Module 9 - Viruses Flashcards
What are viruses?
Small particles that can replicate inside living host cells
How are viruses obligate intracellular parasites?
They rely on taking over the host cell to function
True or false: viruses can infect all forms of life
True
How many viruses exist on the planet?
Millions
How many viruses have been extensively characterized?
5000
How long have viruses plagues humans?
Since before we knew about them
How old is the history of virology?
Nearly as old as the history of life itself
What is virus Latin for?
Poison
When was yellow fever virus discovered?
1901
What did Walter Reed do?
Showed yellow fever was causes by a virus transmitted by mosquitos in 1901
Who discovered yellow fever virus?
Walter Reed
What did Stanley (from Columbia) do?
Crystallized TMV
When was TMV crystallized?
1935
Who crystallized TMB?
Stanley (from Columbia)
How was TMV isolated?
In a filtered, bacteria-free fluid
What is the typical size of a virus?
10-100 nm
What is the typical genome size of a virus?
A few thousand to 200,000 nucleotides
How many genetic molecules do viruses typically have?
One
How can viruses have more than one genetic molecule?
By having a segmented genome
What is the structure of the genetic material in viruses?
Linear or circular, single or double stranded DNA or RNA
What is the host for poliovirus?
Humans
What is the structure of poliovirus?
Non-enveloped, icosahedral
What is the size of poliovirus?
30 nm
What is the genome size of poliovirus?
7.7 kbp
What is the genetic material of poliovirus?
ssRNA
What is the host for TMV?
Tobacco and related plants
What is the structure of TMV?
Non-enveloped, helical
What is the size of TMV?
300x18 nm
What is the genome size of TMV?
6.4 kbp
What is the genetic material of TMV?
ssRNA
What does TMV stand for?
Tobacco mosaic virus
What is the host of T4?
E. coli
What is the structure of T4?
Non-enveloped
What is the size of T4?
200x90 nm
What is the genome size of T4?
170 kbp
What is the genetic material of T4?
dsDNA
What is the host for variola virus?
Humans
What is the structure of variola virus?
Enveloped, complex
What is the size of variola virus?
300x250 nm
What is the genome size of variola virus?
186 kbp
What is the genetic material of variola virus?
dsDNA
What is the most for mimivirus?
Amoeba
What is the structure of mimivirus?
Enveloped, complex
What is the size of mimivirus?
400 nm
What is the genome size of mimivirus?
1200 kbp
What is the genetic material of mimivirus?
dsDNA
What surrounds the viral genome?
A capsid
What is a capsid?
Viral proteins that surround the viral genome
What are capsids composed of?
Capsomeres
What is a capsomere?
A subunit of a capsid
What is a capsomere composed of?
One or more polypeptides
What are the common shapes of a capsid?
Helical or icosahedral
What type of genome do helical viruses have?
ssRNA
What are some examples of helical viruses?
Ebola, TMV
What are some examples of icosahedral viruses?
Rhinovirus, adenovirus, poliovirus
What does rhinovirus do?
Causes the common cold
True or false: capsid shapes are always simple
False: they can have irregular or complex shapes
What is the typical structure of bacterial viruses?
Icosahedral head and a helical tail
What do the tail fibers do in bacteriophages?
Help binding to host cells
What is the nucleocapsid?
The capsid and genome of the virus
What is an enveloped virus?
A virus where a plasma membrane surrounds the nucleocapsid
What is a naked virus?
A virus where there is no plasma membrane surrounding the nucleocapsid
What is another name for a naked virus?
A non-enveloped virus
What are some examples of enveloped viruses?
Influenza and HIV
What are spikes?
Glycoproteins inserted into the lipid membrane of enveloped viruses
What are some examples of spike proteins?
Hemagglutinin and neuraminidase
Which virus has hemagglutinin and neuraminidase?
Influenza
What does hemagglutinin and neuraminidase determine?
Subtype of influenza
What are the 4 steps for viral replication?
- Adhere
- Penetrate and uncoat
- Synthesis
- Assembly and exit
What happens when a virus sticks to the host cell?
It releases its genome into the cell
What happens once the viral genome is inside the host cell?
The host cell expresses the genes to make proteins, replicate genome, and put itself together
What is the most important part of the viral replication cycle?
Entry into the host cell
What does the entry mechanisms depend on?
The host cell
How are animal cell viruses different from bacterial, plant, and fungal viruses?
Animal viruses do not have to contend with cell wall, while bacterial, plant, and fungal viruses do
What does entry of viruses into plant cells depend on?
Some damage on the plant tissue
Why do plant viruses rely on plant tissue damage?
It opens a spot on the cell wall
How can plant tissue be damaged?
Through insects feeding on plants, wind damage, hail/rail damage, fire damage, or human-induced damage
True or false: bacterial viruses enter the host cell
False: they do not enter the host cell after attachment
What happens when bacterial viruses attach to the host cell?
There is a conformational change in the tail protein subunits, which moves DNA from capsid head into bacterial cytoplasm
What happens when animal viruses attach to the host cell?
Some form of virion capsid or viral genome enters the cytoplasm
How do non-enveloped animal viruses enter the cell?
The entire viral particle enters through endocytosis
How do enveloped viruses such as HIV enter the cell?
They undergo a membrane fusion event at the cell surface
How do enveloped viruses such as influenza enter the cell?
They first enter through endocytosis, and then the viral capsid undergoes a specific set of disassembly to release the genome into the cytoplasm
What is the consequence of viruses only being able to replicate within living host cells (in terms of evolution)?
Their origin must be connected with the host cell
What three hypotheses have been proposed for the origin of viruses?
Coevolution, regressive, and progressive
What is another name for the coevolution hypothesis?
The virus first hypothesis
What does the coevolution hypothesis state?
Viruses co-evolved with current cellular hosts, or existed before cells
What are the strengths of the coevolution hypothesis?
It can explain the origin of many RNA viruses
What are the weaknesses of the coevolution hypothesis?
It has little support outside of RNA viruses
What does the regressive hypothesis state?
Viruses were cells that lost their metabolic and replicative features over time, thus depending on the host cell
What are the strengths of the regressive hypothesis?
There is support from nucleocytoplasmic large DNA viruses
What are the weaknesses of the regressive hypothesis?
It does not explain the origin of RNA viruses
What does the progressive hypothesis state?
Existing genetic elements gradually gained the ability to move between cells
What are the strengths of the progressive hypothesis?
There is evidence in the similarity of replication of retroviruses and replication of transposons and retrotransposons
Based on the progressive hypothesis, how did retroviruses evolve?
From eukaryal retrotransposons
How do transposons move within a genome?
By converting DNA to RNA, and then converting back into DNA
How is RNA converted into DNA for transposons?
Through the enzyme reverse transcriptase
What is done with the DNA copy produced by reverse transcriptase in transposons?
It can be integrated into a different location on the chromosome
How are retroviruses similar to retrotransposons?
They also undergo RNA to DNA conversion, and they have a similar genetic organization
True or false: there is evidence for all three hypothesis of viral origin
True: each of them has different evidence
True or false: one hypothesis of viral origin completely explains the origin of viruses
False: each of them have a partial description
What traits of viruses makes them difficult to work with?
They are small and can only replicate within appropriate host cells
What is needed to cultivate viruses?
Host cells must be inoculated with virus, and progeny viruses must be harvested
How are bacteriophages cultivated?
A culture of actively growing bacteria are inoculated with a small sample of phage
How can a researcher tell that a bacteriophage is replicating?
The growth media changes from turbid to clear
What happens after incubation of bacteriophages?
The medium is centrifuged, and the resulting supernatant is filtered
What is done to isolate a viral clone?
Molten nutrient agar is added to the cells and poured on a plate
What is the purpose of the molten nutrient agar?
It inhibits free movement of virus
What does a virus produce when plated?
A visible plaque of dead cells
What does each discrete plaque represent?
A clone (the progeny of a single virus)
What is done to cultivate animal viruses?
A small amount of virus is added to host cells growing in a flask
What do the viruses in the animal cell flask do?
New viral particles are released from infected cells into the medium, and infect other cells
What does the replication of many animal viruses lead to?
CPEs
What is an example of a virus that produces CPEs?
Poliovirus
What does CPE stand for?
Cytopathic effects
What are CPEs?
Visible changes in cellular morphology
What are CPEs often associated with?
Cell damage or death
What are CPEs commonly used as a marker for?
Extent of viral replication
What cell line was used to develop the tools to study animal viruses?
HeLa cells
What is done for simple and relatively crude purifications?
A viral suspension can be centrifuged and filtered through a very small pore filter
What does differential centrifugation do?
Separates particles by mass
What does low speed centrifugation lead to?
Pelleting of large objects, including cells
What does high speed centrifugation lead to?
Pelleting of small objects, such as viruses
What does gradient centrifugation do?
Separates particles by density (concentration)
What is the setup for gradient centrifugation?
The sample is layered on top of a density gradient made up of sucrose concentrations (ranging from 20-70%)
How does gradient centrifugation work?
During centrifugation, particles move down until they encounter a sucrose concentration equivalent to particle density
What is the product of gradient centrifugation?
Bands at different locations in the tube
What is the product of differential centrifugation?
Pellets and supernatant
What are the 4 methods used to quantify viruses?
Direct count, hemagglutination assay, plaque assay, and endpoint assay
How does direct count work?
The absolute number of total viral particles is calculated with an electron microscope
What are the disadvantages of the direct count method?
It requires an expensive, specialized microscope, and it does not differentiate between infectious and non-infectious viral particles
What does the hemagglutination assay rely on?
The properties of some viruses to stick to RBCs, forming a gel mat
What does RBC stand for?
Red blood cell
True or false: hemagglutination assay can be done on all viruses
False: it can only be done on certain viruses
What is hemagglutionation?
The process of RBCs clumping up together due to viruses binding to the RBC surface
True or false: hemagglutination can be seen with the naked eye
True: no microscope is required
What are the advantages of the hemagglutination assay?
It is cheap, easy, fast, and requires no microscope
What are the disadvantages of the hemagglutination assay?
It cannot differentiate between viable and non-viable viruses, and there is no virus number
What type of viruses is the plaque assay useful for?
Phages and plant viruses
What is the plaque assay commonly used for?
To determine infectious titer
What are the steps of a plaque assay?
- A series of dishes with host cells are inoculated with serial dilutions of the virus
- Newly formed viruses infect neighboring cells, resulting in plaques
- Plaques are counted to determine PFU
What is a plaque?
A collection of dead cells
What does PFU stand for?
Plaque forming unit
What is the endpoint assay used for?
Determining the TCID50
What does TCID50 stand for?
Tissue culture infectious dose 50
What are the steps of an endpoint assay?
- Dilutions of viruses are used to infect cells in a growing culture
- Cells are monitored for CPEs, and calculated to find out how much viruses is needed to cause CPE 50% of the time
How is the TCID50 calculated from the endpoint assay?
The number of viruses needed to cause CPE 50% of the time is calculated
How can viruses be named?
Based on the location of discovery, the disease they cause, or appearance
What are some examples of viruses named based on a location?
Ebola, West Nile
What are some examples of viruses named based on diseases?
TMV, Hepatitis A
What are some examples of viruses named based on a physical characteristic?
Coronavirus, Picornaviridae
What are some notes about Ebola virus?
- First recognized outbreak occurred in Zaire (Democratic Republic of Congo) near Ebola River
- Most subsequent outbreaks occurred in central Africa
What are some notes about West Nile virus?
- Initially isolated from a person living near Nile River in Uganda
- First appeared in USA in 1999, now firmly established in North America
What are some notes about TMV?
- Plant infected show distinct discoloration, or mosaic pattern
- First described in 1880s, still causes significant crop loss today
What are some notes about Hepatitis A virus?
- A number of viruses (A, B, C) have been identified
2. All cause damage to liver cells, but differ significantly from each other
What are some notes about coronaviruses?
- Have projections on surface that resemble crowns or coronas
What are some notes about picoronaviruses?
- Have very small (pico) RNA genomes
What does ICTV stand for?
International Committee on Taxonomy of Viruses
Based on the ICTV, how are viruses classified?
Based on order, family, subfamily, genus, and species
What can be used as a common feature to compare viruses?
How they form mRNA
How come mRNA can be used as a common feature to compare viruses?
Because all viruses make mRNA recognized by ribosomes of host cells
How does the Baltimore classification system work?
Each virus is divided into 7 classes based on how they make mRNA
What did David Baltimore do?
Develop the Baltimore system of classification
What is a class I virus?
dsDNA genome
What is an example of a class I virus?
Human herpesvirus
What is a class II virus?
ssDNA genome
What is an example of a class II virus?
Parvoviruses
What is a class III virus?
dsRNA genome
What is an example of a class III virus?
Reoviruses
What is a class IV virus?
ssRNA genome, positive sense
What is an example of a class IV virus?
Poliovirus
What is a class V virus?
ssRNA genome, negative sense
What is an example of a class V virus?
Influenza virus
What is a class VI virus?
ssRNA genome, DNA intermediate
What is an example of a class VI virus?
HIV
What is a class VII virus?
ssRNA genome, RNA intermediate
What is an example of a class VII virus?
Hepatitis B virus
What class of virus has a dsDNA genome?
Class I
What type of virus is human herpesvirus?
Class I
What class of virus has a ssDNA genome?
Class II
What type of virus is parvovirus?
Class II
What class of virus has a dsRNA genome?
Class III
What type of virus is reovirus?
Class III
What class of virus has a ssRNA genome, positive sense?
Class IV
What type of virus is poliovirus?
Class IV
What class of virus has a ssRNA genome, negative sense?
Class V
What type of virus is influenza?
Class V
What class of virus has a ssRNA genome, DNA intermediate?
Class VI
What type of virus is HIV?
Class VI
What class of virus has a dsDNA genome, RNA intermediate?
Class VII
What type of virus is hepatitis B?
Class VII
How is electron microscopy used in virology?
It is useful to see physical differences or how they look like
How is nucleic acid analysis used in virology?
It provides more exact information about virus identity
How is rtPCR different from PCR?
rtPCR uses reverse transcriptase to create cDNA from mRNA, which can then undergo the PCR reaction
What is needed for rtPCR?
Primers, Taq polymerase, nucleotides, and reverse transcriptase
When were viroids first isolated?
1967
How were viroids first discovered?
As infectious agents that caused potatoes to grow abnormally
What do viroids do?
Infect plants
What is the structure of a viroid?
Naked circular ssRNA, with a complicated secondary structure
How do viroids achieve intricate secondary structure?
Through intracellular complementary base pairing
How large is a typical viroid?
400 nucleotides
What is the purpose of the extensive secondary structure of viroids?
It makes it resistant to ribonucleases
What do satellite viruses and satellite RNAs do?
Infect plants
What do satellite viruses and satellite RNAs have in common?
They both have small RNA genomes
How do satellite viruses and satellite RNAs replicate in hosts?
They require a helper virus that co-infects the host cell for replication
Where do satellite viruses get the capsid protein?
From their own gene
Where do satellite viruses get the capsid protein?
From the helper virus
What is an example of a satellite virus?
HDV
What does HDV stand for?
Hepatitis D virus
What is needed for HDV to infect a cell?
HBV also needs to infect the cell for HDV to replicate
True or false: HDV has an envelope
True: it is an enveloped virus
What do prions stand for?
Proteinaceous infectious particles
What is the structure of a prion?
Just protein (no DNA or RNA)
How are prions infectious agents?
They can replicate in the host and cause diseases
What are some specific diseases caused by prions?
Kuru in humans, Scrapie in sheep, mad cow disease in cattle
What types of dieases are caused by prions?
TSEs
What does TSE stand for?
Transmissible spongiform encephalopathies
What are TSEs?
A group of progressive neurological diseases
What are prions?
Misshapen forms of naturally occurring proteins
Where do the prion proteins normally exist?
On the surface of the neuron
What are the two states of the prion protein?
The more common cellular form, or the pathogenic scrapie form
What happens when pathogenic proteins come in contact with the normal cellular proteins?
It causes the cellular molecule to change shape and become pathogenic
What is the consequence of the prion causing a normal protein to change shape?
It can replicate and function as an infectious agent
What can make the prion protein more likely to assume the pathogenic confirmation?
Certain mutations in the gene
True or false: prion-associated diseases can be both infectious or genetic
True: it can arise from another source, or from genetics
What is thought to lead to disease from prions?
The formation of fibrils
How have viruses shaped human history?
Smallpox decimated Native American populations, and influenza influenced the outcome of World War I
What did Dimitri Ivanovski do?
Demonstrated a disease in tobacco plants (TMV) that could be transmitted after using a filter in 1892
What is the official beginning of virology?
Martinus Beijerinck describing TMV as contagium vivum fluidum (soluble living germ) in 1898
What did Frederick Twort and Felix d’Herelle do?
Described bacteriophages in the early twentieth century
What does variola virus do?
It is the agent of smallpox
What is an example of a virus with a segmented genome?
Influenza virus A
How does influenza virus A have a segmented genome?
It has eight segments of ssRNA that code for ten different proteins
What are the largest viruses (in terms of size)?
- Pithovirus sibericum (1.5 um x 500 nm)
2. Mimivirus (400 nm)
What are the largest viruses (in terms of genome)?
- Pandoravirus salinus (2.47 Mbp)
- Megavirus chilensis (1.2 Mbp)
- Mimivirus (1.2 Mbp)
What genes are found in large viruses (such as mimivirus)?
Genes similar to synthesis of nucleotides and amino acids
What is the structure of influenza virus?
Multiple copies of the NP (nucleoprotein) and viral polymerase complex associate with each segment of RNA
What does helical symmetry lead to?
Filamentous, fiber-like, or rod shaped morphology
What is a virion?
Complete viral particle
What is the virion in helical plant and bacterial viruses?
The entire helical nucleocapsid
What do all known animal viruses with helical symmetry have?
An envelope
What does the genome size of a helical virus determine?
How large it is (capsid can grow indefinitely)
How come the genome size of an icosahedral virus is limited?
Only a certain amount of genetic material can be packaged inside the capsid
What is the purpose of a viral envelope?
The associated proteins are important for successful entry into the cell
How many protein units are used for an icosahedral capsid?
60 (3 polypeptides x 20 faces)
What is the advantage of a viral envelope?
It can disguise the virus from the host cell immunity, and helps with attachment
What is the disadvantage of a viral envelope?
The envelope is typically degraded in external environment through desiccation and exposure to chemicals
What is an attachment protein, and what does it do?
It is a protein on the surface of the virus that aids in binding to a host cell
How does adenovirus interact with receptors?
A spike protruding from the vertices
How does poliovirus interact with receptors?
Through amino acid residues in an indentation within the capsid
What receptors does HIV use?
CD4, CCR5, and CXCR4
What breaks down the influenza coat when it enters the cell?
Acidic pH
How do viruses spread within plants?
Through plasmodesmata
True or false: plant viruses recognize specific receptors to enter cells
False: only animal and bacterial viruses do this
How can viral particles exit a cell?
Through budding or cell lysis
What do respiratory viruses do?
Infect respiratory cells
How do respiratory viruses spread?
Through inhalation and exhalation
What do enteric viruses do?
Cause intestinal problems by damaging GI tract cells
What is an example of an enteric virus?
Rotaviruses
How do enteric viruses spread?
Through ingestion (fecal matter)
How do blood-borne viruses spread?
Through bodily fluids (blood, semen)
What cells does HIV affect?
Immune cells
What does NCLDV stand for?
Nucleocytoplasmic large DNA viruses
What are some examples of NCLDVs?
Herpesvirus, poxvirus, and mimivirus
What hypothesis can be made regarding NCLDVs?
Primordial viruses gave rise to the first eukaryal nucleus
What is special about Chlamydia?
It is a bacteria that relies on a host cell for survival
What is Chlamydia missing for survival?
An ETC to synthesize ATP
What does sequence analysis of viral genomes demonstrate?
Genomes of animal viruses show great similarity to host genomes, and no similarity to bacterial genomes
What hypothesis does sequence analysis of viral genomes not support?
The regressive hypothesis
How was Mavirus used in the progressive hypothesis?
It has a mechanism similar to transposons
What was a major advancement in the field of virology for cultivation?
The development of cell culture techniques
What are some examples of CPEs?
The rounding and detachment of the infected cells, or the creation of syncytiums
What is a syncytium?
The fusion of individual, infected cells into a large, multinucleated mass
What is the problem with filtration?
It does not concentrate the viruses
How are the viruses concentrated?
Through ultracentrifugation
What is a viral titer?
Concentration of a virus preparation
What is the purpose of the latex beads in the direct count?
It is used to determine the exact volume, and thus concentration, of the sample
Besides an electron microscope, what can be used to directly count the viruses?
Fluorescent microscopy or flow cytometry
What is the purpose of the serial dilutions in the hemagglutination assay?
It can be used to determine the viral titer maximum concentration that still produces complete hemagglutination
True or false: hemagglutination can occur without viral particles
True: sometimes the viral proteins alone can induce hemagglutination
How come a plaque assay may give a different number than a direct count?
A direct count looks at all particles, while a plaque assay only looks at infectious particles (those that cause cell death)
Why may viruses be defective?
They may have been assembled incorrectly, missing part of the genome, or contain mutations to preclude further replication
What types of viruses are often quantified by an endpoint assay?
Those that cannot form plaques or cause RBCs to aggregate, but still have an observable effect on cells
What does LD50 stand for?
Lethal dose 50
What is the LD50?
The amount of virus to kill 50% of the infected animals
How come an LD50 is not commonly measured?
It requires the use of a lot of lab animals
What is a virus species?
A group whose members share several properties and occupy a common ecological niche
What do Paramyxoviridae and Orthomyxoviridae look like under an electron microscope?
Enveloped, spherical, and 100-150 nm in diameter
How are Paramyxoviridae and Orthomyxoviridae different?
Paramyxoviridae enter the cell by fusing with the cell membrane, and constain a linear ssRNA genome, while Orthomyxoviridae enter the cell by endocytosis, and have a segmented genome
How was an electron microscope helpful and hurtful in the SARS outbreak?
They could identify the virus, but not the specific virus (thought it was paramyxoviridae, not coronavirus)
What is an example of a viroid?
PSTVd
What does PSTVd stand for?
Potato spindle tuber viroid
What is missing from the viroid genome?
Genes that encode for proteins
How can viroids replicate?
By using the cell’s RNA polymerase
How can viroids damage the cell?
By diverting essential resources away from transcription, or interfering with the formation of SRP
What does SRP stand for?
Signal recognition particle
How does a viroid interact with SRP?
The viroid can bind to 7S RNA, interfering with the formation of SRP
What does SRP do?
Directs unfolded polypeptides from the cytoplasm to the ER
How can viroids be transmitted between plants?
Through insects or human activities
How does HBV help HDV?
HBV provides the proteins necessary for the HDV envelope
How are virophages similar to satellite viruses?
They only replicate in host cells coinfected with a helper virus
How are virophages different to satellite viruses?
Virophage replication is detrimental to the helper virus
When was the first virophage discovered?
2008
What is an example of a virophage?
Sputnik
How does Sputnik infect a cell?
It replicates in amoeba infected with mamavirus, inhibiting the production of more mamavirus
What may virophages be used for?
Lateral transfer of gene material
What does CJD stand for?
Creutzfeldt-Jakob disease
How do TSEs affect the brain?
They leave sponge-like holes
Who first studied prions?
Stanley Prusiner
How have viruses been used in research?
They can be used to study the inner workings of cells (DNA replication and gene regulation)
What virus was used to study gene regulation?
Simian virus 40 (SV40)
How were bacteriophages used in research?
They helped show that DNA, not protein, was the genetic material of cells
What did David Baltimore and Howard Temin do?
Discovered reverse transcriptase
What did Harold Varmus and J. Michael Bishop do?
Used virology to study cancer in the 1970s
Which virus was used to study cancer?
Rous sarcoma virus
What is a proto-oncogene?
Genes involved in the normal regulation of the cell cycle
What is an oncogene?
Altered forms of proto-oncogenes that can lead to uncontrolled cell growth and development of tumors
What are oncolytic viruses?
Viruses that infect and kill cancerous cells without harming normal cells
How can reoviruses act as oncolytic viruses?
They preferentially infect cells with activated ras pathways
What is gene therapy?
The process of correcting genetic defects in humans
How can viruses be used in gene therapy?
They can be used to transport and deliver the gene to the host cells
What is nanotechnology?
The development and use of nano-devices
