General Virology Flashcards
What is virus?
Viruses are infectious agents of small size (range 20-300 nm) and simple
structure, able of multiplying in animal, plant, fungal and bacterial cells,
exploiting their biosynthetic apparatus
Viruses, outside the cells, are aggregates of biologically inert
macromolecules, whose genetic information is propagated within suitable
cells
They possess no functional organelles and strictly depend on their cellular
host
Viruses are able to alternate two distinct states: intracellular and extracellular
________________ is required for virus observation
Electron microscopy
Viral morphology
- ovoid or rectangular viruses
- rounded viruses
- filamentous viruses
- bullet viruses, etc.
Viral structure:
The complete extracellular viral particle is called a virion
The virion is composed of a nucleic acid (either DNA or RNA)
and a protein coat, the capsid
capsid + viral genome = nucleocapsid
The capsid protects the genome and it is made up of subunits
called capsomeres (composed of protomers/proteic subunits)
Outside the nucleocapsid, in some viruses, there is a lipoprotein
membrane, the envelope, derived from the host cell
Bacteriophage structure
Different features:
A) Contractile tail, dsDNA (T2, T4);
B) Long tail not contractile, dsDNA (T1, λ);
C) Short tail not contractile, dsDNA (T3);
D) Without tail, large capsomers, ssDNA (φχ 174);
E) Without tail, small capsomers, ssRNA (MS2);
F) Without head, filamentous, ssDNA (M13)
Virion Structure: Naked Capsid
Icosahedral (cubic) symmetry
Icosahedron: 12 vertices. 30 edges, 20 faces
In smaller viruses (i.e., Poliovirus)
protein subunits form trimers
organized into pentamers (or pentons)
Capsid assembly of the icosahedral capsid
of a picornavirus.
Individual proteins associate into subunits,
which associate into protomers,
capsomeres, and an empty procapsid.
Inclusion of the (+) RNA genome triggers its
conversion to the final capsid form
Virion Structure: Naked Capsid
Icosahedral (cubic) symmetry
Larger capsid virions are constructed by
inserting structurally distinct capsomeres
between the pentons at the
vertices. These capsomeres have six
nearest neighbors (hexons).
In medium-sized viruses 12 pentamers
are localized at the vertices of the
icosahedron and 20 hexons are localized
on the faces (i.e., Caliciviruses).
Larger viruses have 12 pentons at the
vertices of the icosahedron and a variable
number of hexons on the faces and edges
(60 for Papillomaviruses and
Polyomaviruses, 150 for Herpesviruses,
240 for Adenoviruses)
Adenovirus:
12 pentons with fibers and 240 hexons
Virion Structure
Helical symmetry
Helical structures appear as
rods, and are observed
within the envelope
of most negative-strand
RNA viruses
The envelope
It is a lipid bilayer containing highly specialized viral proteins (glycoproteins and
matrix proteins)
It is acquired by budding through cellular membranes
Presence of antigens important for the immune response
Glycoproteins functions:
* mediate the interaction of the virus with the target cell (viral attachment
protein, VAP*)
* allow the fusion of the envelope with the cell membrane
Matrix proteins functions:
* connect the viral nucleocapsid with the glycoproteins and provide added
rigidity to the virion
* play a fundamental role in the assembly of virions
* In naked capsid viruses, specific capsid proteins function as VAPs
Naked capsid viruses:
1)Component: Protein
2) Properties: resistant to temperature, acid, proteases, detergents, drying
3) Consequences: easily spread, can dry out and retain infectivity, can survive the adverse conditions of the gut, resistant to detergents, antibody might be sufficient for immunoprotection.
Enveloped viruses:
1) Components: membrane, lipids, proteins, glycoproteins
2) properties: disrupted by acid, detergents, drying, heat
3) consequences: cannot survive the gastrointestinal tract, spreads in large droplets, secretions, organ transplants, blood transfusions; doesnt need to kill the cell to spread, may need antibody and cell-mediated immune response for protection, elicits hypersensitivity and inflammation to cause immunopathogenesis
Viral nucleic acid:
The viral genome is a single nucleic acid (haploid, except Retroviridae) DNA or RNA
(monocatenary or bicatenary; circular or linear; whole or segmented)
Double-stranded DNA (dsDNA) viruses:
Linear (Herpesviridae, Adenoviridae, Poxviridae)
Circular (Papillomaviridae, Polyomaviridae)
Single-stranded DNA (ssDNA) viruses:
Linear (Parvoviridae)
Partially double-stranded DNA
Circular with a break on a filament
(Hepadnaviridae)
Single-stranded RNA viruses:
Linear, positive (Coronaviridae, Flaviviridae, Togaviridae, Matonaviridae,
Astroviridae, Caliciviridae, Picornaviridae)
Linear, negative (Paramyxoviridae, Rhabdoviridae, Filoviridae)
Linear, negative or ambisense, segmented (Arenaviridae, Bunyavirales)
Linear, positive, diploid (Retroviridae)
Linear, negative, segmented (Orthomyxoviridae)
What are positive and negative RNA viruses?
Positive and negative sense RNA viruses are the two types of ssRNA viruses. Positive sense RNA viruses have a genome containing viral mRNA that can be readily translated into proteins. However, negative sense RNA viruses consist of a genome containing viral RNA that is complementary to the mRNA.
Double-stranded RNA viruses:
Linear, segmented (Reoviridae)
Viral proteins:
- Structural proteins
- Proteins regulating some functions or components of the host cell (e.g., the
transcription of cellular DNA) to the advantage of the virus - Polymerases for nucleic acid replication (DNA or RNA polymerases)
- Enzymes that:
- regulate the interaction with the surface of the host cell (neuraminidase);
- transcribe the viral genome into mRNA (DNA-dependent RNA polymerase);
- add end groups to the viral mRNA (poly (A) polymerase);
- copy the viral RNA to DNA (RNA-dependent DNA polymerase);
- other functional enzymes (protein kinases)
Other chemical constituents….
Lipids are present in the envelope, where a small amount of protein-bound
carbohydrates is also found
Classification of viruses
Classification based on structural, physicochemical
and replicative characteristics
Properties of virions
Properties of the genome
Properties of viral proteins
Replicative properties of the genome
Physical properties
Biological properties
Properties of virions:
Dimensions
Form
Presence of envelope
Symmetry of the capsid
Structure of the capsomers
Properties of the genome:
Type and size of the nucleic acid
Mono / bicatenary
Linear / circular
Positive, negative or ambisense
Number and size of segments
Presence of cap-5’ terminal
Presence of covalently linked 5’ terminal polypeptide
Presence of poly(A)-3’ terminal
Nucleotide sequence
Replicative properties of the genome:
Nucleic acid replication strategy
Characteristics of transcription
Translation and post-translation processing features
Site of protein accumulation, assembly and maturation
Cytopathology
Formation of inclusions
Properties of viral proteins:
Number of proteins
Protein size
Functional activities of proteins
Amino acid sequence
Physical properties:
Stability to pH
Thermal stability
Stability to cations
Stability to solvents
Stability to detergents
Radiation stability
Biological properties:
Serological correlations
Host spectrum
Pathogenicity
Tissue tropism
Transmission
Relationship with vectors
Geographical distribution
Enteric viruses:
Viral agents acquired by ingestion that multiply in the intestinal tract:
Families Reoviridae, Coronaviridae, Picornaviridae, Adenoviridae, and Caliciviridae
Respiratory viruses:
Viral agents acquired by inhalation that multiply in the respiratory tract:
Families Orthomyxoviridae, Paramyxoviridae, Coronaviridae, Adenoviridae, and
Picornaviridae
Neurotropic viruses:
Viral agents acquired through different ways that multiply first at the site of entry
and in other organs recognizing their final target in the nervous system:
Families Picornaviridae, Rhabdoviridae, Paramyxoviridae, Herpesviridae,
Arenaviridae, Polyomaviridae, and Arbovirus
Dermotropic viruses:
Viral agents acquired through different ways that multiply first at site of entry and
in other organs recognizing the final target in the skin or mucous membranes or
that multiply exclusively at the level of the skin/mucous membranes:
Families Poxviridae, Paramyxoviridae, Herpesviridae, Picornaviridae,
Matonaviridae, and Papillomaviridae
Arboviruses:
Viral agents that multiply in bloodsucking arthropods and are transmitted through
their sting to a vertebrate host:
Families Togaviridae, Flaviviridae, Reoviridae, and Bunyaviridae
Oncogenic viruses:
Viral agents that are acquired by different modes of transmission, have a specific
tissue tropism and establish persistent infections causing transformation or
immortalization of the cells:
Families: Herpesviridae, Poxviridae, Adenoviridae, Polyomaviridae,
Papillomaviridae, Hepadnaviridae, and Retroviridae
Steps in viral replication:
- Recognition of the target
- attachment
- penetration
- uncoating
- macromolecular synthesis
a) early mRNA and nonstructural protein synthesis: genes for enzymes and nucleic acid-binding proteins
b) replication of the genome
c) late mRNA and structural protein synthesis
d) posttranscriptional modification of protein - assembly of virus
- budding of enveloped viruses
- release of virus
Adsorption or Attachment:
Adsorption involves the attachment of viral surface proteins or glycoproteins to the
receptors on the target cell surface
This step determines the preferential virus infectivity for certain tissues of the
host organism
However
* some viruses recognize more than one receptor;
* different receptors can act in sequence (first contact and subsequent
stabilization);
* the cell entry of some viruses could be receptor-independent.
Some viruses (e.g., HIV) have a double attachment process, involving co-receptors:
Phase 1: low binding affinity with a cell receptor which has the purpose of
bringing the virus closer to a second cell receptor
Phase 2: the second cell receptor promotes the formation of a strong bond and
the virus initiates the penetration
Virus penetration into the target cell:
While attachment also occurs at 4°C, virus penetration occurs only at 37°C and
requires energy
The phenomenon is still poorly understood in its molecular details.
Different viruses use a preferential entry mechanism
Some enveloped viruses enter cells by
direct fusion of plasma membrane and
envelope
Lipids and proteins of the viral envelope are
incorporated into the cytoplasmic
membrane, allowing the entry of the
nucleocapsid into the cytoplasm
Fusion glycoproteins are present on the viral
envelope
Enveloped virus penetration by fusion:
Subsequent steps of
adsorption,
fusion of the envelope with the plasma membrane of the target
cell, and release of the nucleocapsid into
the cytoplasm
Virus endocytosis by target host cell:
Other enveloped (and
naked viruses) are taken
in by receptor-mediated
endocytosis (viropexis)
The viruses (enveloped and
not) engaged in receptormediated endocytosis are
inserted into clathrin-coated
(or caveolin-coated or
uncoated) vesicles which,
after removal of the coat,
fuse with endosomes.
Enveloped viruses will fuse
their envelope with the
membrane of the endosome.
In some cases, only the genome penetrates into the target cell:
__________________
Pore-mediated penetration of Picornaviridae genome
Translocation or direct penetration:
Following a conformational change (invagination) of the cytoplasmic membrane some
viruses spontaneously enter the cell, without interacting with cell receptors
The nucleic acid of_____________________ enters the cell by direct injection,
bacteriophages
Uncoating:
Process that allows the exposure of viral nucleic acid and the subsequent
beginning of the synthesis processes; viral and cellular enzymes can participate
in this process
Macromolecular synthesis
Site of viral replication:
Depending on the type of nucleic acid and its characteristics, viruses
replicate in different ways and districts (cytoplasm, nucleus) of the host cell
Viruses with a DNA genome replicate in the nucleus
Exception: poxviruses replicate in the cytoplasm because they have their
own DNA-dependent RNA polymerase
Viruses with an RNA genome replicate in the cytoplasm
Exception: retroviruses and influenza virus replicate in the nucleus
Viral gene expression:
Viruses can synthesize a molecule of mRNA for each gene (monocistronic RNA),
or mRNA that include the information of multiple genes, which will give rise to
polyproteins that will be subsequently cleaved
Early translation (nonstructural proteins)
proteins translated from mRNAs transcribed from the genome of the infecting
virus
enzyme for nucleic acid replication
regulatory proteins
Late translation
proteins translated from mRNA transcribed from the newly synthesized viral
genome
viral structural proteins
proteins inhibiting early protein synthesis and replication of viral nucleic acids
Replication of the viral genome:
Some DNA viruses use their DNA-dependent DNA polymerase (Adenoviruses,
Herpesviruses, Poxviruses), while others use the cellular DNA polymerase
(Polyomavirus, Parvovirus, Papillomavirus)
All RNA viruses have their own enzymes for their replication (RNA-dependent
RNA polymerases, replicases and transcriptases)
Negative-strand and double-strand RNA viruses bring the machinery for these
processes into the cell together with the genome as part of the nucleocapsid
Hepadnaviruses and Retroviruses have a peculiar enzyme for their replication
(RNA-dependent DNA polymerase or reverse transcriptase)
Replication of Retroviruses:
diploid genome consisting of
two identical positive-sense
linear ssRNA molecules
* Viral reverse transcriptase
(dsDNA) and integrase
* Cellular DNA-dependent RNA
polymerase produces the
transcripts (subgenomic and
genomic)
Replication of
Herpes simplex virus:
1) Attachment and Entry: HSV binds and fuses with the host cell membrane.
2) Transport to the Nucleus: The capsid moves to the nucleus, where DNA is released.
3) Gene Expression: IE, E, and L genes are expressed in stages, controlling replication.
4) DNA Replication: Viral DNA is replicated in the nucleus.
5) Assembly and Envelopment: New virions are assembled and acquire their envelope.
6) Release: Virions exit the cell through exocytosis, potentially causing cell death.
7) Latency: HSV establishes latency in neurons and can reactivate
Replication of Parvoviruses:
Linear ssDNA
* the cells must be actively
multiplying and in S phase
* cellular DNA polymerase makes the
bicatenary genome (replicative
intermediate)
* Cellular DNA-dependent RNA
polymerase II makes the
transcription
* a viral protein cuts the dsDNA giving
rise to two chains of which the
original one, devoid of the repeated
sequences transferred to the newly
formed molecule, is then completed
in 3‘;
* the two chains are then separated
by helicases, leading to the
formation of two molecules that
begin a new replicative cycle
Replication of Hepatitis B virus:
- Genomic DNA (L+S strand)
enters the nucleus and is
converted to dsDNA; - the filament L serves as a
template for transcription by
cellular DNA-dependent RNA
polymerase II; - two types of mRNA are formed:
pregenomic RNA (replicative
intermediate) and subgenomic
RNA (mRNA for protein
synthesis); - encapsidated by core proteins,
the pregenomic RNA is
retrotranscribed into a singlechain DNA by the viral DNA
polymerase and then degraded
by it (ribonuclease activity); - the synthesis of the filament S
follows
Replication of +RNA viruses:
Astroviridae, Caliciviridae, Picornaviridae, Coronaviridae, Flaviviridae, Togaviridae
Linear positive ssRNA
* Viral RNA acts as mRNA
* the viral RNA-dependent RNA
polymerase is translated
* The polymerase generate a
replicative intermediate linear
negative ssRNA to generate a
new positive-sense genome
Virion release by budding (enveloped viruses):
Human-enveloped viruses acquire
lipid bilayer membrane by
budding from a cellular
membrane
The exit from the cell occurs through
exocytosis (in the case of envelope
formation across intracellular
membranes) or budding at the level of
the cytoplasmic membrane, in some
cases also enveloped viruses can be
released by cell lysis
Acquisition of the lipid bilayer membrane by budding from a cellular membrane. Viral spikes are
expressed on the cell surface followed by synthesis of matrix protein that associates near the plasma
membrane where viral spikes are present. The matrix protein attracts the assembled nucleocapsid
(genome + nucleoprotein) near the plasma membrane expressing viral spikes followed by envelope
membrane wrapping and release of the virus particle
The initial budding rarely causes cell death but many progeny viruses released result in loss of cell
membrane permeability
Assembly of naked capsid viruses and nucleocapsids:
Capsids and nucleocapsids selfassemble from preformed
capsomeres
Icosahedral capsids are
preassembled and the genomes
are complexed with condensing
proteins
The process of enclosing the viral
genome in a protein capsid is
called encapsidation
Helical nucleocapsids are
assembled by adding protein
subunits to the RNA genome to
form a helix
For _____ viruses (without envelope) the cell membrane lyses and releases the virions
lytic
Each infected cell may produce as many as 100,000 particles; however, only ________ of
these particles may be infectious. The yield of infectious virus per cell, or burst size, and the
time required for a single cycle of virus reproduction are determined by the properties of the
virus and the target cell
1% to 10%
