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Summary Abstract Infectious Agents and Immunity Biomedische Wetenschappen
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Abstract Infectious Agents and Immunity, Biomedical Sciences, Leiden University, English
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VirologyVirus particle is very small. Virus can only replicate in the host. What is a virus:
• RNA or
• DNA
• Protein Coat
• Membrane envelope
The size of a virus is around 100 nm. Virus is not alive and don’t have their own metabolism, they
cannot grow and multiply on their own. It has to enter the host cell and replicate. Also, maintaining
itself by transporting to another host. A virus particle can have either DNA or RNA, never both. Virus
has all kinds of different forms. RNA and DNA need to be protected from degradation by encapsulate
(protein). Many viruses do also have a membrane which are proteins sticking out and this is
important to enter a host cell (spikes).
Characteristics of viruses:
• An infectious, obligate, intracellular parasite.
• Viral genome compromise either DNA or RNA.
• Within a cell a viral genome is replicated and directs the synthesis, by host cellular systems,
of other viral components.
• Progeny infectious virus particles (virions) are formed by the novo assembly from newly
synthesized components in the host cell (not the membrane of the virus, stolen from host in
ER or outer membrane host).
• Progeny virions (new virus particles) are the vesicles for the transmission of the viral genome
to the next host cell, disassembly leads to the beginning of the next infectious cycle.
Virus will go open to replicate when it is in a host cell. Electromicroscope is the only way to see the
virus particles. Bacteriophages are viruses which infect bacteria.
Virus classification:
Viruses are classified according to four main characteristics:
• Nature of the nucleic acid (DNA or RNA, positive strand can be translated, negative first have
to be transcribed into positive to be translated)
• Symmetry of the protein shell
• Presence or absence of lipid membrane (envelope)
• Dimensions of virion and capsid
Genomics had become increasingly important.
Baltimore classification:
• Classification describes the relationship between the viral genome and mRNA.
• mRNA is the central focus of this scheme.
• By knowing the nature of the virus genome, the basic steps to produce mRNA can be
deduced, simplifying comprehension of
complex viral live cycles.
• The Baltimore scheme lacks information
on viral genome synthesis, the second
universal function of viral genomes.
mRNA is necessary to make new protein. Positive
stranded RNA virus can directly transcribe their
genome by making negative strand and copy this
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,back into positive strand to translate the RNA. Negative stranded RNA virus, first copy into positive
RNA strand to be able to translate the genome and form mRNA.
DNA single stranded you first have to make double stranded RNA to translate. Double stranded RNA
can be made into mRNA.
Retrovirus positive RNA stranded virus, first copy RNA back into DNA (humans never do) by using
reverse transcription. Enzyme is reverse transcriptase and only retroviruses do have this enzyme.
Classification RNA viruses based on what their protein shell looks like. Protect by helical (enveloped)
or Icosahedral: naked (no membrane) or enveloped (membrane). Negative stranded RNA need to be
copied negative strand into positive strand and need an enzyme that the host doesn’t have (human
never copy RNA into RNA). RNA viruses have to bring their own polymerase (virion polymerase in
virus particle).
DNA viruses have the same principle. Complex (enveloped) or
Icosahedral: naked (no membrane) or enveloped (membrane).
Virus life cycle:
Virus particle inside the host cell. Attachment of the virus,
penetration and uncoating. Copy genetic material, make new viruses
and get out of the host cell to infect another cell or another host.
Functions of viral proteins I (structural):
• Protection of the viral genome.
Assembly of a stable, protective protein shell. Specific recognitions and the packaging of the
nucleic acid genome. Interaction with the host cell membranes to form the envelope.
• Delivery of the genome.
Binding to host cell receptors. Transmission of signals that induce uncoating of the genome.
Induction of fusion with host cell membranes. Interactions with cell components to direct
transport of viral genome to the appropriate site.
Structure and (protein) components of a virus particle, and how they enter the cell.
The nucleocapsid: a protective coat
• A protein structure enwrapping the viral genome.
• Genetic economy dictates that this protein shell is built by using the same type if molecule
over and over again.
• The structural properties of the capsid proteins permit regular and repetitive interactions
among them.
• The coat of most viruses displays a helical or icosahedral symmetry.
Helical symmetry:
Coat protein molecules engage in identical, equivalent interactions with one another and with the
viral genome to allow construction of a large, stable structures form a single protein unit. Tabacco
Mosaic Virus (TMV), Vesicular Stomatis Virus nucleocapsid (Rabdovirus), Influenza virus.
Icosahedral symmetry:
Most economical way to build a closed symmetric shell with the
smallest number of the identical subunits, maximal internal
volume, with nonsymmetric proteins. Solid with 20 faces, each an
equilateral triangle. 12 vertices 5:3:2 axes of rotational symmetry.
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,Complex symmetry:
Some viruses are more complex, being composed of several separate capsomeres with separate
shape and symmetry. They do not have icosahedral or helical symmetry. Adenovirus, bacteriophage,
vaccinia virus.
Viral envelope glycoproteins:
Integral membrane glycoproteins (stolen from host). Ectodomain: attachment, antigenic sites, fusion.
Internal domain: assembly (interaction with RNP via M protein). Coronavirus.
Viral matrix proteins:
Structural proteins that link the viral envelope with the virus core. They play a crucial role in virus
assembly. Vesicular stomatis virus, Human Immunodeficiency Virus (HIV).
Viral spike proteins form oligomers that are homomeric or heteromeric in structure. Viruses use
spike proteins as keys to stuck into lock of the surface of the host cell.
Virus particles are not inert structures:
• Virions are meta-stable structures. They have not yet attained the minimum free energy
conformation.
• This is only achieved when an unfavorable energy barrier is surmounted, followed by
irreversible conformational changes during attachment and entry. Energetically elevated,
does not need energy to get into the host cell. Energetic state is higher and will be broken
down to be able to enter the next cell. Spike protein bind receptor, conformational change,
lower energetic levels and because of that the virus can enter the host cell.
• Virions are molecular machines that play an active role in delivery of the genome.
Virus entry: the start of infection
1. Binding to the receptor
2. Penetration of the membrane
3. Uncoating to allow replication,
transcription and translation.
Right image: virus is taken up into an
endosome. Endosome and virus envelope fuse
together and the virus is in the cytosol of the
host cell. This called uncoating.
Enveloped and none-enveloped viruses have
different penetration strategies. None-
envelope also have receptors binding to the
host cell surface to enter the host cell.
pH independent and acid activated virus-host
cell membrane fusion.
pH independent fusion (plasma membrane):
• Most retroviruses (HIV),
• Herpesviruses,
• Paramyxoviruses (RSV, measles),
• Some coronaviruses
NH4Cl can be added to the medium to determine the route of entry.
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, Acid activated fusion (endosomal membrane):
• Filoviruses (Ebola),
• Flaviviruses (dengue, YFV),
• Rhabdoviruses (VSV, Rabies),
• Orthomyxoviruses (influenza),
• Some coronaviruses.
Fusion of a retrovirus (HIV) at
the plasma membrane. HIV
entry of the host cell requires
the use of two different two
in a fixed order: CD4 and
CCR5.
Flu virus fusion at the endosome. Conformational change that
enables encountering of the two membranes together so that
fusion can take place. Don’t need to know details.
Cell surface molecules serve as specific virus receptors:
• Binding to the receptor does not require energy and is
temperature independent
• Initial binding is usually weak
• Affinity versus avidity, it all depends on how well the
spikes bind to the receptor. Strength depends on the
number of spikes binding the receptor.
• The role in virus transmission
Virus tropism: which kinds of organs/cell types a virus tragets.
The surface receptors used by the virus (largely) determine which effects/symptoms the virus causes:
• Hepatitis
• Respiratory symptoms
• Intestinal symptoms
• Skin symptoms
ACE II SARS coronavirus
CD46 Measles
Intergin avB 3/5 Adenovirus
Scavenger receptor DC81, claudin, including HCV
Siaclic acid (carbohydrates) Influenza
CD4, CCR4, CCR5 HIV
Strategies for viral replication and transcription.
Replication and transcription:
The nature of the genome and/or the site of replication and transcription will determine which of the
enzymes needed for replication and transcription have to be encoded by the virus. Generally, the
nature of the genome determines where replication and transcription take place: DNA viruses
nucleus (except poxviruses). RNA viruses cytoplasm (except orthomyxoviruses; Flu).
General characteristics of DNA virus replication.
• DNA comes in different shapes and sizes.
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