Chapter 3
virus and subvirus
Section 1
Virus structure
Euvirus,at least contains two components—— nucleic
acid and
protein
Subvirus,molecular pathogen includes：
viroid（类病毒） ——independent infectious RNA
only
virusoid（拟病毒） ——non-independent infectious
RNA only
prion（朊病毒） ——protein only
Viruses are obligate intracellular parasites which can
only be viewed with the aid of an electron microscope,
They vary in size from approximately 20-200 nm,In order
to persist in the environment they must be capable of
being passed from host to host and of infecting and
replicating in susceptible host cells,
1,definitions
A virus particle has thus been defined
as a structure which has evolved to
transfer nucleic acid from one cell to
another,
The nucleic acid found in the
particle is either DNA or RNA,is
single- or double-stranded and linear
or segmented,In some cases the
nucleic acid may be circular,
The simplest of virus particles consists of a protein
coat (sometimes made up of only one type of protein
which is repeated hundreds of times) which surrounds
a strand of nucleic acid.
More complicated viruses have their nucleic acid
surrounded by a protein coat which is further
engulfed in a membrane structure,an envelope
consisting of virally coded glycoproteins derived
from one of several regions within the infected cell
during the maturation of the virus particle,The
genetic material of these complex viruses encodes
for many dozens of virus specific proteins.
The complete fully assembled virus is termed the
virion,It may have a glycoprotein envelope which has
peplomers (包膜粒 )(projections,spike突起,刺突 ) which
form a?fringe边缘? around the particle,The protein coat
surrounding the nucleic acid is referred to as the
capsid,The capsid is composed of morphological
units or capsomers（衣壳粒）,The type of capsomer
depends on the overall shape of the capsid,but in the
case of icosahedral capsids the capsomers are either
pentamers or hexamers（五邻体或六邻体）,The
combined nucleic acid-protein complex which
comprises the genome is termed the nucleocapsid（核衣壳）,which is often enclosed in a core within the
virion.
Nucleic acid （ DNA or RNA）
nucleocapsid
Viron Capsid （ protein）
Envelope （ glycoprotein）
Structure of the virus
Fig,(a) unenveloped/helical (tobacco mosaic virus),(b) unenveloped/icosahedral
(adenovirus); (c) enveloped/helical (paramyxovirus),(d) enveloped/ icosahedral
(herpesvirus),
180nm
Diagrammatic representation of the structure of virus particles
RNA
Reverse
transcriptase
Lipid
membrane
100nm
Rabies virus(l)and HIV(R) have tight-fitting envelopes.
herpes simplex (l) has a loose-fitting envelope,
whereas adenovirus (R) is non-enveloped,
Diagrammatic representation of the structure of virus particles
Glycoprotein
envelope
Icosahedral
capsid
containing
DNA
90nm
45nm
While the electron microscope (EM) had been known for many
years,the invention of the negative-staining technique in 1959
revolutionized studies on virus structure,In negative-contrast EM,
virus particles are mixed with a heavy metal solution (e.g,sodium
phosphotungstate磷钨酸盐 ) and dried onto a support film,The
stain provides an electron-opaque background against which the
virus can be visualized。
2,Methods of study（ 1）
Negative-staining
technique
Observation under the electron microscope has thus
allowed the definition of virus morphology at the 50-
77A resolution level,In addition,negative staining of
thin sections of infected cells has allowed definition of
structures which appear during virus maturation and
their interactions with cellular proteins,
Methodes of study （ 2）
Electron
microscopy
Immunoelectron microscopy is used to study
those viruses which may be present in low
concentrations or grow poorly in tissue culture
(e.g,Norwalk virus),These clumps of virus are
more readily observed,
Methods of study（ 3）
Immunoelectron
microscopy
Electron cryomicroscopy （电子低温显微术）
reduces the risk of seeing artifacts as may be
unavoidable by negative staining,High
concentrations of virus are rapidly,frozen in liquid
ethane（乙烷） while on carbon grids,Electron
micrographs can be digitized and three-dimensional
reconstruction performed,Resolutions of 9A have
been achieved using this method,
Electron
cryomicroscopy
Methods of study（ 4）
X-ray diffraction of virus crystals is the ultimate in
determining the ultrastructure of virion morphology,（是对病毒形态和超显微结构分析的主要方法） At present,only simple
viruses can be crystallized,More complex viruses are
analyzed by attempting to form crystals of sub-particular
molecules,The X-ray diffraction pattern of the virion particle
allows mathematical processing,which can predict the
molecular configuration（分子构型） of the virus particle,
X-ray
diffraction
Methods of study（ 5）
Summarize
methods of studying
Negative-staining technique
Electron microscopy
Immunoelectron microscopy
Electron cryomicroscopy
X-ray diffraction
Three-dimensional reconstruction of an
icosahedrally symmetric virus particle.(一个二十面体对称病毒粒子的三维重建 )
Helical symmetry can be loosely
described as having a?spiral staircase?
structure,The structure has an obvious
axis down the center of the helix,The
subunits are placed between the turns of
the nucleic acid,A diagram of such a
structure (tobacco mosaic virus) is
shown in the left Fig.,Animal viruses with
a similar capsid structure include
measles,rabies and influenza,
3,Virus symmetry（ helical）
The capsids of virions tend to have one of two
symmetries ——helical or cuboid,
Most animal viruses have spherical or cuboid symmetry,
Obtaining a true sphere is not possible for such structures and
hence subunits come together to produce a cuboid structure
which is very close to being spherical,
Virus symmetry （ cuboid）
The 'closed shell' capsid is usually based on the structure referred to
as an icosahedron.
A regular icosahedron,formed from assembly of identical subunits,
consists of 20 equilateral triangular faces,30 edges and 12 vertices
and exhibits 2-,3- and 5-fold symmetry,
The minimum number of capsomers required to construct an
icosahedron is 12,each composed of five identical subunits,Many
viruses have more than 12,
Diagrammatical representation of isosahedral symmetry
Although in adenoviruses projecting fibers are also present,
which distinguishes this capsid from that of other viruses,The
maturation and assembly of these structures is very complex;
indeed,much of how it happens is unknown,
Axes of
rotation
Many viruses in addition to having a capsid also contain a
virus-encoded envelope,Most enveloped viruses bud from a
cellular membrane (plasma membrane,e.g,influenza virus,or
nuclear membrane,e.g,herpes simplex virus),Within this
virus lipid / protein bilayer are a number of inserted virus-
encoded glycoproteins,The envelopes can be amorphous
(e.g,the herpes virion) or tightly bound to the capsid (e.g,
HIV),Thus,the lipid of the envelope is derived from the cell,
the glycoprotein being encoded by the virus,Quite how the
process of budding occurs is largely unknown.
4,Virus envelopes
Viruses are obligate intracellular parasites and
vary from 20-200 nm in size,They have varied
shape and chemical composition,but contain
only RNA or DNA,The intact particle is termed a
'virion' which consists of a capsid that may be
enveloped further by a glycoprotein/lipid
membrane,Viruses are resistant to antibiotics,
Key Notes
definitions
Virus morphology has been determined by
electron microscopy (EM) (using negative
staining),thin-section EM (using negative
staining),immunoelectron microscopy (using
negative staining),electron cryo-microscopy
and X-ray crystallography.
Key Notes
Methods of
study
Virus capsids have helical or icosahedral
symmetry,In many cases the capsid is engulfed
by a membrane structure (the virus envelope),
Helical symmetry is seen as protein sub-units
arranged around the virus nucleic acid in an
ordered helical fashion,The icosahedron is a
regular shaped cuboid which consists of
repetitions of many protein sub-units assembled
so as to resemble a sphere.
Key Notes
Virus
symmetry
Virus envelopes are acquired by the capsid as it
buds through nuclear or plasma membranes of the
infected cell,Envelopes may contain a few
glycoproteins,for example,human
immunodeficiency virus (HIV),or many
glycoproteins,for example,Herpes simplex virus
(HSV),The virus envelope contains the receptors,
which allow the particle to attach to and infect the
host cell.
Key Notes
Virus
envelopes
The classification of viruses involves the use
of a wide range of characteristics (morphology,
genome,physicochemical and physical
properties,proteins,antigenic and biological
properties) to place viruses in orders,families,
genera and species.
Section 2 Virus Taxonomy
These are groupings of families of viruses that share common
characteristics.
These are groupings of genera of viruses that share common
characteristics and are distinct from the members of other
families,They are designated by the suffix -viridae.
These are groupings of species of viruses which share common
characteristics,These are designated by the suffix -virus.
These represent a polythetic class of viruses that constitutes a
replicating lineage and occupies a particular ecological niche.
Virus orders
Virus families
Virus genera
Virus species
initial attempts to classify viruses were based on their
pathogenic properties,and the only common feature to many of the
viruses placed together in such groupings was that of organ
tropism (器官趋性 e.g,viruses causing hepatitis or respiratory
disease),There were more important aspects (e.g,virus structure
and composition) which led virologists to believe that these initial
attempts of classification were far from adequate,In the late 1950s
and early 1960s,hundreds of new viruses were beginning to be
isolated and the need for a different classification method became
essential,In 1966 the International Committee on Nomenclature of
Viruses (ICNV) was established at the International Congress of
Microbiology held in Moscow,As the present classification scheme
has evolved,an acceptance of the characteristics to be considered
and their respective weighting has become universal.
In 1995 the sixth report of the ICTV (International
Committee on Taxonomy of Viruses) recorded a
universal taxonomy scheme consisting of one
order,71 families,11 subfamilies and 164 genera
(with more than 4000 members),The system still
contains hundreds of unassigned viruses,
largely because of lack of data,Also,new viruses
are still being discovered.
Viral proteins,coded by the viral genome,are
either structural (capsid,envelope) or non-
structural (e.g,enzymes,oncogenes,inhibitors
of cell macromolecular synthesis and interaction
with MHC presentation),They may be essential
or non-essential in tissue culture replication.
Section C Virus proteins
Structural proteins are studied,following virus purification,using
a range of techniques including,
1,sodium dodecyi sulfate (SDS)-polyacrylamide gel electrophoresis,
2,Western blotting（蛋白质印迹法）,
3,Immunoprecipitation（免疫沉淀法）,
Non-structural proteins are examined by,for example,pulse-
chase experiments（脉冲追踪实验）,use of protease and
glycosylation inhibitors（糖基化抑制剂）,
methodology
Viral proteins are synthesized by the translation of viral
mRNAs on cellular ribosomes,Proteins are often processed
following synthesis (e.g,proteolytic cleavage,glycosylation,
myristylation,acylation and palmitoylation蛋白酶剪切、糖基化、
十四烷基化、酰化作用、十六烷酰化 ),In many viruses,protein
synthesis is controlled at the levels of transcription and
translation,which makes virus replication quite an efficient
process,This control is usually directed by the virus genome.
Protein synthesis
and complexity
Structural proteins are either nucleocapsid,matrix or envelope
proteins,They have a role in protecting the viral genome and in
delivering the genome from one host to another via receptors on
host cells,They also have a major role in the assembly of the virion,
In most viruses,structural proteins are produced in abundance late
in the replicative cycle.
These may be carried in the virion (but are not part of the virion
architecture) where they have enzymic activity which is necessary
for initiating infection,Others are not destined for the virion but
have roles in the infected cell,These roles include switching off
host-cell nucleic acid and protein synthesis,polymerase,protease
and kinase activities,DNA binding activity and gene regulation.
Structural proteins
Non structural proteins
Types of viral genome
Viral genomes are diverse in size,structure
and nucleotide make up,They are linear,circular,
dsDNA,ssDNA,dsRNA,ssRNA,segmented or
non-segmented（分段的或不分段的）,
Section 4 virus nucleic acid
Many viral genomes have been sequenced and the
repertoire of their coding potential determined,
Genomes are studied by a range of techniques
including：
1,restriction enzyme analysis,
2,buoyant density,
3,thermal denaturation,
4,nuclease sensitivity
5,EM.
Techniques of
study
Herpesviruses and adenoviruses have large DNA
genomes which vary in their structures,DNA
viruses often have terminal inverted repeats as
part of their genome structure,They may have
coding capacity for up to 80 virus proteins.
Parvovirus (ssDNA) and polyoma viruses (dsDNA)
are small DNA genomes,The coding capacity
may be increased by use of overlapping genes
and both strands of DNA.
Small DNA viruses
Large DNA viruses
These are either positive sense (e.g,picornaviruses,
coronaviruses/ flaviviruses and togaviruses) or negative
sense (e.g,orthomyxo-viruses,paramyxoviruses and
rhabdo viruses),Positive-sense genome^ act as mRNAs,
negative sense genomes need a cRNA to act as,mRNA.
Segmented viral genomes (e.g,orthomyxoviruses) are
those which are divided into two or more physically
distinct molecules of nucleic acid packaged into a single
virion.
Segmented RNA viruses
Non-segmented RNA viruses
Characterization of the viral genome is based on a
number of parameters,
(1) composition of the nucleic acid (i.e,DNA or
RNA);
(2) size and number of strands;
(3) terminal structures;
(4) nucleotide sequence;
(5) coding capacity;
(6) regulatory signal elements,transcriptional
enhancers,promoters and terminators.
dsDNA genome,pox,herpes,adeno,papova,irido
mRNA Protein
dsDNA dsDNA
(b) ssDNA genome,parvo
mRNA Protein
ssDNA ———— > dsDNA Assembly
ssDNA
(c) ss/dsONA genome using ssRNA intermediate,hepadna
ss/dsDNA mRNA ————? Protein ———— > Assembly
dsDNA ss/dsDNA
,Protein
(d) dsRNA genome,reo,birna
Protein
dsRNA —— r mRNA
' Assembly (dsRNA)
Assembly
(g) ssRNA genome using ds DNA intermediate,retro
ssRNA ———— >,dsRNA ——— >,Integration ——?,mRNA
a(e) +sense ssRNA genome; picorna,calici,corona,toro,toga
Protein ^ —,____(cleavage)
^
+RNA +RNA
-RNA
(f) -sense ssRNA genome,orthomyxo,paramyxo,rhabdo,filo
(bunya,arena)
^ Protein ~^ -RNA ————— >? +RNA ^ ^ Assembly
^^- -RNA ^
The complexity and range of virus types is echoed in the various strategies
they adopt in their replicative cycles,
Viruses,as obligate intracellular parasites,must attach to or enter host
cells in order to undergo a 'reproductive' cycle.
This cycle is highly dependent on the metabolic machinery of the cell,
which in most cases the virus takes over and orchestrates towards its own
replication,usually inhibiting host-cell protein and nucleic acid synthesis,
The outcome is the production of hundreds of progeny virions which leave the
infected cell (by lysis or budding),killing the cell and spreading to infect more
host cells and tissues,This replicative or growth cycle can be analyzed in
tissue culture cells and is often referred to as the one-step growth cycle,
The cycle has a number of stages - attachment and penetration,nucleic
acid synthesis and tran scription,protein synthesis,maturation,
assembly and release,A typical pattern for a growth curve is shown in the
Fig,Of next slide.
Replicative cycle
replicative cycle
Viruses are obligate intracellular parasites.
This cycle is highly dependent on the metabolic machinery of the
cell,the virus takes over and orchestrates towards its own
replication,usually inhibiting host-cell protein and nucleic acid
synthesis.
one-step growth cycle,The cycle has a number of stages -
attachment and penetration,nucleic acid synthesis and
tran scription,protein synthesis,maturation,assembly and
release.
A typical,one-step” growth or replicative cycle of viruses
Cell death
time
Following attachment and penetration by virus,cells are
lysed and titrated for infectious virus particles (pfus) at
various times post-infection,Plotting log10 pfu versus time
gives the characteristic curve which has an eclipse period
(where no new virions have been formed) followed by a
logarithmic expansion phase until peak virus liters are
reached when the cell usually dies and virions are released,
The shape of this curve varies greatly between viruses - for
most bacteriophage it takes less than 60 min and for many
animal viruses it can exceed 24 h before maximum titers are
reached,
Attachment is mediated by a specific interaction between the
virus and a receptor on the plasma membrane of the cell,Indeed it is
the presence of such a receptor that determines the cell tropism and
species tropism (细胞趋向性和种类趋向性 )of the virus,These
receptors have cellular functions other than providing a binding site
for viruses,but have been paramount in affecting virus evolution,
Attachment,penetration and uncoating
Thus,the herpes simplex virus (HSV) binds to receptor via at
least two viruscoded envelope glycoproteins.
One of the four proteins in the poliovirus capsid attaches to a
receptor of the Ig protein superfamily (only on primate cells),
HIV,via its major envelope glycoprotein (gpl20),attaches to the
CD4 receptor found predominantly on human T4 lymphocytes,
Recently,two further ligand receptors were shown to have a
role in HIV attachment.
Penetration
For HSV and HIV,penetration of the virus across the plasma
membrane is achieved by fusion of the viral envelope with the
membrane,releasing the nucleocapsid into the cytoplasm of the cell,
The naked capsid of poliovirus,however,is taken up by the process
of endocytosis,the membrane invaginating to engulf the capsid,
resulting in the formation of a vacuole which transports the capsid into
the cytoplasm,The virion is later released from this vacuole,
Methods of virus entry.
(i) HSV,HSV,a large DNA virus,replicates mainly in the
nucleus of the cell,although of course protein synthesis
and post-translational modification take place in the
cytoplasm,The genome encodes for dozens of virus
specific proteins,many with enzymic activity (e.g.
thymidine kinase,DNA polymerase) - such proteins are
usually non-structural (i.e,will not finish up in the virion),
Others are structural proteins and will form the capsid,
envelope and tegument (间层,the structure between the
capsid and the envelope).
Transcription and translation---HSV
Viruses need proteins at different times and in different
concentrations throughout their growth cycles and hence
the virus shows transcriptional control.
Depending on the timing of their expression in the virus
replication cycle,HSV genes are classified as either
immediate early,early or late (α,βorγ),
The mRNA produced encodes proteins that have control
functions,switching on subsequent genes.
All proteins,of course,are formed on cytoplasmic host-
cell ribosomes and remain in the cytosol or are directed
to the endoplasmic reticulum where they undergo the
post-translational events (e.g,glycosylation,
phosphorylation) that give them their final identity,
Eventually,these proteins find their way (specifically
directed,i.e,chaperoned) back to the nucleus for
assembly.
The double-stranded viral DNA is synthesized by
the viral DNA polymerase in association with a
number of DNA-binding proteins,This enzyme has
formed the target for a number of antiviral drugs as
it is significantly different to the host-cell DNA
polymerase.
Herpes simplex virus replication (a dsDNA virus) showing regulation
of and by immediate early (IE),early (E) and late (L) proteins.
Poliovirus is much simpler in its replicative procedures and
control,indeed it lacks fine control! The poliovirus genome RNA
strand also acts as mRNA (termed a positive-sense RNA virus)
and is immediately translated into one long polyprotein which is
subsequently cleaved into a number of structural and non-structural
poliovirus proteins,Included are the structural proteins VP1 and
VPS and the precursor protein VPO,Non-structural proteins
include a protease and RNA,polymerase,Replication takes place
in
Transcription and translation---poliovirus
the cytoplasm,indeed enucleate cells will support
poliovirus replication,The ss RNA,under the direction
of the viral RNA polymerase and cellular factors,
replicates via a series of ds replicative intermediate
molecules which act as template for the synthesis of
new positive strands,These are then destined to act
as mRNA for further rounds of protein synthesis,or
become genomes in newly formed progeny virions
Fig,Poliovirus replication,
(iii) HIV is a member of the unique family of viruses (Retroviridae) that carry
a reverse transcriptase enzyme in their particles,the enzyme catalyzing
the formation of DNA from a RNA template,Thus,HIV goes through a series
of events (see fig,5),which terminates in the formation of a ds DNA
circularized molecule,formed from an initial input of HIV ss RNA,
Transcription and translation---HIV
This molecule,under the direction of a virally encoded integrase,is inserted
into the host DNA as a provirus(原病毒 ),DNA synthesis is now under the
control of the cell - when a daughter cell is produced the provirus is
reproduced at the same time,
The transcription of viral mRNA is under viral control
(from the long terminal repeat (LTR) region of its genome)
and a series of mRNA molecules of various sizes are
transcribed.
Translated proteins are in some cases proteolytically
cleaved by virus protease into smaller functional
proteins,HIV envelope proteins (gpl20 and gp45) are
further processed in the endoplasmic reticulum before
being laid down(定位于 ) in the plasma membrane of the
cell,Full-length copy RNA molecules are also
transcribed from the provirus DNA,these forming
progeny RNA strands destined to be encapsidated.
As proteins and nucleic acid are synthesized in the
infected cell they are channeled to various locations for
virion assembly,Capsids assemble in the nucleus or the
cytoplasm,The steps of capsid assembly vary,depending
on the complexity of the mature capsid,and for enveloped
viruses the site of envelope acquisition is either the nuclear
membrane,plasma membrane and rarely the
endoplasmic reticulum,Prior to capsids 'budding' through
these membranes,virus-specific proteins would have been
laid down in the membrane,
Maturation,assembly and release
Mature HSV capsids are assembled in the nucleus via a number of
precursor forms,Assembly is assisted by scaffolding proteins,
which do not finish up in the mature capsid but facilitate protein-
protein and protein-nucleic acid bonding as the subunits of the
capsid come together,The mature capsid (containing the DNA
genome) buds through the nuclear membrane to acquire its
envelope,Virions are channeled through the ER to the plasma
membrane where they are released,Many herpesviruses invade
adjacent cells by the process of cell-cell fusion,Thus,the plasma
membrane of an infected cell fuses with an adjacent normal cell,
facilitating the entry of progeny virions which undergo a further
replication cycle,In tissue culture this phenomenon can be seen as
large areas of multinucleate fused cells (syncytia)(多核的融合细胞,
多核体 )
(i) HSV.
Poliovirus is a relatively simple icosahedral capsid with four
proteins making up the capsid (VP1,VP2,VPS and VP4),A
further virus-coded protein,VPg,is attached to the ssRNA,
serving as a recognition protein,This capsid self-assembles
without the need for scaffolding proteins,but does produce
an 'immature' capsid form prior to the RNA being inserted
into the virion,Thus,the sub-units of the capsid assemble
via 'pentamers' to form a nucleic acid-free capsid shell
containing VPO,VP1 and VPS,As the RNA is sequestered
into the capsid,VPO is cleaved into VP2 and VP4 and the
mature virion is formed,Poliovirus exits the cell by lysis,
releasing several hundreds of progeny virions.
(ii) Poliovirus.
The capsid of HIV assembles in the cytoplasm,Capsid assembly
of the icosahedron follows the normal pattern,but the control
mechanisms are obviously important here as the mature virion
contains within its central core many components,proteins,two
identical strands of RNA and the reverse tran-scriptase,
integrase and protease complex of polymers,
Budding of HIV is via the plasma membrane.Many viruses (e.g,
influenza,reovirus) have multisegmented genomes,Each
segment,during infection,codes for a virus protein essential in
replication,In order to be infectious the virion must,therefore,
contain a copy of each segment of RNA,Quite how this is
achieved remains a mystery!
(iii) HIV.
HIV
replication
Replicative cycle
As obligate intracellular parasites,viruses 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,maturation and assembly of the virions
and their subsequent release from the cell by
budding or lysis(裂解 ).
Key notes
Attachment,penetration and
uncoating
Attachment is a very specific interaction between
the virus capsid or envelope and a receptor on the
plasma membrane of the cell,Virions are either
engulfed into vacuoles by 'endocytosis' or the virus
envelope fuses with the plasma membrane to
facilitate entry,Uncoating is usually achieved by
cellular proteases 'opening up' the capsid.
Key notes
Transcription and translaation
Using cellular and virus-encoded enzymes and
'helper' proteins,nucleic acid is usually transcribed in
a controlled fashion,Control is also exercised at the
level of mRNA concentration (apart from some simple
viruses,e.g,polio),Nucleic acid is synthesized by
virus-encoded enzymes,Translated proteins may
undergo post-transitional modification (e.g,cleavage,
glycosylation,phosphorylation).
Key notes
maturation,assembly and release
Subunits of capsids assemble via?sub-assembly?
structures,with or without the help of scaffolding
proteins(骨架蛋白 ),Envelopes,when present,(在有包膜的病毒中 )are acquired by capsids budding through
the nuclear or plasma membrane.
Key notes
Prokaryote virus ——bacterophage
Phage or bacteriophage is reffered to as
prokaryote viruse,They widely existed in the
environment where there is prokaryotes,This group
is composed of the following members,
bacteriophage (噬细菌体 )
actinophage(噬放线菌体 )
cyanophage(噬蓝细菌体 )
Reproduction of phage consists of five stages:
(1) attachment (absorption)
(2) penetration (injection)
(3) replication (synthesis of DNA and proteins)
(4) maturity (self assembly)
(5) release (lysis)
Virulent phage can successively finish the five
replicative steps in a short time,which usually cause the
lysis of the host cells,It’s replicative course is called lytic
cycleor productive cycle,(裂解性周期或增殖性周期 )
The genome of temperate phage can integrate into that
of the host cell after invasion (penetration),and replicate
simoutaneously with the host cell,thus it don’t result in
the lysis of the host cell,We call this lysogeny(The host
cell is called Lysogenic bacteria(溶源菌 ),which can coexist
with the temperate phage for a long time and without
detrimental affect.
Virulent phage and temperate phage
Complex symmetry(复合对称 ),
head,icosahedron(cuboid symmetry)
tail,helical symmetry
Tail,different proteins with head,the
outer part is called tail sheath (尾鞘 ),the
internal is empty called tail marrow(尾髓 ),
Some tails has following appendages;
collar(颈环 )
tail fiber(尾丝 )
base plate(基板 )
spike(刺突 )E,coli T4 phage
collar
tail
fiber
on
base
platespike
T4噬菌体正在侵染大肠杆菌
T4 phage
（ 1） Viroid,obligate intracellular molecular pathogen
composed of
only RNA,and now only found in plants.
subvirus(亚病毒 )
subvirus,molecular pathogen composed of either nucleic acid or
protein,It include viroid,virusoid,prion
（ 2） Prion,(abbreviation for protein infection),a group of
proteinaceous infectious elememts,
（ 3） Virusoid,an extremely tiny group of deficient
viroid wraped in euvirus,Composed only by
naked RNA or DNA,The euvirus parasited by
virusoid is called helper virus(辅助病毒 ) in that the
replication of virusoid have to depend on the help of
it,Thus,virusoid might interfere with the replication
of euvirus and alleviate it?s damage to the host cell.
Phage and fermentation
Bacteriophage may greatly endanger the
fermentation industry,When a big fermenter（发酵罐）
is contaminated by phages,fermentation period might
be extended,fermentative liquid changes clearer,and
the product is hard to form,More severely,it might
lead to great economic losses because of fermenter
pouring（倒罐） and the cease of production,This is
a common scene in the production of glutamic acid,
bacteria amylase fermentation,acetone 丁醇
fermentation and antibiotic fermentation,
adenovirus
bacteriophage
bacteriophage
Influenza A virus
Nature budding of HIV
T phage
polio virus
SARS virus
Tobacco mosaic virus
HIV infection
狂犬病病毒 Rabies virus
心脏病毒 Cardiovirus,Molecular surface of Mengovirus,
radially depth cued,as solved by X-ray crystallography
口蹄疫病毒 Aphthovirus,Molecular surface of
Foot and Mouth Disease Virus,radially depth
cued,as solved by X-ray crystallography
病毒 （ viruses）
流感病毒 Influenza Virus
乳头瘤病毒 Papilloma viruses are also found
associated with human penile,uterine and cervical
carcinomas and are very likely to be their cause;
moreover,genital warts can convert to carcinomas.
DNA肿瘤病毒 DNA tumor viruses
腺病毒 Adenovirus
These viruses are highly oncogenic in animals
and only a portion of the virus is integrated into
the host genome.
天花病毒 Pox virus
SV40 virus,a polyoma virus
Mammalian Reovirus Virion
脊髓灰质炎病毒 polio virus
人 T-淋巴细胞病毒,攻击一个 T- 淋巴细胞
Human T-lymphocyte Virus Attacking a T-lymphocyte (TEM x26,400)
HTLV-1 (human T-cell
lymphotropic virus),Causes
Adult T-cell leukemia
(Sezary T-cell leukemia)
which is found in some
Japanese islands,the
Caribbean,Latin America
and Africa,HTLV-1 is
sexually transmitted
真菌 Fungi are eukaryotic organisms
念珠菌
Sputum smear from patient with
pulmonary candidiasis,Gram stain,
烟曲霉菌的瓶状分生孢子
Conidia,phialoconidia of
Aspergillus fumigatus
Gram-stain of vaginal smear showing Candida
albicans （ 白色念珠菌 ） epithelial cells and
many gram-negative rods,(1,000X oil)
virus and subvirus
Section 1
Virus structure
Euvirus,at least contains two components—— nucleic
acid and
protein
Subvirus,molecular pathogen includes：
viroid（类病毒） ——independent infectious RNA
only
virusoid（拟病毒） ——non-independent infectious
RNA only
prion（朊病毒） ——protein only
Viruses are obligate intracellular parasites which can
only be viewed with the aid of an electron microscope,
They vary in size from approximately 20-200 nm,In order
to persist in the environment they must be capable of
being passed from host to host and of infecting and
replicating in susceptible host cells,
1,definitions
A virus particle has thus been defined
as a structure which has evolved to
transfer nucleic acid from one cell to
another,
The nucleic acid found in the
particle is either DNA or RNA,is
single- or double-stranded and linear
or segmented,In some cases the
nucleic acid may be circular,
The simplest of virus particles consists of a protein
coat (sometimes made up of only one type of protein
which is repeated hundreds of times) which surrounds
a strand of nucleic acid.
More complicated viruses have their nucleic acid
surrounded by a protein coat which is further
engulfed in a membrane structure,an envelope
consisting of virally coded glycoproteins derived
from one of several regions within the infected cell
during the maturation of the virus particle,The
genetic material of these complex viruses encodes
for many dozens of virus specific proteins.
The complete fully assembled virus is termed the
virion,It may have a glycoprotein envelope which has
peplomers (包膜粒 )(projections,spike突起,刺突 ) which
form a?fringe边缘? around the particle,The protein coat
surrounding the nucleic acid is referred to as the
capsid,The capsid is composed of morphological
units or capsomers（衣壳粒）,The type of capsomer
depends on the overall shape of the capsid,but in the
case of icosahedral capsids the capsomers are either
pentamers or hexamers（五邻体或六邻体）,The
combined nucleic acid-protein complex which
comprises the genome is termed the nucleocapsid（核衣壳）,which is often enclosed in a core within the
virion.
Nucleic acid （ DNA or RNA）
nucleocapsid
Viron Capsid （ protein）
Envelope （ glycoprotein）
Structure of the virus
Fig,(a) unenveloped/helical (tobacco mosaic virus),(b) unenveloped/icosahedral
(adenovirus); (c) enveloped/helical (paramyxovirus),(d) enveloped/ icosahedral
(herpesvirus),
180nm
Diagrammatic representation of the structure of virus particles
RNA
Reverse
transcriptase
Lipid
membrane
100nm
Rabies virus(l)and HIV(R) have tight-fitting envelopes.
herpes simplex (l) has a loose-fitting envelope,
whereas adenovirus (R) is non-enveloped,
Diagrammatic representation of the structure of virus particles
Glycoprotein
envelope
Icosahedral
capsid
containing
DNA
90nm
45nm
While the electron microscope (EM) had been known for many
years,the invention of the negative-staining technique in 1959
revolutionized studies on virus structure,In negative-contrast EM,
virus particles are mixed with a heavy metal solution (e.g,sodium
phosphotungstate磷钨酸盐 ) and dried onto a support film,The
stain provides an electron-opaque background against which the
virus can be visualized。
2,Methods of study（ 1）
Negative-staining
technique
Observation under the electron microscope has thus
allowed the definition of virus morphology at the 50-
77A resolution level,In addition,negative staining of
thin sections of infected cells has allowed definition of
structures which appear during virus maturation and
their interactions with cellular proteins,
Methodes of study （ 2）
Electron
microscopy
Immunoelectron microscopy is used to study
those viruses which may be present in low
concentrations or grow poorly in tissue culture
(e.g,Norwalk virus),These clumps of virus are
more readily observed,
Methods of study（ 3）
Immunoelectron
microscopy
Electron cryomicroscopy （电子低温显微术）
reduces the risk of seeing artifacts as may be
unavoidable by negative staining,High
concentrations of virus are rapidly,frozen in liquid
ethane（乙烷） while on carbon grids,Electron
micrographs can be digitized and three-dimensional
reconstruction performed,Resolutions of 9A have
been achieved using this method,
Electron
cryomicroscopy
Methods of study（ 4）
X-ray diffraction of virus crystals is the ultimate in
determining the ultrastructure of virion morphology,（是对病毒形态和超显微结构分析的主要方法） At present,only simple
viruses can be crystallized,More complex viruses are
analyzed by attempting to form crystals of sub-particular
molecules,The X-ray diffraction pattern of the virion particle
allows mathematical processing,which can predict the
molecular configuration（分子构型） of the virus particle,
X-ray
diffraction
Methods of study（ 5）
Summarize
methods of studying
Negative-staining technique
Electron microscopy
Immunoelectron microscopy
Electron cryomicroscopy
X-ray diffraction
Three-dimensional reconstruction of an
icosahedrally symmetric virus particle.(一个二十面体对称病毒粒子的三维重建 )
Helical symmetry can be loosely
described as having a?spiral staircase?
structure,The structure has an obvious
axis down the center of the helix,The
subunits are placed between the turns of
the nucleic acid,A diagram of such a
structure (tobacco mosaic virus) is
shown in the left Fig.,Animal viruses with
a similar capsid structure include
measles,rabies and influenza,
3,Virus symmetry（ helical）
The capsids of virions tend to have one of two
symmetries ——helical or cuboid,
Most animal viruses have spherical or cuboid symmetry,
Obtaining a true sphere is not possible for such structures and
hence subunits come together to produce a cuboid structure
which is very close to being spherical,
Virus symmetry （ cuboid）
The 'closed shell' capsid is usually based on the structure referred to
as an icosahedron.
A regular icosahedron,formed from assembly of identical subunits,
consists of 20 equilateral triangular faces,30 edges and 12 vertices
and exhibits 2-,3- and 5-fold symmetry,
The minimum number of capsomers required to construct an
icosahedron is 12,each composed of five identical subunits,Many
viruses have more than 12,
Diagrammatical representation of isosahedral symmetry
Although in adenoviruses projecting fibers are also present,
which distinguishes this capsid from that of other viruses,The
maturation and assembly of these structures is very complex;
indeed,much of how it happens is unknown,
Axes of
rotation
Many viruses in addition to having a capsid also contain a
virus-encoded envelope,Most enveloped viruses bud from a
cellular membrane (plasma membrane,e.g,influenza virus,or
nuclear membrane,e.g,herpes simplex virus),Within this
virus lipid / protein bilayer are a number of inserted virus-
encoded glycoproteins,The envelopes can be amorphous
(e.g,the herpes virion) or tightly bound to the capsid (e.g,
HIV),Thus,the lipid of the envelope is derived from the cell,
the glycoprotein being encoded by the virus,Quite how the
process of budding occurs is largely unknown.
4,Virus envelopes
Viruses are obligate intracellular parasites and
vary from 20-200 nm in size,They have varied
shape and chemical composition,but contain
only RNA or DNA,The intact particle is termed a
'virion' which consists of a capsid that may be
enveloped further by a glycoprotein/lipid
membrane,Viruses are resistant to antibiotics,
Key Notes
definitions
Virus morphology has been determined by
electron microscopy (EM) (using negative
staining),thin-section EM (using negative
staining),immunoelectron microscopy (using
negative staining),electron cryo-microscopy
and X-ray crystallography.
Key Notes
Methods of
study
Virus capsids have helical or icosahedral
symmetry,In many cases the capsid is engulfed
by a membrane structure (the virus envelope),
Helical symmetry is seen as protein sub-units
arranged around the virus nucleic acid in an
ordered helical fashion,The icosahedron is a
regular shaped cuboid which consists of
repetitions of many protein sub-units assembled
so as to resemble a sphere.
Key Notes
Virus
symmetry
Virus envelopes are acquired by the capsid as it
buds through nuclear or plasma membranes of the
infected cell,Envelopes may contain a few
glycoproteins,for example,human
immunodeficiency virus (HIV),or many
glycoproteins,for example,Herpes simplex virus
(HSV),The virus envelope contains the receptors,
which allow the particle to attach to and infect the
host cell.
Key Notes
Virus
envelopes
The classification of viruses involves the use
of a wide range of characteristics (morphology,
genome,physicochemical and physical
properties,proteins,antigenic and biological
properties) to place viruses in orders,families,
genera and species.
Section 2 Virus Taxonomy
These are groupings of families of viruses that share common
characteristics.
These are groupings of genera of viruses that share common
characteristics and are distinct from the members of other
families,They are designated by the suffix -viridae.
These are groupings of species of viruses which share common
characteristics,These are designated by the suffix -virus.
These represent a polythetic class of viruses that constitutes a
replicating lineage and occupies a particular ecological niche.
Virus orders
Virus families
Virus genera
Virus species
initial attempts to classify viruses were based on their
pathogenic properties,and the only common feature to many of the
viruses placed together in such groupings was that of organ
tropism (器官趋性 e.g,viruses causing hepatitis or respiratory
disease),There were more important aspects (e.g,virus structure
and composition) which led virologists to believe that these initial
attempts of classification were far from adequate,In the late 1950s
and early 1960s,hundreds of new viruses were beginning to be
isolated and the need for a different classification method became
essential,In 1966 the International Committee on Nomenclature of
Viruses (ICNV) was established at the International Congress of
Microbiology held in Moscow,As the present classification scheme
has evolved,an acceptance of the characteristics to be considered
and their respective weighting has become universal.
In 1995 the sixth report of the ICTV (International
Committee on Taxonomy of Viruses) recorded a
universal taxonomy scheme consisting of one
order,71 families,11 subfamilies and 164 genera
(with more than 4000 members),The system still
contains hundreds of unassigned viruses,
largely because of lack of data,Also,new viruses
are still being discovered.
Viral proteins,coded by the viral genome,are
either structural (capsid,envelope) or non-
structural (e.g,enzymes,oncogenes,inhibitors
of cell macromolecular synthesis and interaction
with MHC presentation),They may be essential
or non-essential in tissue culture replication.
Section C Virus proteins
Structural proteins are studied,following virus purification,using
a range of techniques including,
1,sodium dodecyi sulfate (SDS)-polyacrylamide gel electrophoresis,
2,Western blotting（蛋白质印迹法）,
3,Immunoprecipitation（免疫沉淀法）,
Non-structural proteins are examined by,for example,pulse-
chase experiments（脉冲追踪实验）,use of protease and
glycosylation inhibitors（糖基化抑制剂）,
methodology
Viral proteins are synthesized by the translation of viral
mRNAs on cellular ribosomes,Proteins are often processed
following synthesis (e.g,proteolytic cleavage,glycosylation,
myristylation,acylation and palmitoylation蛋白酶剪切、糖基化、
十四烷基化、酰化作用、十六烷酰化 ),In many viruses,protein
synthesis is controlled at the levels of transcription and
translation,which makes virus replication quite an efficient
process,This control is usually directed by the virus genome.
Protein synthesis
and complexity
Structural proteins are either nucleocapsid,matrix or envelope
proteins,They have a role in protecting the viral genome and in
delivering the genome from one host to another via receptors on
host cells,They also have a major role in the assembly of the virion,
In most viruses,structural proteins are produced in abundance late
in the replicative cycle.
These may be carried in the virion (but are not part of the virion
architecture) where they have enzymic activity which is necessary
for initiating infection,Others are not destined for the virion but
have roles in the infected cell,These roles include switching off
host-cell nucleic acid and protein synthesis,polymerase,protease
and kinase activities,DNA binding activity and gene regulation.
Structural proteins
Non structural proteins
Types of viral genome
Viral genomes are diverse in size,structure
and nucleotide make up,They are linear,circular,
dsDNA,ssDNA,dsRNA,ssRNA,segmented or
non-segmented（分段的或不分段的）,
Section 4 virus nucleic acid
Many viral genomes have been sequenced and the
repertoire of their coding potential determined,
Genomes are studied by a range of techniques
including：
1,restriction enzyme analysis,
2,buoyant density,
3,thermal denaturation,
4,nuclease sensitivity
5,EM.
Techniques of
study
Herpesviruses and adenoviruses have large DNA
genomes which vary in their structures,DNA
viruses often have terminal inverted repeats as
part of their genome structure,They may have
coding capacity for up to 80 virus proteins.
Parvovirus (ssDNA) and polyoma viruses (dsDNA)
are small DNA genomes,The coding capacity
may be increased by use of overlapping genes
and both strands of DNA.
Small DNA viruses
Large DNA viruses
These are either positive sense (e.g,picornaviruses,
coronaviruses/ flaviviruses and togaviruses) or negative
sense (e.g,orthomyxo-viruses,paramyxoviruses and
rhabdo viruses),Positive-sense genome^ act as mRNAs,
negative sense genomes need a cRNA to act as,mRNA.
Segmented viral genomes (e.g,orthomyxoviruses) are
those which are divided into two or more physically
distinct molecules of nucleic acid packaged into a single
virion.
Segmented RNA viruses
Non-segmented RNA viruses
Characterization of the viral genome is based on a
number of parameters,
(1) composition of the nucleic acid (i.e,DNA or
RNA);
(2) size and number of strands;
(3) terminal structures;
(4) nucleotide sequence;
(5) coding capacity;
(6) regulatory signal elements,transcriptional
enhancers,promoters and terminators.
dsDNA genome,pox,herpes,adeno,papova,irido
mRNA Protein
dsDNA dsDNA
(b) ssDNA genome,parvo
mRNA Protein
ssDNA ———— > dsDNA Assembly
ssDNA
(c) ss/dsONA genome using ssRNA intermediate,hepadna
ss/dsDNA mRNA ————? Protein ———— > Assembly
dsDNA ss/dsDNA
,Protein
(d) dsRNA genome,reo,birna
Protein
dsRNA —— r mRNA
' Assembly (dsRNA)
Assembly
(g) ssRNA genome using ds DNA intermediate,retro
ssRNA ———— >,dsRNA ——— >,Integration ——?,mRNA
a(e) +sense ssRNA genome; picorna,calici,corona,toro,toga
Protein ^ —,____(cleavage)
^
+RNA +RNA
-RNA
(f) -sense ssRNA genome,orthomyxo,paramyxo,rhabdo,filo
(bunya,arena)
^ Protein ~^ -RNA ————— >? +RNA ^ ^ Assembly
^^- -RNA ^
The complexity and range of virus types is echoed in the various strategies
they adopt in their replicative cycles,
Viruses,as obligate intracellular parasites,must attach to or enter host
cells in order to undergo a 'reproductive' cycle.
This cycle is highly dependent on the metabolic machinery of the cell,
which in most cases the virus takes over and orchestrates towards its own
replication,usually inhibiting host-cell protein and nucleic acid synthesis,
The outcome is the production of hundreds of progeny virions which leave the
infected cell (by lysis or budding),killing the cell and spreading to infect more
host cells and tissues,This replicative or growth cycle can be analyzed in
tissue culture cells and is often referred to as the one-step growth cycle,
The cycle has a number of stages - attachment and penetration,nucleic
acid synthesis and tran scription,protein synthesis,maturation,
assembly and release,A typical pattern for a growth curve is shown in the
Fig,Of next slide.
Replicative cycle
replicative cycle
Viruses are obligate intracellular parasites.
This cycle is highly dependent on the metabolic machinery of the
cell,the virus takes over and orchestrates towards its own
replication,usually inhibiting host-cell protein and nucleic acid
synthesis.
one-step growth cycle,The cycle has a number of stages -
attachment and penetration,nucleic acid synthesis and
tran scription,protein synthesis,maturation,assembly and
release.
A typical,one-step” growth or replicative cycle of viruses
Cell death
time
Following attachment and penetration by virus,cells are
lysed and titrated for infectious virus particles (pfus) at
various times post-infection,Plotting log10 pfu versus time
gives the characteristic curve which has an eclipse period
(where no new virions have been formed) followed by a
logarithmic expansion phase until peak virus liters are
reached when the cell usually dies and virions are released,
The shape of this curve varies greatly between viruses - for
most bacteriophage it takes less than 60 min and for many
animal viruses it can exceed 24 h before maximum titers are
reached,
Attachment is mediated by a specific interaction between the
virus and a receptor on the plasma membrane of the cell,Indeed it is
the presence of such a receptor that determines the cell tropism and
species tropism (细胞趋向性和种类趋向性 )of the virus,These
receptors have cellular functions other than providing a binding site
for viruses,but have been paramount in affecting virus evolution,
Attachment,penetration and uncoating
Thus,the herpes simplex virus (HSV) binds to receptor via at
least two viruscoded envelope glycoproteins.
One of the four proteins in the poliovirus capsid attaches to a
receptor of the Ig protein superfamily (only on primate cells),
HIV,via its major envelope glycoprotein (gpl20),attaches to the
CD4 receptor found predominantly on human T4 lymphocytes,
Recently,two further ligand receptors were shown to have a
role in HIV attachment.
Penetration
For HSV and HIV,penetration of the virus across the plasma
membrane is achieved by fusion of the viral envelope with the
membrane,releasing the nucleocapsid into the cytoplasm of the cell,
The naked capsid of poliovirus,however,is taken up by the process
of endocytosis,the membrane invaginating to engulf the capsid,
resulting in the formation of a vacuole which transports the capsid into
the cytoplasm,The virion is later released from this vacuole,
Methods of virus entry.
(i) HSV,HSV,a large DNA virus,replicates mainly in the
nucleus of the cell,although of course protein synthesis
and post-translational modification take place in the
cytoplasm,The genome encodes for dozens of virus
specific proteins,many with enzymic activity (e.g.
thymidine kinase,DNA polymerase) - such proteins are
usually non-structural (i.e,will not finish up in the virion),
Others are structural proteins and will form the capsid,
envelope and tegument (间层,the structure between the
capsid and the envelope).
Transcription and translation---HSV
Viruses need proteins at different times and in different
concentrations throughout their growth cycles and hence
the virus shows transcriptional control.
Depending on the timing of their expression in the virus
replication cycle,HSV genes are classified as either
immediate early,early or late (α,βorγ),
The mRNA produced encodes proteins that have control
functions,switching on subsequent genes.
All proteins,of course,are formed on cytoplasmic host-
cell ribosomes and remain in the cytosol or are directed
to the endoplasmic reticulum where they undergo the
post-translational events (e.g,glycosylation,
phosphorylation) that give them their final identity,
Eventually,these proteins find their way (specifically
directed,i.e,chaperoned) back to the nucleus for
assembly.
The double-stranded viral DNA is synthesized by
the viral DNA polymerase in association with a
number of DNA-binding proteins,This enzyme has
formed the target for a number of antiviral drugs as
it is significantly different to the host-cell DNA
polymerase.
Herpes simplex virus replication (a dsDNA virus) showing regulation
of and by immediate early (IE),early (E) and late (L) proteins.
Poliovirus is much simpler in its replicative procedures and
control,indeed it lacks fine control! The poliovirus genome RNA
strand also acts as mRNA (termed a positive-sense RNA virus)
and is immediately translated into one long polyprotein which is
subsequently cleaved into a number of structural and non-structural
poliovirus proteins,Included are the structural proteins VP1 and
VPS and the precursor protein VPO,Non-structural proteins
include a protease and RNA,polymerase,Replication takes place
in
Transcription and translation---poliovirus
the cytoplasm,indeed enucleate cells will support
poliovirus replication,The ss RNA,under the direction
of the viral RNA polymerase and cellular factors,
replicates via a series of ds replicative intermediate
molecules which act as template for the synthesis of
new positive strands,These are then destined to act
as mRNA for further rounds of protein synthesis,or
become genomes in newly formed progeny virions
Fig,Poliovirus replication,
(iii) HIV is a member of the unique family of viruses (Retroviridae) that carry
a reverse transcriptase enzyme in their particles,the enzyme catalyzing
the formation of DNA from a RNA template,Thus,HIV goes through a series
of events (see fig,5),which terminates in the formation of a ds DNA
circularized molecule,formed from an initial input of HIV ss RNA,
Transcription and translation---HIV
This molecule,under the direction of a virally encoded integrase,is inserted
into the host DNA as a provirus(原病毒 ),DNA synthesis is now under the
control of the cell - when a daughter cell is produced the provirus is
reproduced at the same time,
The transcription of viral mRNA is under viral control
(from the long terminal repeat (LTR) region of its genome)
and a series of mRNA molecules of various sizes are
transcribed.
Translated proteins are in some cases proteolytically
cleaved by virus protease into smaller functional
proteins,HIV envelope proteins (gpl20 and gp45) are
further processed in the endoplasmic reticulum before
being laid down(定位于 ) in the plasma membrane of the
cell,Full-length copy RNA molecules are also
transcribed from the provirus DNA,these forming
progeny RNA strands destined to be encapsidated.
As proteins and nucleic acid are synthesized in the
infected cell they are channeled to various locations for
virion assembly,Capsids assemble in the nucleus or the
cytoplasm,The steps of capsid assembly vary,depending
on the complexity of the mature capsid,and for enveloped
viruses the site of envelope acquisition is either the nuclear
membrane,plasma membrane and rarely the
endoplasmic reticulum,Prior to capsids 'budding' through
these membranes,virus-specific proteins would have been
laid down in the membrane,
Maturation,assembly and release
Mature HSV capsids are assembled in the nucleus via a number of
precursor forms,Assembly is assisted by scaffolding proteins,
which do not finish up in the mature capsid but facilitate protein-
protein and protein-nucleic acid bonding as the subunits of the
capsid come together,The mature capsid (containing the DNA
genome) buds through the nuclear membrane to acquire its
envelope,Virions are channeled through the ER to the plasma
membrane where they are released,Many herpesviruses invade
adjacent cells by the process of cell-cell fusion,Thus,the plasma
membrane of an infected cell fuses with an adjacent normal cell,
facilitating the entry of progeny virions which undergo a further
replication cycle,In tissue culture this phenomenon can be seen as
large areas of multinucleate fused cells (syncytia)(多核的融合细胞,
多核体 )
(i) HSV.
Poliovirus is a relatively simple icosahedral capsid with four
proteins making up the capsid (VP1,VP2,VPS and VP4),A
further virus-coded protein,VPg,is attached to the ssRNA,
serving as a recognition protein,This capsid self-assembles
without the need for scaffolding proteins,but does produce
an 'immature' capsid form prior to the RNA being inserted
into the virion,Thus,the sub-units of the capsid assemble
via 'pentamers' to form a nucleic acid-free capsid shell
containing VPO,VP1 and VPS,As the RNA is sequestered
into the capsid,VPO is cleaved into VP2 and VP4 and the
mature virion is formed,Poliovirus exits the cell by lysis,
releasing several hundreds of progeny virions.
(ii) Poliovirus.
The capsid of HIV assembles in the cytoplasm,Capsid assembly
of the icosahedron follows the normal pattern,but the control
mechanisms are obviously important here as the mature virion
contains within its central core many components,proteins,two
identical strands of RNA and the reverse tran-scriptase,
integrase and protease complex of polymers,
Budding of HIV is via the plasma membrane.Many viruses (e.g,
influenza,reovirus) have multisegmented genomes,Each
segment,during infection,codes for a virus protein essential in
replication,In order to be infectious the virion must,therefore,
contain a copy of each segment of RNA,Quite how this is
achieved remains a mystery!
(iii) HIV.
HIV
replication
Replicative cycle
As obligate intracellular parasites,viruses 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,maturation and assembly of the virions
and their subsequent release from the cell by
budding or lysis(裂解 ).
Key notes
Attachment,penetration and
uncoating
Attachment is a very specific interaction between
the virus capsid or envelope and a receptor on the
plasma membrane of the cell,Virions are either
engulfed into vacuoles by 'endocytosis' or the virus
envelope fuses with the plasma membrane to
facilitate entry,Uncoating is usually achieved by
cellular proteases 'opening up' the capsid.
Key notes
Transcription and translaation
Using cellular and virus-encoded enzymes and
'helper' proteins,nucleic acid is usually transcribed in
a controlled fashion,Control is also exercised at the
level of mRNA concentration (apart from some simple
viruses,e.g,polio),Nucleic acid is synthesized by
virus-encoded enzymes,Translated proteins may
undergo post-transitional modification (e.g,cleavage,
glycosylation,phosphorylation).
Key notes
maturation,assembly and release
Subunits of capsids assemble via?sub-assembly?
structures,with or without the help of scaffolding
proteins(骨架蛋白 ),Envelopes,when present,(在有包膜的病毒中 )are acquired by capsids budding through
the nuclear or plasma membrane.
Key notes
Prokaryote virus ——bacterophage
Phage or bacteriophage is reffered to as
prokaryote viruse,They widely existed in the
environment where there is prokaryotes,This group
is composed of the following members,
bacteriophage (噬细菌体 )
actinophage(噬放线菌体 )
cyanophage(噬蓝细菌体 )
Reproduction of phage consists of five stages:
(1) attachment (absorption)
(2) penetration (injection)
(3) replication (synthesis of DNA and proteins)
(4) maturity (self assembly)
(5) release (lysis)
Virulent phage can successively finish the five
replicative steps in a short time,which usually cause the
lysis of the host cells,It’s replicative course is called lytic
cycleor productive cycle,(裂解性周期或增殖性周期 )
The genome of temperate phage can integrate into that
of the host cell after invasion (penetration),and replicate
simoutaneously with the host cell,thus it don’t result in
the lysis of the host cell,We call this lysogeny(The host
cell is called Lysogenic bacteria(溶源菌 ),which can coexist
with the temperate phage for a long time and without
detrimental affect.
Virulent phage and temperate phage
Complex symmetry(复合对称 ),
head,icosahedron(cuboid symmetry)
tail,helical symmetry
Tail,different proteins with head,the
outer part is called tail sheath (尾鞘 ),the
internal is empty called tail marrow(尾髓 ),
Some tails has following appendages;
collar(颈环 )
tail fiber(尾丝 )
base plate(基板 )
spike(刺突 )E,coli T4 phage
collar
tail
fiber
on
base
platespike
T4噬菌体正在侵染大肠杆菌
T4 phage
（ 1） Viroid,obligate intracellular molecular pathogen
composed of
only RNA,and now only found in plants.
subvirus(亚病毒 )
subvirus,molecular pathogen composed of either nucleic acid or
protein,It include viroid,virusoid,prion
（ 2） Prion,(abbreviation for protein infection),a group of
proteinaceous infectious elememts,
（ 3） Virusoid,an extremely tiny group of deficient
viroid wraped in euvirus,Composed only by
naked RNA or DNA,The euvirus parasited by
virusoid is called helper virus(辅助病毒 ) in that the
replication of virusoid have to depend on the help of
it,Thus,virusoid might interfere with the replication
of euvirus and alleviate it?s damage to the host cell.
Phage and fermentation
Bacteriophage may greatly endanger the
fermentation industry,When a big fermenter（发酵罐）
is contaminated by phages,fermentation period might
be extended,fermentative liquid changes clearer,and
the product is hard to form,More severely,it might
lead to great economic losses because of fermenter
pouring（倒罐） and the cease of production,This is
a common scene in the production of glutamic acid,
bacteria amylase fermentation,acetone 丁醇
fermentation and antibiotic fermentation,
adenovirus
bacteriophage
bacteriophage
Influenza A virus
Nature budding of HIV
T phage
polio virus
SARS virus
Tobacco mosaic virus
HIV infection
狂犬病病毒 Rabies virus
心脏病毒 Cardiovirus,Molecular surface of Mengovirus,
radially depth cued,as solved by X-ray crystallography
口蹄疫病毒 Aphthovirus,Molecular surface of
Foot and Mouth Disease Virus,radially depth
cued,as solved by X-ray crystallography
病毒 （ viruses）
流感病毒 Influenza Virus
乳头瘤病毒 Papilloma viruses are also found
associated with human penile,uterine and cervical
carcinomas and are very likely to be their cause;
moreover,genital warts can convert to carcinomas.
DNA肿瘤病毒 DNA tumor viruses
腺病毒 Adenovirus
These viruses are highly oncogenic in animals
and only a portion of the virus is integrated into
the host genome.
天花病毒 Pox virus
SV40 virus,a polyoma virus
Mammalian Reovirus Virion
脊髓灰质炎病毒 polio virus
人 T-淋巴细胞病毒,攻击一个 T- 淋巴细胞
Human T-lymphocyte Virus Attacking a T-lymphocyte (TEM x26,400)
HTLV-1 (human T-cell
lymphotropic virus),Causes
Adult T-cell leukemia
(Sezary T-cell leukemia)
which is found in some
Japanese islands,the
Caribbean,Latin America
and Africa,HTLV-1 is
sexually transmitted
真菌 Fungi are eukaryotic organisms
念珠菌
Sputum smear from patient with
pulmonary candidiasis,Gram stain,
烟曲霉菌的瓶状分生孢子
Conidia,phialoconidia of
Aspergillus fumigatus
Gram-stain of vaginal smear showing Candida
albicans （ 白色念珠菌 ） epithelial cells and
many gram-negative rods,(1,000X oil)
