Download Virology

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Introduction to Virology
Scribe: Kratika Pareek
Proof: Angi Gullard
Page 1 of 6
Introduction to Virology [S1]
a. For my particular parts on the exam, you will be responsible for what’s on the slides.
b. Talk about introduction to virology, viral replication.
c. Viruses are obligate intracellular parasites – that means that they need a cell to grow in, they just don’t
grow outside of cells in tubes.
d. Viral pathogenesis - that’s how virus replication causes disease and how viruses escape and interact with the
immune systems.
e. Viruses themselves actually do not cause that much disease; it is the immune response to viruses that
causes a lot of the symptoms that you get, and we will talk about that with the common cold.
The DNA  RNA Protein Pathway [S2]
a. Viruses follow the dogma of molecular biology, which is DNA to RNA to Protein.
b. DNA viruses go to the nucleus and utilize cellular proteins in the nucleus for their gene expression.
c. RNA viruses replicate in the cytoplasm, and use proteins in the cytoplasm for their replication. All of the
viruses that we are going to talk about use the host cell machinery for translation – that is RNA to Protein.
They do not encode enough genetic information for translation by themselves. So they are going to steal
elements of the host translational machinery.
Characteristics of Viruses [S3]
a. Early on, they described viruses as filterable agents. They pass through filters that capture bacteria.
b. They found that they could take mixtures and filter out the bacteria and take that clear supernatant and put
that back on to certain bacteria, and it would kill that. That is how they got the word viruses.
c. It started with the word “phage”. They called them bacteriophages. What they found through these studies is
that they are obligate intracellular parasites. They have minimal genetic information compared to eukaryotic
DNA genome. You have 20,000-50,000 proteins; viruses don’t encode 1/10 of that. They rely on the host to
complete the replication cycle.
 Viruses are mainly assembled from building blocks, meaning that they don’t divide like cells. Most of the
time, viruses main goal in their life is to make new viruses. They make a lot of new viruses because they
want to infect cells. They absolutely require a host cell for replication to produce proteins.
For Viruses to be Successful: [S4]
a. Viruses have to be able to transmit through harsh environmental conditions.
b. Most viruses are transmitted through in a fecal/oral manner. That means viruses like to live in your gut, you
excrete them into the environment, they pass through the environment and you re-ingest them. Those are
called enteroviruses. Other viruses are exhaled.
c. When a person sneezes on you, viruses are in these droplets being shot out and landing on you and trying to
get into your lungs to replicate.
d. One of the major organs to protect you against viruses is the skin. Viruses have developed ways to get
around this – through your mucosal tissues. Once viruses get into a cell, it’s not immediately successful. They
have adapted to actually use the biochemical machinery of the host for replication. They are going to steal
your host cell machinery – convert your cells into virus factories.
e. Viruses have developed numerous methods to escape elimination by the host’s immune system. You have
an immune system that protects you from viruses and infection. Viruses devise ways to get around the
immune system.
Basic Components of a Virion [S5]
a. They are very simple – either DNA or RNA. All of your genetic information is DNA. DNA viruses are like your
chromosomes. They have structural proteins which surround this nucleic acid in order to protect from the
environment. Some viruses have enzymes and nucleic acid binding proteins that are in the virions. It is
important to know which ones have these enzymes because that means they are different virus from viruses
that don’t have enzymes.
b. This forms a nucleocapsid which can also be a naked capsid virus. It can also be encapsulated by an
envelope, a term virologist like to use. The best way to view an envelope is it is like a soap bubble that
encapsulates the virus. Embedded in this soap bubble are viral proteins that help it enter cells
Virus Classification [S6]
a. There are many ways to classify viruses: size, morphology, genome type, and means of replication.
b. DNA viruses are generally enveloped or naked capsid. Envelope viruses are the one with the soap bubble
around them. Some viruses that you have heard about: herpes and smallpox. Naked capsid viruses include
Papilloma and Polyoma viruses,
c. RNA viruses can be subdivided into several different categories. One is a plus-strand RNA virus; one is a
negative-strand RNA virus. Both are single-stranded RNA viruses. You will not be tested on negative-strand
RNA viruses. There are some viruses that have double-stranded RNA. Finally, there is one type of virus that
Fundamentals 11:00-12:00
Scribe: Kratika Pareek
Thursday, 10/28/10
Proof: Angi Gullard
MORROW
Introduction to Virology
Page 2 of 6
is backwards compared to the DNA to RNA to Protein. These viruses are called retroviruses; these go RNA
to DNA to RNA to Protein. Retroviruses are important for you because one of the most well-known
retroviruses is HIV.
VII. Relative Sizes of Viruses [S7]
a. It is important to realize viruses are small. They are smaller than cells because they obligate intracellular
parasites. As you can see, compared to E.Coli (can’t be seen with naked eye), most viruses are considerably
smaller than E.Coli with the exception of the poxvirus. You cannot see viruses with the naked eye – must use
an electron microscope.
b. The one exception is the poxvirus, which causes smallpox. Supposedly you can see it if you have very good
eyesight – may not be the case.
VIII. General Structure of Viruses [S8]
a. Virus Shapes. Since we can’t see virus shapes, a lot of these have been determined by a 3D structural
analysis that you will hear about a lot tomorrow. In general, viruses come in 2 different shapes. One is an
icosahedral virus which is analogous to a soccer ball. A lot of them are made in the same way of just patching
together common subunits.
b. Another type of virus structure is what we call nucleocapsid which is the viral RNA-genome (in this case)
bound by proteins. I don’t want to confuse you because nucleocapsid is used in both terms for the viral
nucleic acid surrounded by the icosahedral virus as well as this particular structure (picture on slide). We are
going to compare icosahedral viruses to non-icosahedral viruses (nucleocapsids).
c. Either one of these two structure can be found in an envelope virus. Surrounding the nucleic acid is a
membrane – a lipid bilayer with viral proteins embedded in it. This lipid bilayer is analogous to the soap
bubble. This is attained as the virus exits the cell – it picks up some of the host’s cell membrane to surround
it. It uses the layer in its infection process.
IX. Genome Contents of Viruses [S9]
a. For RNA viruses, you can have single-strand, double-strand, linear, or segmented. We will focus mostly on
single and double-stranded RNA virus.
b. DNA virus are mostly double-stranded, but you will also hear about a few which are single-stranded, linear,
or circular.
c. Not important to memorize this slide. I just want to you appreciate the fact that viruses come in lots of
different shapes and sizes
X. Naked vs. Enveloped Viruses [S10]
a. This is an important slide! Naked vs. Enveloped virus. Naked capsids are these viruses that form these
nice icosahedral shells. In contrast, envelope viruses can also have icosahedral components, but they’re
surrounded by this lipid bilayer. Embedded in the bilayer are viral proteins.
b. The difference between a naked capsid virus and an envelope virus with respect to how to kill them is very
important. A naked capsid does not have an envelope - just tightly-bound, compacted proteins around the
nucleic acids allowing it to withstand harsh environmental conditions. Transmitted normally fecal/orally or
sometimes during a spray. They are resistant to drying, acids, detergents – mainly detergents. What this
means is that if you put Lysol on a tabletop, you cannot kill naked capsid viruses. One of the major naked
capsid viruses is rhinovirus, one of the agents for the common cold.
c. In contrast, the enveloped viruses are much more fragile. They don’t dry, not stable in acid, and generally
remain in body fluids. When you add Lysol to these viruses, you pop the bubble thereby inactivating the virus
making it non-infectious. Example is influenza, the flu virus. It is important to realize the difference between
the naked capsid and envelope viruses – envelope viruses can be readily inactivated by drying them out or by
using detergents to remove the lipid bilayer.
XI. Icosahedral Capsid Assembly [S11]
a. People have studied the assembly of these icosahedral viruses for a long time. Basically, these highlight the
point that they are built from small blocks of proteins that self-assemble into these capsids. They start out as
singular proteins; they self-aggregate; they form pentamers; which then form further aggregates; eventually
form an icosahedral virus. This virus looks like a soccer ball. Once they form the complete capsid structure, it
is a very stable structure. These viruses are the ones transmitted in a fecal/oral manner.
XII. Examples of Icosahedral Capsids [S12]
a. 3D structures. Look very similar. Most of these are transmitted in a fecal/oral manner. Some of these are
plant viruses.
b. The Rotavirus and Reovirus cause a significant amount of disease in humans.
XIII. General Enveloped Virus Structure [S13]
a. In contrast, enveloped viruses included HIV and influenza virus. They have a similar structure in that they
have this envelope surrounding the viral capsid core (a nucleocapsid). They are not the same as the
Fundamentals 11:00-12:00
Scribe: Kratika Pareek
Thursday, 10/28/10
Proof: Angi Gullard
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Introduction to Virology
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icosahedral structure. The envelope protects the core from the environment. Embedded in the envelope are
viral proteins which the virus uses to interact with the host cell in order to invade it.
XIV.
Example Envelope Glycoprotein Influenza Hemagglutinin [S14]
a. This is influenza virus. This is the molecule that interacts with the cell that it infects and in doing so it
redistributes this protein, which inserts into the host cell membrane to open it up and go through an infection.
These are negative stranded RNA viruses.
XV. Steps of Virus Replication Cycle [S15]
a. This is a very important slide. Important to remember the steps in replication – I am going to ask you this
question on the test!
b. We will start out talking about the attachment part and the interaction of the virus with the host cell receptor
and the penetration part. We have 2 different types of viruses here: One is the icosahedral virus and the other
is the enveloped virus. As you can see they enter in different ways to get to the point of uncoating.
XVI.
Attachment [S16]
a. Viruses are intracellular parasites. So they need to interact with something on the cell in order to get into the
cell. It is usually this point of interaction that determines a lot of the pathogenesis of the virus. For example,
HIV, the viral glycoprotein, the GP120 that is embedded in the envelope of this virus interacts with a cellular
protein called CD4 and then another cellular protein called CCR5 or CXCR4. That is why HIV preferentially
infects CD4 positive cells. So people that develop AIDS lose their CD4 positive cells because HIV replicates
inside those cells and kills them. HIV does not replicate in a CD8 positive cell. Because CD4 is not CD8, and
HIV cannot enter those cells.
b. In contrast Flu interacts with sialic acid that is found on many different cells. So Flu can get into a lot of
different cells such as epithelial cells because of the sialic acid cell receptor. Depending upon the receptor,
the virus will enter different set cells.
XVII. Steps of Replication Cycle [S17]
a. We have this process of recognition, attachment, and then penetration. So it is going from the outside to the
inside of the cell. This particular process for the icosahedral ones is engulfed into a lysosome, and then [once
inside] busts out of the lysosome to release its nucleic acids
b. In contrast, Flu viruses or HIV will interact with the cell surface and because they have a lipid envelope. They
will fuse with the cell surface and release their nucleic acids into the cell. These are the two different paths for
how these viruses infect.
XVIII. Synthesis of New Viral Components [S18]
a. Once they are in the cytoplasm of the cell, viruses will have different ways to express their nucleic acids,
which are the mRNA encoding viral proteins such as make new viral genomes for encapsidation as well as
viral proteins – enzymes and other proteins required for transcription and genome replication and structural
proteins.
XIX.
The DNA RNA Protein Pathway [S19]
a. The first slide, we talked about the central dogma of DNA to RNA to Protein. Viruses utilize this pathway in
their replication. DNA viruses will go to the nucleus. They will encode several different proteins, but they use
a lot of the RNA polymerase II molecules that make mRNA from the DNA template. They will steal these to
make their own messenger RNAs which will be translocated to the cytoplasm to make viral proteins and then
that will begin to take over the cell.
b. RNA viruses do not use the nucleus mainly. They will just initially make their RNAs in the cytoplasm and then
they will also become translated
XX.
DNA Virus Transcription [S20]
a. DNA virus transcription uses host cell’s DNA dependent RNA polymerase II to make mRNAs. In your
nucleus, the way you make an mRNA is you have a polymerase (RNAP II). RNAP I is used for ribosomal
RNA. RNAP II makes mRNA. The DNA viruses will steal RNAP II to make the viral mRNAs. The DNA viruses
have to get to the nucleus, so they will infect on the plasma membrane and will be transported to the nucleus.
They will release their DNA and begin to steal the RNAP II to make viral message.
b. There is one exception that you should know: the Poxvirus. It is referred to as the smallpox virus. This is a
huge DNA virus that somehow in evolution got lost. This virus replicates only in the cytoplasm of the cell, so it
does not use the host cells RNA-polymerase. It is so big that it makes its own RNAP II. This is the only DNA
virus that replicates in the cytoplasm
XXI.
RNA Virus Transcription [S21]
a. RNA viruses, in contrast, they don’t rely on the nucleus too much. They mostly replicate in the cytoplasm of
the cell.
b. Flu virus, however, replicates in the nucleus.
c. They must encode their own enzymes. One is called RNA-dependent RNA-polymerase. It is RNA-dependent
meaning that it needs an RNA genome; and it makes a new RNA – it’s an RNA-polymerase.
Fundamentals 11:00-12:00
Scribe: Kratika Pareek
Thursday, 10/28/10
Proof: Angi Gullard
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Introduction to Virology
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d. The Host cell has no enzymes for generating new viral RNA genomes using an RNA template. You will hear
in the next 5-10 years about the development of many therapeutic compounds designed to inhibit RNAdependent RNA-pol, because these are enzymes that viruses uses but the host does not. This is what people
would refer to as the “magic bullet” – kill the virus without hurting the host cell. They are currently in
development, but you have heard of a few of these such as AZT which is used against HIV. AZT targets the
reverse transcriptase, which is not found in normal cells
e. 2 points from this slide that you want to know for the test: Know distinction between + strand and – strand
RNA viruses
i. +strand have the same sense as the mRNA, which means that they can be directly translated just like
mRNA.
ii. –strand viruses are genomes that have an opposite sense of mRNA, which means that they cannot be
directly translated. They must be copied first to produce +strands in order to be translated. –strand RNA
viruses cannot be translated because the cell does not recognize it. Within their virions however, they carry
an enzyme that makes +strand RNA
XXII. Replication of Viral Genomes [S22]
a. Replication of viral genomes. DNA viruses use an enzyme called DNA-dependent DNA-pol which requires
DNA to make new DNA. Some of these will use host’s cellular DNA-pols, while others create their own.
b. RNA viruses use RNA-dependent RNA-pols to make new RNA copies. It is encoded exclusively by viruses.
Not found in normal cells meaning they are excellent targets for antivirals.
c. Retroviruses such as HIV are technically RNA viruses. It packages an enzyme called reverse transcriptase
which goes form RNA to DNA and that gets integrated into the chromosomal DNA. Then the new viral DNA
genomes are transcribed by the host cell. Although it sounds relatively simple now, in the 1970’s, this was
such a radical concept that it was awarded the Nobel Prize to David Baltimore and Howard Timmon. It also
helps that retroviruses cause a significant amount of disease.
XXIII. Viral Protein Synthesis [S23]
a. Viral protein synthesis occurs in a couple of different ways. All viruses depend on the host cell translation
machinery, which includes ribosomes, tRNA, post translational modifications. They use a couple of different
strategies because they have less genetic information. One is that they use separate mRNAs for each viral
protein. That is pretty bland.
b. I want you to remember this polyprotein strategy – which means that multiple proteins are encoded at one
mRNA. Individual proteins are derived from a polyprotein by enzymatic cleavages catalyzed by proteases,
sometimes viral proteases, sometimes host cell proteases that they steal.
XXIV. Polyprotein Strategy [S24]
a. These viruses are long +strand RNAs that make one single, long polyprotein, which is then cleaved at
specific amino acid pairs to yield different sets of proteins. These form the caps, and the replication proteins.
They are cleaved by 3CPro which is a viral protease. As the polyprotein is being made, once it gets past
3CPro, it bites itself out, goes and recognizes these different sites and cleaves these polyproteins to make
the virus protein.
b. This is important because since this is a specific viral protease which the virus absolutely needs for
replication, it becomes an excellent target for drugs. Developing drugs for the Rhinovirus. HIV uses this
polyprotein strategy, and there are drugs called protease inhibitors used (in combination with inhibitors for
reverse transcriptase) to knock down HIV
XXV. Assembly and Release [S25]
a. The first three steps are invariant. Steps 5, 6, and 7 can sometimes change depending upon the virus. When
I ask a question about this, I will distinguish between that – not try to trick you.
b. After that, the virus has to get released from cells. It is released in two different ways:
i. For envelopes, it fuses with the plasma membrane and then buds off from the cell.
ii. Naked viruses assemble their capsid in the cytoplasm and generally release through the cell via cell lysis,
meaning that they explode the cell – called lytic viruses.
XXVI. Lytic Virus Growth Curve [S26]
a. These viruses, Picornavirus in particular, grow very fast in cells and grow to such high titers. They explode
the cells. They are lytic viruses.
b. Other viruses such as retroviruses are more passive in their release from cells and generally they do not kill
the cells. Instead the cells become viral factories. This is important because this will dictate the immune
response that you will get towards the viruses
XXVII. Viral Budding from Cell Membrane [S27]
a. This is a picture of a virus budding, which is a very elegant process. Picture of HIV budding from host cells.
As you can see it assembles on the plasma membrane and then buds off. The plasma membrane surrounds
Fundamentals 11:00-12:00
Scribe: Kratika Pareek
Thursday, 10/28/10
Proof: Angi Gullard
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Introduction to Virology
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the virus becoming the envelope. Embedded on the viral envelope are viral proteins that are used to re-infect
the cell.
XXVIII. Viral Pathogenesis [S28]
a. Now we will talk about viral pathogenesis. Viral pathogenesis is the interaction between the host and the
virus. General steps:
i. Entry into the body by several different routes.
ii. You want to distinguish between the primary site of replication and the secondary site. Generally the
secondary site is a result of viremia, meaning viruses found in the blood. Usually it is the secondary site
that causes most of the viral pathogenesis. If the viruses would stay where they initially infected you, they
would go through the infection process, you would be able to handle the virus. It is usually when they go
through a viremic phase to a secondary site where they cause a problem.
XXIX. Example: Ebola [S29]
a. In the initial infection process, it infects macrophages. If these macrophages stayed where the infection was,
they would be able to control the infection and that would be the end of it. Macrophages like to migrate.
However, and when they do, they induce an immune response. The immune response is what causes the
problems such as extracellular bleeding.
XXX. Outcomes of Virus Infection at the Cellular Level [S30]
a. Most of the time virus infections fail – they are aborted. That is good for us because otherwise we would be
dead. They are not very effective at infecting us. When cells do get infected, you can have a couple of
different features:
i. Lytic – viruses can replicate in high enough amounts causing the cell to explode and release the virus.
ii. Many times as part of the evolutionary process, the cells undergo apoptosis – which is programmed cell
death. This means that the cell senses that it is being infected by viruses so it kills itself so it will not
produce new viruses. This prevents the total body from being infected by killing the cell at an early stage.
b. You can also have infection without cell death. This is generally what you get with chronic infection – no cell
lysis and new viruses are produced. Retroviruses are known for chronic cell infection
c. You can have latent infection. This is typified by Herpes Simplex Virus. This is where you become infected
with Herpes, you clear it, you go out in the sun and all of sudden you have a lesion appearing. This is a latent
reactivation of Herpes virus. Usually stimulated by stress or changes in your immune system’s response to
the virus.
d. Finally, you can have transformation. These are oncogenic viruses. Initially there was a lot of interest in
oncogenic viruses such as retroviruses especially in chickens. They found that retroviruses were oncogenic.
There have been a few cases of human oncogenic viruses. The other oncogenic viruses that you have heard
of are papilloma viruses. In replicating, they produce new cells, but also new viruses. These new cells
replicate without mind for the tissue that they are in. They can cause tumors and other serious problems.
XXXI. Host Defenses Against Viruses [S31]
a. This is an important slide because it tells you how your body defends itself against viruses. Remember the
four general categories.
i. The natural barriers of the body (the skin). The skin is the most important organ of the body to defend
against viruses. If viruses can’t get in, then they can’t infect. When you are dealing with your patients, you
do not want to have exposed sores on your body.
ii. You have an innate immune defense, which means it is not antigen dependent or virus dependent/specific.
This includes the interferon response, a cytokine made in response to virus infections in order to inhibit viral
infections. Macrophages go around and engulf viruses. Dendritic cells kill viruses and present the antigen
to different cells. Natural killer cells go around and kill everything that they can.
iii. You also have antigen-specific immune responses, which include antibodies. The premise of most
vaccines that we use is to make antibodies so we immunize you against the virus. You make these
antibodies which bind to the virus. Antibody binding prevents the virus from getting into the cell, which
stops it from making new viruses. Because antibodies circulate, they can prevent a virus from infection a
secondary site which was critical in the development of the polio virus. There are also Helper T-cells, which
actually help the B cells to make antibodies.
iv. Cell-mediated immunity is the process by which virus infected cells are eliminated. This is an important
concept that was again awarded the Nobel Prize in the mid 1990’s for MHC restriction. The CD8 cells (not
CD4) are killer cells, which when they become immunized, can recognize virus infected cells and kill those
cells, thereby protecting you from viral infections.
XXXII. Viral Strategies to Evade Host Defenses [S32]
a. Viruses have strategies to counteract the actions our immune system takes. It is a constant battle between
the two. They can prevent the interferon action. Interferon is generally stimulated by double-stranded RNA.
Because of the interferon response, if you make too much double-stranded RNA, you will blunt the interferon
Fundamentals 11:00-12:00
Scribe: Kratika Pareek
Thursday, 10/28/10
Proof: Angi Gullard
MORROW
Introduction to Virology
Page 6 of 6
response so the virus will try to produce just enough dsRNA so as to not to block the interferon response. If
the interferon response works, it shuts down translation and that eventually leads to the degradation of the
viral RNA because it cannot produce its own proteins
b. One of the big ways that viruses get around the host’s immune response is by changing the viral antigens. All
of you have heard about this in 2 prominent viruses: HIV and Flu. The way they do that is the viral
polymerases – the RNA-dependent RNA-pol for Flu and the reverse transcriptase for HIV – are very errorprone. This is a time where it is actually good to make a lot of mistakes because in doing that you have a lot
of genomes that when the host makes an immune response which is very specific for one particular strain,
there are some strains that are still that that are not neutralized by the antibody or killed by the cytotoxic Tcells and they get to keep growing. By making this high error rate in the viral polymerases, that allows them to
begin to evade the immune system. It is important recognize here this viral polymerase, not the host’s
polymerase. This is a very important distinction. The viral polymerases can make many mistakes, not the host
cell enzyme.
c. Viruses are spread cell to cell many times, meaning that viruses are spread by cells fusing together or cell
contact. So viruses do not have to become extracellular where they could be potentially neutralized.
d. Finally, viruses have ways to suppress the antigen presentation and lymphocyte function. So when HIV will
infect a cell, many times it will make that cell incapable of functioning as an immune cell. It will inactivate
these processes. So basically this cell becomes a virus producing factory that cannot help the generation of
immune response to the virus.
XXXIII. Viral Immunopathogenesis [S33]
a. In the last slide, we will talk about viral pathogenesis. Viral pathogenesis many times is your host immune
response to the virus, not the virus causing the response. When you have Flu-like symptoms, these are a
result of interferon and cytokines (respiratory viruses). Flu-like symptoms include sniffling, higher
temperature, sputum. These are not caused by the virus. It is caused by the immune response to the virus.
You body raises its temperature because viruses do not like to replicate in temperatures above 37 degrees.
This temperature increase is a response to cytokines. Many times you develop mucus; you sneeze to get the
virus out. The mucus develops and is swallowed transporting the virus into the stomach. Many of these
viruses are not stable in the low pH (2) environment of the stomach. These are all grouped together as Flulike symptoms.
b. The other things here are much more diverse and they are basically the response or over-response of your
immune system to the virus. Delayed type hypersensitivity means that some of the response to these viruses
cross-react to other tissues in your body. That allows the symptoms of delayed-type hypersensitivity, immune
complex disease, hemorrhagic disease, post-infection cytolysis, and even immunosuppression. Some viruses
actually cause immunosuppression like HIV and cytomegalovirus. It is that immunosuppression that is caused
by virus infection but also sometimes by the stimulation of host cell proteins that actually result in the actual
response to the virus infection.
[End 51:57 mins]