Virology Test 1

Lectures 1-6 combined study material

Why are we studying virology?

• improvements in human health (ex: life expectancy, eradication of epidemics)

• Viruses affect every living organism!!!!

• understanding new emergent viruses and viral mechanisms

What did Pasteur and Koch discover that is important to the history of virology, and when did they discover this?

Discovered that microscopic organisms can be the causative agents of disease

Late 1800s

What is filtering, and which scientists FIRST used this? Which virus did they study, and what was their main discovery?

Filtering: A process of separating solids from liquids or gases using a porous material or a sieve to remove impurities.

Ivanovsky (1892) and Beijerinck (1898) discovered the tobacco mosaic virus using this filtering approach.

Main Discovery: realized that they can be smaller than bacteria!!!!

Which scientists studied foot and moth disease and what did their discoveries lead to?

Loeffler and Bosch (1898)

This was the first recognition and identification of the viral particle.

Who is Louis Pasteur and what did he do?

produced the first rabies vaccine… but he didn’t even know what viruses were!

• produced “attenuated viruses of different strengths” (LIVE viruses of different strengths)

• the weakest level was used for the first dose, and only 1/350 people actually got infected with rabies after the injection

Who made the first vaccines for polio? What was the difference between them?

Salk made the first inactivated vaccine for polio in 1954. Sabin developed an attenuated vaccine in 1959.

Attenuated: weakened live viruses that can replicate in the body, and can cause an asymptomatic infection.

Inactive: contain killed or inactive viruses that cannot replicate in the body.

Who was the person who studied yellow fever virus? What is notable about this virus, and what did he study specifically about it?

How did he test this?

Walter Reed discovered the yellow fever virus, which is the first human virus that was able to be studied. He studied the transmission cycle.

To do this, he tested the infection by using a mosquito vector on human subjects.

What important discovery was made in the year 1911?

Viruses play an important role in the development of certain tumors.

What important discovery was made in the year 1915? How did this help microbiologists?

Bacteria have viruses too.

This helped microbiologists understand DNA to be the genetic code.

What important discovery was made in the year 1930?

Electron microscopy****

This opened our view of virus shapes and sizes by increasing the SCALE

We cut the surface and then look at the inside. What important discovery was made in the year 1915?

What important discovery was made in the 1940s and onward?

New viruses continued to be discovered.

Ex: Hepatitis, HIV, SARS, COVD

What is the virosphere? Why is it important??

“Viruses are everywhere”. Viruses are more abundant than bacteria.

Many viruses have important ecological roles as PHAGES while some do not have harmful effects such as human gut microbiome.

What category do viruses fall under?

Acellular, composed of protein and nucleic acid

What category do viroids, satellites, and prions fall under, and what are each of them composed of??

All are acellular.

Viroids: composed of RNA

Satellites: composed of nucleic acid enclosed in a protein shell

Prions: composed of protein

Generally, what are some key components that viruses contain?

Proteins, genomes, lipid membranes (sometimes)

Notably, what do viruses NOT contain? What can they NOT do?

ribosomes, organelles, multiple nucleic acid types.

cannot divide via meiosis, mitosis, or binary fission, and are not metabolically active on their own

What is an important difference between viruses and other types of unicellular microorganisms and viruses??

What does this mean about viruses and the treatment for their effects?

Viruses have many infectious nucleic acids. They persist as nucleic acid integrated into the host genome for the LIFETIME of the host.

It means that they have a harder time treating them, because they do NOT follow the principles of antibiotics.

What is the hypothesized origin of viruses?

It’s unknown, but there are some theories.

• Could be escaped eukaryotic genes

• Maybe degenerate forms of intracellular parasites

• A random origin as an alternative form to pack nucleic acid enzymes

What’s important to remember about giant viruses, and what are some examples of them?

They have massive genomes!!!! They can be seen with a light microscope, and their genomes are larger than some bacterial genomes.

• Mimivirus

• Megavirus

• Pandoravirus

What are key elements of a non enveloped virus?

1. capsid

2. nucleic acid

What are they key elements of an enveloped virus?

1. envelope

2. spikes

3. capsid

4. nucleic acid

What two components does a nucleocapsid contain?

• nucleic acid

• protein capsid

What is the envelope made of?

lipids

What three categories of infectious molecules are NOT viruses, even though they’re similar?

1. Viroids

2. Satellites

3. Prions

What are viroids? How do they infect hosts, and how large are they?

They are covalently closed, ssRNA molecules.

They hijack the host DNA-dependent RNA polymerase for replication!!

They’re around 200-300 nucleotides long (really not that big at all lol)

What are satellites, and how to they differ from viroids?

Although they are similar to viroids, they are composed of DNA OR RNA, and sometimes can require a helper virus to replicate.

What are prions and how do they infect?

What are these associated with?

Prions are infectious abnormal proteins with configurations that turn normal cell forms into abnormal cell forms!!

They’re associated with some neurodegenerative diseases.

What are viruses?

small, infectious, obligate intracellular parasites

What are the role of virions, and are they considered a complete viral particle?

Yes, they are complete viral particles. A virion’s role is to:

-protect the genome of environmental damage

-facilitate passage to a host, including entry

What are the key structures of a virion, and what are their functions?

-Capsid: (protein, made of capsomeres or protomers)

-envelope (lipid, taken from the host)

What type of technology has helped discover details of protein capsid arrangement and assembly at very small scales?

X-ray crystallography. The colored images here are computer generated; put together via what X-ray crystallography has allowed us to figure out, showing monomers and arrangement.

Why is the level of detail that X-ray crystallography supplies important and useful to us?

-it allows us to see how the virus is structured- if we treated a virus that looks like this one, maybe a similar treatment would work for this one, too.

-We can see proteins on the surface and how they interact with the host

What are three examples of how the analysis of protein structure can help us to better understand viruses?

• Structure of hemagglutinin (HA) in influenza viruses allowed for understanding location of neutralizing epitopes

• Variations of amino acid is

  currently used in

  development of updated vaccines

• Individual proteins like neuraminidase (NA) in influenza can be analyzed at 2-3A resolution to develop antivirals

what makes up the protein coat or capsid?

protomers or capsomers

what is the function of the capsid?

protection of the genome

Capsid + genome =

nucleocapsid

True or false: the nucleocapsid and an envelope are the same thing.

False- Enveloped viruses have an additional lipid layer surrounding the nucleocapsid.

What are the proteins that may be inserted onto the envelope?

peplomers

How many proteins do the most important viruses code for?

5-10

True or false: the size of the genome is correlated to the amount of proteins it encodes for.

True

why would making a capsid from just one kind of protein (or protomer, single) be beneficial for a virus?

Simplification; allows the rest of the genome to do other things. Example of this is in the tobacco mosaic virus.

Structural proteins encompass:

capsomeres or protomers (may be one or more polypeptide)

Non-structural proteins (not generally present in virion) encompass:

-enzymes

-replicases or polymerases

-reverse transcriptase

-transcriptases

-proteases, helicases, ligases

-integrases (take DNA and adds to site onto host genome)

-RNA processing enzymes

Are peplomers (spikes) on the envelope of a virus glycosylated?

Yes. (glycoproteins like HA, NA) with oligosaccharides using the sugar composition of the host (mostly N-glycosidic, rarely O-glycosidic)

What are matrix proteins, where are they, and are they glycosylated?

Provide structural integrity, located inside envelope of orthomyxoviruses, rhabdoviruses, and retroviruses. Non-glycosylated.

Why is it a bad thing for our immunity if host proteins become included in a viral protein component?

Having our components included in the virus will make the virus look different- and harder for our immune system to recognize.

True or False: peplomers are only in a perpendicular orientation (spikes).

False. peplomers can also be parallel/flat.

Are viruses with perpendicular or parallel peplomers harder to target via detergent?

Parallel. The flat structure helps to mimic the shape of the envelope, which coats the envelope as a result. This makes it harder for detergents to target the envelope, which is made of lipids, because it is now protected via the peplomers. Detergents would still work, but might need to be stronger.

Which type of viral nucleic acid is most similar to viral mRNA, and as such, doesn’t need to be transformed to translate its material into the host? (the path of least resistance)

Positive strand RNA

What would need to happen for a virus with a positive-strand RNA genome to begin the translation of its material into the host?

Nothing- it is ready to go.

What would need to happen for a virus with a negative-strand RNA genome to begin the translation of its material into the host?

First, would need to be converted to DNA via reverse transcriptase.

Then, DNA polymerase can make a complimentary strand- getting to the positive strand RNA.

What would need to happen for a virus with a positive-strand DNA genome to begin the translation of its material into the host?

Transcription of the negative strand

What would need to happen for a virus with a negative-strand RNA genome to begin the translation of its material into the host?

Would need to transcribe to RNA, which would give the + strand.

What is the difference between a monopartite and segmented nucleic acid?

Monopartite viruses have a single nucleic acid molecule protected in a shell made of proteins forming the virus particle.

The genome of segmented viruses is divided into two or more nucleic acid segments that are all encapsulated together in a single virus particle.

In which category of viruses is the genome diploid (two copies of each gene)?

retroviruses

Some DNA viruses that have circular, supercoiled genomes. Why is this, and how can the virus’s genetic material be expressed?

This occurs for packing purposes, or protection for the genome.

Uncoiling must take place for expression. Machinery is needed, either from the host or from non-supercoiled parts of the virus.

How many bases does a gene normally have?

1000, or 1kb.

Where do envelope lipids come from?

The host.

The lipid bilayer is collected through budding, and the lipid composition varies based on the host.

Depending on which organelle the lipids come from, determines the composition of the lipids.

~60% phospholipids, ~40% cholesterol

what is budding?

when the membrane of the virus is acquired in the late stage of viral assembly.

What are the three types of virion symmetry?

-helical

-icosahedral

(both of the above are symmetrical)

-complex

Describe helical symmetry.

-RNA genome forms a spiral within the nucleocapsid

-single protein repetition

-plant helical viruses are unenveloped.

-some vertebrate helical viruses are wound further and are enveloped

-other vertebrate helical viruses are enveloped and segmented (such as influenza!)

Describe Icosahedral symmetry.

Icosahedron: 12 corners, 30 edges, 20 faces

Can be enveloped or unenveloped!

T= Triangulation number (tells you how many structural units per face)

Describe Complex symmetry.

-not a lot of organization

-no helical/ icosahedral shape

-no axis

-weird morphology

-often found in large viruses (such as pandoravirus)

What are the functions of the capsid and envelope?

-Binding to receptors

-Membrane fusion (having the right proteins available for fusion, which is involved in entry and release)

-uncoating

-receptor modification

What temperature causes protein denaturation, and what temperature is good for preservation in viruses?

>55-60 C, -70 C

What are the latin names for the order, family, and genus of viruses?

order (-virales)

family (-viridae)

Genus (-virus)

What are the main stages of the replication cycle?

-Attachment and Recognition

-Entry

-Regulation of internal cell events

-Formation of new viral particles

-Release from cell

What are the seven classes of viral genomes?

1. dsDNA

2. ssDNA

3. dsRNA

4. ssRNA (+)

5. ssRNA (-)

6. ssRNA (+) with DNA intermediate

7. Gapped dsDNA

What is an eclipse period?

from infection until production of first virions (intracellular)

What is the latent period?

from infection until release of virions

What is unique about the latent and eclipse period of enveloped viruses?

They occur at the same time- as the viral particle is being made, we see a release.

How does attachment occur?

Binding between viral attachment proteins and receptors on the plasma membrane of the cell.

-depends what is on the outermost layer of cell and virus (peplomers on the envelope)

True or false- some viruses from different families use the same receptor.

True

True or false- some viruses bind to multiple receptors.

True!

-some proteins enhance protein interaction and initiate fusion of the membrane/attachment

-the first interactions are weaker, and then more get exposed.

How does fusion with the cell membrane begin in the case of HIV?

-Binds to CD4 molecules on the target cells through gp120 (glycoprotein peplomer on the virus!)

-Recall that CD4 helps immune system recognize antigens. As the gp120 binds, it changes shape, exposing a chemokine receptor binding site and binds to chemokine.

-This proves changes gp41, another glycoprotein on the virus, exposing a fusogenic domain in gp41, which allows the target cell to fuse with the virus.

What is the key role of HA (hemagglutinin) in the attachment process in the case of orthomyxoviruses?

Hemagglutinins bind to sialic acid in the glycoproteins of the host.

True or false- adenovirus recognizes only one receptor in target cells.

False. Adenovirus recognizes two receptors in target cells: Cocksackievirus and Adenovirus Receptor (CAR).

-CAR is not usually seen or available to the virus. It is only able to bind when the virus is present and the body detects it.

How can adenovirus bind to target receptors?

-CAR is only made visible when the virus is present and the body detects it. This happens when the body starts producing signals (interleukins) IL8, which makes the receptors visible and accessible for the virus to bind.

True of false: The mechanisms of viral entry can occur via diffusion.

False. Mechanisms of entry require work and changes in configuration.

What are examples of proteins at the plasma membrane that can interact with the virus and “help” it get in?

-clathrin

-dynamin

-caveolin

-flotillin

In viral entry, what leads to conformational changes in viral proteins and fusion?

Acidification

What is the purpose of viral unpacking?

to remove the capsid and expose genetic material- now genome replication and expression can happen.

How are membranes brought together in HIV?

gp41, when bound to a membrane, changes configuration. It curls, bringing the membranes closer together.

Protein changes in influenza are ___

pH-mediated

True or false- do non-enveloped viruses bind to receptors on the membrane?

True. They get engulfed.

List some viruses whose genome replication takes place via a replication fork.

-papillomaviruses

-polyomaviruses

-herpesviruses

-retroviral proviruses

What type of genomes can replicate via replication fork?

Ds circular genome (DNA)

True or false- only linear DNA genomes can replicate via strand displacement.

False. This can occur in linear and circular genomes, via “rolling circle replication.”

Does strand displacement replication use a primer?

Yes. The primer binds at the very end and places a cytosine there. Now, a strand can begin adding, 5’-3’.

What are some examples of viruses that replicate via strand displacement?

adenoviruses (protein)

parvoviruses (DNA hairpin)

poxviruses (DNA hairpin)

Some viruses require the cell’s machinery for replication (papillomavirus, polyomavirus). What makes many viruses with larger genomes different?

They tend to synthesize everything they need, themselves. They come with the materials needed via packaging.

What needs to happen to gapped dsDNA viruses before replication?

They need to be repaired by the nucleus of the host before proceeding (made into dsDNA).

In viruses, is there RNA transcription from RNA?

Yes, the viruses carry RNA polymerase that reads RNA to make RNA.

An RNA-depended RNA polymerase is required.

What is the replication pathway for a virus with a (-) strand RNA genome?

-makes a complimentary strand via RNA pol, and makes mRNA (capped and adenylated).

What is the replication pathway for a virus with an ambisense RNA genome?

Only the 5’ (+) region can be read by a ribosome- needs to be complimented first via mRNA synthesis

What is the replication pathway for a virus with an double stranded RNA genome?

uses (+) strand to turn into protein and template strands.