mode by which
animal viruses penetrate
The mode by which animal viruses bud
off and release,
2.Vertebrate animal virus persistence
Some of virus do not kill host cell nut integrated its
DNA into host genome or exist in host cell as plasmids
after infecting the host, This kind of viral nucleic acid
is called as protovirus,
The characters of persistence,
1） The persistent infected animal cells can keep normal function for many years,
2)The virus dose not duplicate and stay in persistence state befoe re activated,
3） The expression of integrated protovirus gene sometimes assign host cell new
features,
4） Protoviruses are activated by environmental agents such as UV,then they are
duplicated,matured and released,departing from the chrosome,
5)Some herper virus can,turn off/on” multiplication of virion,Under stimulus such as
cold,heat,press or immune suppression,herper virus staying in organism cell all the
life time will be reactivated to duplication and lysis of host cell,resulting in deasees,
then come back to persistence state,Thereby,this kind of persistence os also celled as
latency,
6） Some viruses lead to slow virus infections,Measles virus can hidden in brain
cells for mang years,causing progressive damage and loss of function,
3,Virus and tumorgenesis
Tumor,An abnormal mass of tissue that results from excessive cell
division,Tumors perform no useful body function,They may be either
begin or malignat,Benign tumors,do not invade neighboring tissues
and do not seed metastases,but may locally grow to great size,They
usually do not return after surgical removal,Malignant tumors are
called cancer:,Cancer has the potential to invade and destroy
neighboring tissues and create mtastases,There many complex
factors,such as physical,chemical and biological factors,causing
the human and vertebrate animal tumorgenesis,
Some animal viruses enter their host cell and permanently alter its
genetic material,leading to cancer,These viruses are termed
oncovirus those are mainly dsRNA viruses and retroviruses,Their
effect on the cell is called transformation,
It is estimated that 15 % of human cancers are caused by
virus infection,
Some human cancers which may be caused by viruses
Oncovirus cancer type
Epstein-Barr(EB) Burkitt leucoma
（ epstein-barr virus）
hepatitis b virus hepatoma
hepatitis c virus hepatoma
retrovirus many animals leucemia
htlv huaman adenolymphoma
papovavirus each animal tumors; huamnuternine
cervix cancer
Conspicuous character of oncovirus,
can integrated its nucleic acid into host
cell genome like lysogenic phage,The
transformed cells’ growth rate increases uickly,
The chromosome and cell surface molecules
are changed,The cell can infinite division and
lost the contact
The mechanism of cell transformation by oncovirus
（ 1） The integration of protovirus,
（ 2） The expression of specific gene related with transformation,
These special transformation-related gene is termed Viral
oncogenes,which is homologue of human and vertebrate animals
proto-oncogene and is mutation of normal cell proto-oncogene,It is
considered that the proto-oncogenes in normal host cell are very
important regulating genes,which encoding proteins are very
important in regulating cell proliferation and multiplication,The
mutation proteins encoded by mutant proto-oncogenes will lead to
cell aggressive growth,Some of human cancers are induced by
several proto-oncogenes mutating at the same time,such as colon
carcinima,Viruses may also induce cell abnormal growth,For
example,the tumor viruses alter the proto-oncogenes activities or
abnormal expression,therefor resulting in cell transformation and
tumorgenesis,
4.Emerging virus
Emerging viruses are the viruses those are regional low lever of
infection and have interspecies barrier enlarge their host to other
species,resulting in wide-ranging human infectious diseases,Such
as ebola virus,lassa virus,AIDS virus,Recently emerging SARS
virus and birds influenza virus are belonged to this kind of virus,
We should pay much attention to these defection diseases caused by
them,
The causes of emerging virus,
1） The environment are destroyed by human activity,。
2） The modern transportation,development of tourism and
large scale population migration,
3） The mutation of virus gene change the host range,
4） The intimate contact between human and animals,
References
Prescott LM,Harley JP,and Klein DA.,Microbiology (5th ed.),Higher education
press and McGraw-Hill Companies,Inc.2002
Michael TM,John MM,Jack P,Brock.,Biology of Micoorganisms,International
edition,Pearson Education,Inc.2003
Talaro K,P,Foundations in Microbiology (Fifth Edition),Higher education press
and McGraw-Hill Companies,Inc.2005
Zhou De-qing,Microbiology textbook,second edition,high education publishing
house,2002
The concept of viruses
Viruses are a unique group of tiny infectious
particles that are obligate parasites of cells,are
not cells but resemble complex molecules
composed of DNA or RNA,Most of them are so
small (0.02-0.3μm) that an electron microscope
is necessary to detect them,
Classification of the viruses,
Viruses
Subviral
agents
Viroids
Prions
Satellites and Deltavirus
Non-cell organism
Characteristics of virions (virus particles),
1） are tiny particles that are ultramicroscopic size,can go through the bacteria filter,
2） are not cell but composed of protein and nucleic acid
3） Nucleic acid can be either DNA or RNA but not both,
4） use themselves nucleic acid to replicate and apply the assembling of viral protein
and nucleic acid to multiply massively,
5） are obligate intracellular parasites and lack enzymes for most metabolic processes
and synthesizing protein,multiply by taking control of host cell’s metabolism and
synthetic machinery,
6） are abiotic macromolecular and contain the infectivity for a long time outside of
the host cell,
7） are not sensitive to antibiotic but sensitive to interferon,
8） Some of them can be integrated into the host cell’s genome in provirus,
Significance of virus research,
1) Control and eliminate the aversive viruses,which do harm to the
human health and the domestic animals,The national economy is
severely affected by the virus diseases,In fermentation
industry,contamination of phages will have bad influence in the
fermentation production,
2) By study of the virus,we can upgrade the species,cultivate live
virus vaccine strain,protect the ecological environment,apply
virus as insecticida and use them as vectors for gene engineering,
Section 1.The General structure and
Chemical Composition of Viruses
1.Size of the virus particle
Most of them are so small and vary widely （ 0.02-0.3μm） that an electron
microscope is necessary to detect them,their size relegates them to the realm
of the ultramicroscopic,
The tiniest circoviridae,17nm in diameter,is a little bigger than ribosome,
while the maximum Poxviruses,200nm in diameter,is as big as the minimum
bacteria,even to be detected by light microscope,
2,Structure of viruses
The mode of naked nucleocapsid virus 有囊膜病毒模式结构
Capsid
capsomere
Nucleic
acid
ca
ps
id
Spike
Virus
particle
Nucleocapsid
(Basic Unit)
Envelopewith
Spike
(nonbasic Unit）
Centrel
core
Capsid
DNA/RNA
Genome:Double/single strand
sectile/unsectile
多肽
（ 结构亚单位 ）
Capsomer
Component of virus
particle
3,Morphology and symmetry of viruses
3.1 Morphology of Virus
3.2 Architecture type of Virus
helical symmetry
icosahedral symmetry
complex symmetry
Naked
envelope
habditiform,TMV etc
silkiness,Bacterium coli M13phage etc
coiling,Influenza virus etc
bullet,Wut virus etc
Envelope
Naked
envelope
Envelope,herper virus
small,Poliovirus
big,adenovirus
Envelope, poxvirus（ Brick shape）
Naked envelope,Bacterium coli T phage (tadpole shape)
Architecture
type of Virus
1,Helical symmetry
A typical virus helical symmetry is the
tobacco mosaic virus( TMV),This is a RNA
virus in which the 2130 protein subunits (each
158 amino acids in length) are arranged in
helix,In TMV,the helix has 16 ? subunits
per turn and the overall dimensions of the
virus particles are 18*300 nm,The lengths of
helical viruses are determined by the lengths
of the nucleic acid,but the width of the
helical viruses particles is determined by the
size and packing of the protein subunits,
2,Icosahedral symmetry
Take adenovirus for example,The icosahedral capsid (70 to 100 nm) is made up of 252
capsomeres,240 hexons forming the faces and 12 pentons at the vertices,Each penton bears
a slender fiber and is composed of a pentamer(Ⅲ ) and a trimer fibrin(Ⅳ ) but each hexamere
is not hexamer but trimer constituted by three 110K polypeptide Ⅱ,
Sense and antisense single strand,
sense（ +）,identical to the mRNA base sequence,
antisense（ -）,complementary to the mRNA base sequence,
Sense/antisence（ ± ）,complementary double strands,
+RNA,as mRNA template for translation to protein,
-RNA,complementary to +RNA,can not as mRNA template for translation to
protein,
+DNA,complementary to-DNA,not as template for transcription to mRNA,
-DNA,as template for transcription to mRNA。
Segmentation and amerism,
Some RNA viruses are not strictly ?antisense' but ambisense,since they are
part (-)sense & part (+)sense,
4,Proteins of viruses
1.Constitutive protein,constitute the morphological maturity
and infectious virus particle,including capsid,peplos and
enzymes accounting for 30-70% per particle,
（ 1） capsid protein,the protein covering of a virus?s
nucleic acid core,exhibit symmetry due to the subunits called
capsomers,
Functions of capsid protein,constitutes the virus capsid
to shield the nucleic acid; naked virus?s capsid participates
the absorption,penetration,determination the host tropsim
and surface antigen,
(2） peplomere protein,are composed of peplos glycoprotein
and matrix protein,located in peplos surface,
Peplos glycoprotein,are the chief surface antigen (SA) of virus;
most of them are virus attachment protein by interaction with cell
receptor to switch to the infection,
Some of them may mediate the penetration of virus,agglutinate
vertebrate animal akaryocyte,cell fusion and enzyme activity,
Matrix protein,is the submembrane structure between lipid bilayer
and nucleocapsid for supporting the peplos and virus structure,It can
also mediate the recognition between nucleocapsid and peplos
glycoprotein and is very important in virus budding off,
(3) Virion enzyme,exist in virocapsomer,categorized as follow by
function,
One kind is mediate penetration and release of virus,such as T4
phage lysozyme,flu virus neuramidinase,
Another is involved in virus macromolecule synthesis,such as
retrovirus,hepadnavirus,the dsRNA virus,antisense RNA virus,As
for some complicate viruses,for instance the poxvirus duplicated in
cytoplasm have many enzymes involved in DNA duplication and
RNA transcript fabrication,
2,Non-structure protein (NS protein),it means proteins encoded
by virus genome have function but do not bind the virus particles in
duplicate process,
The quantities and quality of them are dependent on the virus
species,complex of virus genome and the periods of virus
duplication,Mostly NS proteins have enzyme activities and
involved in regulating virus replication and transcription,Recently
data show that part of viruses have the ability to antiapoptosis and
inhibition antigen presentation,For example,the 3ABC protein in
foot and mouth disease virus is used to classify the wild virus and
attentuated vaccine immune,
3,Virus lipoid,virus lipoid is formed from the host cell during the release
of virus,mainly resides in virus peplos,The lipoid accounts for 20-35%
in the structural composition,the poxvirus lipoid is 5% and the rabies
virus is up to 50%,
4.Viral carbohydrate Some of viruses contain a few carbohydrate,It is
present in virus carbohydrate and glucolipide by oligosacharide lateral
chain or mucopolysaccharides,Except for the enveloped viruses ’
glucoprotein ecphyma,some of complex virus particles have internal
glucoprotein or glycosylated capsid protein,Glucoprotein is significant
immunigen,for instance,anti - influenza virus hemagglutinin serum
have conspicuous virus neutralization,
5.Other composition There are some positive ionic compounds(such as
tetramethylenediamine,apermidine,spermine) in some animal viruses,
plant viruses and phage viruses,It is reported that there is metal
positive ion in several plant viruses,These minimal organic positive ion
or inorganic positive ion bind randomly with virus nucleic acid and
affect the conformation of nucleic acid,The combining weight of them
is relevant to the correlated ion concentration in environment and
acquire the unconstant ingredient from environment when virus
assembly,
Section 3 Reproduction and taxnomy
of viruses
1,Principle groups and classification system
Number character
1 Nature of host（ animal,plant,bacteria,insect,mycetes）
2 Nature of nucleic acid（ DNA or RNA； single or double strands；
molecular mass； segmentation or not,how many
segments(RNA virus)； sense or antisense genome
3 Capsid symmetry——icosahedron,helical,complex symmetry
4 With or without envelope,sensitive to ether
5 Diameter of virus particle of nucleocapsid
6 Numbers of icosahedron
7 Immune character
8 Number of genome and genetic map
9 Location of virus in cell duplication
10 DNA replicative intermediate(ssRNA virus)； reverse
11 Mode of release
12 Specific clinical symptom,propagative pathway
International Committee on the Taxonomy of Viruses( ICTV) is the "international court"
of experts that rules on names and relationships of all viruses,but only to the level of
species,,The ICTV virus classification system apply order,family,subfamily,genus and
species as categorization units,Below this level,the nomenclature of serovar,genotype,
toxicity,variant,isolation are determined by received international experts,It is reported
that all the recoganized viruses are categorized into 233 families,1550 species and 204
families are belonged to 64 orders,Since the sixth report,the viruses are categorized into
DNA viruses,DNA and RNA retroviruses and RNA viruses,On the basis of virus evolution
genetics,ICTV set up 3 orders based on part families in the 7th report,which are
Caudovirales,Mononegavirales,Nidovirales, The classification of different genera in a
subfamily is based on the virus’s immunology properties and host specificity,But the
viral specie is a kind of uncertain taxonomical unit,In 1990,ICTV make a definition
that the species is a group of viruses with generation relation and occupancy of
some niche,It also means that,under the preconditions having same family and
genus features,the virus having some similar secondory features but not same are
classified into the same kind if viruses,
Virus Nomenclature,
The principal style changes are that the virus family,subfamily,and genus names
should be capitalized and printed in italics,When such a name is used formally,the
term for the taxon should precede the term for the taxonomic unit,for example,“the
family Bunyaviridae” and,the genus Tospovirus”,When used formally,a virus
species name should also be printed in italics,with the first word of any subsequent
proper noun capitalized,for example,Avian leukosis virus,Lucerne Australian
latent virus,Queensland Kashmir bee virus,Generally,the designation of the
taxonomic unit,species” need not precede the species name,for example,Rous
sarcoma virus need not be written as,the species Rous sarcoma virus”,The first
use of a virus species name in a paper should usually be treated formally and
therefore should appear in italics with the first word capitalized,Subsequent
reference to the same virus should be an accepted acronym,which is not
italicized,for example,AMV for Alfalfa mosaic virus.Virus names presented in tables
should be written formally,The name of a tentative species whose taxonomic status
is uncertain should not be written in italics,but its first word (and any proper nouns)
should be capitalized,
2,Bacteriophage
Phages are a kind of virus that infect protocaryon
microorganism (bacteria,ray fungus and cyanobacteria et al) and
distributes widespread,They are divided into dsRNA virus,ssDNA
virus,dsRNA virus and ssRNA virus without envelope,They are in
the shape of tadpole,microballoons and silk(Fig 4-19),The
quantities and qualities of fermentation badly contaminated by
phages will result in heavy loss,It is extensively used in molecular
biology research,such as the colibacillary λ phage as gene
engineering vector; colibacillary M13 phage as phage display
technique for expression of polypeptide and protein as well as
protein-protein interaction,
Bateriaphage pantomorphia（ source from Richard ）
1.Virulent bacteriaphage and reproductive mode
This kind of phages makes cell release virion by lysis cell
when they penetrate host cell,Therefor they are called virulent
phage,such as T4 phage,
The cycle of virus mutiplication,
The cycle is separated into adsorption,penetration,duplication,assembly
,maturation and release,This process iscalled lytic cycle,
1,Adsorption
2,Penetration
Nucleic acid Type
Nucleic Acid Structure
Virus Examples
Single-Stranded
Double-stranded
Linear,single stranded,positive
strand
Linear,single stranded,negative strand
Linear,single
stranded,segmented,positive strand
Linear,single
stranded,segmented,diploid (two
identical single strands),positive
strand
Linear,single stranded,segmented,
negative strand
Linear,double stranded,segmented
Picornaviruses(polio,rhinoviruses)
,togaviruses,RNAbacteriophage
s,TMV,and most plant viruses
Rhabdoviruses(rabies),paramyxov
-iruses(mumps,measles)
Brome mosaic virus(individual
segments in separate virions)
Retroviruses(Rous sarcoma virus,
human immunodeficiency
virus)
Paramyxoviruses,orthomyxovirus
es(influenza)
Retroviruses,wound-tumor virus
of plants,cytoplasmic
polyhdrosis virus of
insects,phage Ф 6,many
mycoviruses
Types of Viral Nucleic Acids(RNA)
3,Biosynthesis
± DNA +mRNA Translation Proteins
New virions
Transcription
Replication
（ a） The Reproduction of Double-Stranded DNA
（ T4 Bacteriophages）
+DNA
Bacterial
DNA
polymerase ± DNA
(Replicative form)
+DNA
+mRNA
Translation
Transcription
Replication
New virions
Proteins
（ b） The Reproduction of ФX174,a +Strand DNA
＋ RNA ± RNA
(replicative form)
RNA replicase
＋ RNA genomes
Replication Translation
＋ RNA
New virions Virus Proteins
mRNA
activity
（ c） The Reproduction of Single-Stranded RNA
Bacteriophages
Viral replicase
New virions
+RNA Proteins(after processing by host and
virus-coded proteinases
± RNA
Replicative
form
+RNA
（ a） positive single-stranded RNA viruses(picornaviruses)
RNA Animal virus Reproductive Strategies,
RNA-dependent RNA polymerases*
(Transcriptases)
＋ mRNA
New virions
± RNA Proteins
RNA-dependent
RNA polymerase
(Replicase)
± RNA
(b) Double-stranded RNA viruses (reoviruses)
－ RNA ＋ mRNA proteins
RNN-dependent
RNA polymerase
(viral replicase) ± RNA
Replicative
form
－ RNA
RNA-dependent RNA polymerase+
(Transcriptase)
New
virions
（ c） Negative single-stranded RNA viruses (paramyxoviruses-
mumps and measles;orthomyxoviruses-influenza
＋ mRNA
New virions
RNA-dependent DNA polymerase
Reverse transcriptase+
Proteins
+RNA
Ribonuclease H
Component of
RT
Reverse
transcriptase+
+RNA/-DNA Proviral DNA ± DNA -DNA
+RNA（ virion）
Transcription
(d )Retroviruses (Rous sarcoma virus,HIV)
4,Assembly and
maturation
5.Release(lysis)
（ 1 ） Eclipse period, it is the period from the virus
penetrating host cell to the releasing of virion,
Latent prophase or called as eclipse phase means the
period during which virus nucleic acid penetrates host cell and
assembly the first virion,At that time there are not complete,
infectious mature virion,
Latency anaphase,During this period,the titer of active
virus particles inside cell rises dramatically,but are not release
from host cell,which marks the end of latency,
（ 2） Burst phase,During this period,the number of virion
increases rapidly with lysis of host cell,
（ 3） Platform phage,It is the period that all of the host
cells are lysated and the valence of virus reaches the apogee,
Two characteristic data
Eclipse period:,it is the minimum course from the
penetration of virus to virion release,It is different from
different viruses,such as phage’s eclipse period is counted by
minute,animal and plant viruses are by hour or day,
Burst size,it is the average number of released virion,which is
equal to the number of all the released virion divided by
infected cell numbers in eclipse period and is also equal to the
ratio between viral valence in stable phage and viral valence in
eclipse period,Determined by one step growth curve,the
phage’s burst size is generously from a few to a few hundred
and plant and animal viruses’ burst size are up to a few
hundred even to ten thousand,
3.Template phage and lysogeny
Some of phages integrate their genome into the host
genome and duplicate along with host material at the time
of cell division but do not induce host cell lysis after they
penetrating the host cell,Therefore, they are called
temperate phage,The concurrent state is called lysogeny,
the infected cells called lysogen,the virus integrated into
cell genome called as prophage,
细胞反复分裂
溶原途径
裂解途径
The mode of λphage lysis
and lysogenic pathway
诱导
The characters of of lysogeny,
（ 1） lysogenic conversion,The prophage will result in
the phenotypic alternation of host cell,which is not directly
related to the completion of life cycle and are known as
lysogenic conversion,
（ 2） Immunity,Although a lysogenic bacterium may be
susceptible to other viruses,it can not be infected by virus
particles of the type for which it is lysogenic,The λ repressor
protein expressed by prophage gene can inhibits the
duplication of virus in host cell,
3.Pathogenicity conversion,Some of prophages result
in pathogenicity conversion,For instance,Corynebecterium
diphtheriae and Clostridium botulinum are not toxic to
human,Once infected by template phages,they are converted
into toxogenic strains,resulting in damage to infected tissue
and diphtherea and botulism toxic symtom,
4.Lysogeny is reversible, The prophages can be
reactivated spontaneously of under outside stimulus,and
enter lytic cycle with lysis of host cells,The probability of
this process is very low(1/10000-1/100000 or so）,
3.Vertebrate animal virus
There many virus parasitize in all kind s of vertebrate
animals,but only those associated with human healthy
and domestice livestock poultry are investigated much
more,There are more than 300 kind of viruses associated
with human health and more than 900 with other
vertebrate animals,70-80% of human contagious diseases
are caused by viruses,The vertebrate animals viruses are
categorized into dsRNA,ssDNA,daDNA,dsRNA and
ssRNA,Some of them have envelope or not; Some of
them have spike protein outside envelope or not,
1.Vertebrate animal
Viruses multiplication 1.Adsorption.The virus
attaches to its host cell by
specific binding of its
spikes to cell receptors,2.Penetration,The virus is engulfed into a vesicle and
its envelope is uncoated,
thereby freeing the viral
RNA into cell cytoplasm,
Duplication,Under the control of
viral genes,the cell synthesizes
the basic components of new
viruses,RNA molecule,
capsomers,spikes,
4.Assembly,Viral
spike proteins are
inserted into the
cell membrane for
viral envelope;
nucleocapsid id
formed form RNA
and capsomers,
5,Release,Enveloped viruses
bud off of the membrane,
carrying away an envelope
with spikes,This complete
virus of virion id ready to
infect another cell,
The mode by which animal
viruses adsorb to the host
cell membrane,
1） Naked virus direct
penetration,
2） Virus with envelope
penetrates by endocytosis,
3） Virus with envelope penetrate by fusion of cell membrane
The mode by which
animal viruses penetrate
The mode by which animal viruses bud
off and release,
2.Vertebrate animal virus persistence
Some of virus do not kill host cell nut integrated its
DNA into host genome or exist in host cell as plasmids
after infecting the host, This kind of viral nucleic acid
is called as protovirus,
The characters of persistence,
1） The persistent infected animal cells can keep normal function for many years,
2)The virus dose not duplicate and stay in persistence state befoe re activated,
3） The expression of integrated protovirus gene sometimes assign host cell new
features,
4） Protoviruses are activated by environmental agents such as UV,then they are
duplicated,matured and released,departing from the chrosome,
5)Some herper virus can,turn off/on” multiplication of virion,Under stimulus such as
cold,heat,press or immune suppression,herper virus staying in organism cell all the
life time will be reactivated to duplication and lysis of host cell,resulting in deasees,
then come back to persistence state,Thereby,this kind of persistence os also celled as
latency,
6） Some viruses lead to slow virus infections,Measles virus can hidden in brain
cells for mang years,causing progressive damage and loss of function,
3,Virus and tumorgenesis
Tumor,An abnormal mass of tissue that results from excessive cell
division,Tumors perform no useful body function,They may be either
begin or malignat,Benign tumors,do not invade neighboring tissues
and do not seed metastases,but may locally grow to great size,They
usually do not return after surgical removal,Malignant tumors are
called cancer:,Cancer has the potential to invade and destroy
neighboring tissues and create mtastases,There many complex
factors,such as physical,chemical and biological factors,causing
the human and vertebrate animal tumorgenesis,
Some animal viruses enter their host cell and permanently alter its
genetic material,leading to cancer,These viruses are termed
oncovirus those are mainly dsRNA viruses and retroviruses,Their
effect on the cell is called transformation,
It is estimated that 15 % of human cancers are caused by
virus infection,
Some human cancers which may be caused by viruses
Oncovirus cancer type
Epstein-Barr(EB) Burkitt leucoma
（ epstein-barr virus）
hepatitis b virus hepatoma
hepatitis c virus hepatoma
retrovirus many animals leucemia
htlv huaman adenolymphoma
papovavirus each animal tumors; huamnuternine
cervix cancer
Conspicuous character of oncovirus,
can integrated its nucleic acid into host
cell genome like lysogenic phage,The
transformed cells’ growth rate increases uickly,
The chromosome and cell surface molecules
are changed,The cell can infinite division and
lost the contact
The mechanism of cell transformation by oncovirus
（ 1） The integration of protovirus,
（ 2） The expression of specific gene related with transformation,
These special transformation-related gene is termed Viral
oncogenes,which is homologue of human and vertebrate animals
proto-oncogene and is mutation of normal cell proto-oncogene,It is
considered that the proto-oncogenes in normal host cell are very
important regulating genes,which encoding proteins are very
important in regulating cell proliferation and multiplication,The
mutation proteins encoded by mutant proto-oncogenes will lead to
cell aggressive growth,Some of human cancers are induced by
several proto-oncogenes mutating at the same time,such as colon
carcinima,Viruses may also induce cell abnormal growth,For
example,the tumor viruses alter the proto-oncogenes activities or
abnormal expression,therefor resulting in cell transformation and
tumorgenesis,
4.Emerging virus
Emerging viruses are the viruses those are regional low lever of
infection and have interspecies barrier enlarge their host to other
species,resulting in wide-ranging human infectious diseases,Such
as ebola virus,lassa virus,AIDS virus,Recently emerging SARS
virus and birds influenza virus are belonged to this kind of virus,
We should pay much attention to these defection diseases caused by
them,
The causes of emerging virus,
1） The environment are destroyed by human activity,。
2） The modern transportation,development of tourism and
large scale population migration,
3） The mutation of virus gene change the host range,
4） The intimate contact between human and animals,
References
Prescott LM,Harley JP,and Klein DA.,Microbiology (5th ed.),Higher education
press and McGraw-Hill Companies,Inc.2002
Michael TM,John MM,Jack P,Brock.,Biology of Micoorganisms,International
edition,Pearson Education,Inc.2003
Talaro K,P,Foundations in Microbiology (Fifth Edition),Higher education press
and McGraw-Hill Companies,Inc.2005
Zhou De-qing,Microbiology textbook,second edition,high education publishing
house,2002
