BIOL 3_Ch 6 (Intro to Viruses)

What is the most well known bacteriophage?

"T-even" bacteriophage infect E. coli - T-2 and T-4 - Most widely studied bacteriophage - Go through similar stages as animal viruses

Nucelocytoplasmic large DNA viruses

- Closely related to each other - Distantly related to other viruses - May constitute a new order of viruses The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes.

Viral envelope How does it evolve?

- Composed of the membrane system of the host. - When virions are released from the host cell, they take a bit of the host's cell membrane, nuclear membrane or ER depending on where they bud off from. - Host's regular membrane proteins are replaced with viral proteins - Viruses then proceed to use this modified host cell membrane as their envelope - Viruses also add its own proteins (glycoprotein spikes) to the envelope.

It is difficult to design therapies against viruses. Discuss what current antiviral drugs target and their overall effectiveness.

- Current antiviral drugs target host cells to block virus replication (thus causing severe side effects) or one of the steps in the viral life cycle. - But they are often less effective than antibiotics.

How do you detect the effects of viral multiplication in bird embryos? List 3 signs.

- Death of the embryo - Defects in embryonic development - Pocks (in raw eggs): discrete, opaque spots indicating localized areas of damage

Who discovered bacteriophage? What does it infect? What is the effect on the infected bacteria?

- Discovered in 1915 by Frederick Twort and Felix d'Herelle - Parasitize every known bacterial species - Often make the bacteria they infect more pathogenic for humans

b. Benefits of using bird embryos

- Embryonic development occurs in a protective shell - - Intact and self-supporting unit with its own sterile environment and nourishment - Furnishes several embryonic tissues that support viral multiplication

Surprising factors and medical significance of prion infection

- Exact mode of infection is unknown - Protein composition of prions has revolutionized ideas of what can constitute an infectious agent - Questions about how prions replicate given that they have no nucleic acid

a) Primary cell cultures

- Freshly isolated animal tissue is placed in a growth medium - Cells undergo mitotic division, producing a monolayer - Retain the characteristics of the original tissue from which they were derived - Generally have limited existence

b) Continuous cell cultures

- Have altered chromosome numbers - Grow rapidly - Show changes in morphology - Can be continuously subcultured if they are given fresh nutrient media

2) satellite viruses What they do, a type of disease that they cause, and how they infect cells.

- Viruslike agents and defective forms that cause human disease - They are dependent on other viruses for replication

At minimum, viruses must carry genes for synthesizing the viral ____ and ____ for regulating the actions of the host and for packaging the mature virus.

- capsid (protein sell, a.k.a. capsid in all) - genetic material (nucleic acids; DNA or RNA)

What are the 6 viral components? Which of those are found in ALL viruses?

1) Capsids 2) Envelopes (not in all viruses) 3) Nucleic Acids (RNA or DNA) 4) Matrix proteins 5) Enzymes (not in all viruses) 6) Spikes (not in all viruses)

What are the three shapes of capsid?

1) Helical capsid: Rod-shaped capsomeres that form a continuous helix around the nucleic acid 2) Icosahedral capsid: Three-dimensional, 20-sided figure with 12 evenly spaced corners 3) Complex capsids: Found in bacteriophage, the viruses that infect bacteria - Have multiple types of proteins - Take shapes that are not symmetrical

Describe the structures of icosahedral, helical, and complex viruses.@

1) Helical capsid: Rod-shaped capsomeres that form a continuous helix around the nucleic acid 2) Icosahedral capsid: Three-dimensional, 20-sided figure with 12 evenly spaced corners (20/12) 3) Complex capsids: Found in bacteriophage, the viruses that infect bacteria - Have multiple types of proteins - Take shapes that are not symmetrical

2 methods in which viruses are cultivated (name 3 ways using these methods)

1) In vivo methods: viral cultivation in lab animals or embryonic bird tissues. a. Live animal inoculation b. Using bird embryos 2) In vitro methods: viral cultivation in cell or tissue culture. c. Using cell/tissue culture techniques

What are the two common types of cytopathic effects (CPEs)?

1) Inclusion bodies: Compacted masses of viruses or damaged cell organelles in the nucleus or cytoplasm 2) Syncytia (singular, syncytium): Fusion of multiple host cells into single large cells containing multiple nuclei

3 unique properties of viruses

1) Infectious particles - Rather than organisms 2) Active or inactive - Rather than alive or dead 3) Obligate intracellular parasites: - Cannot multiply unless they invade a specific host cell - Must instruct the genetic and metabolic machinery of the host cell to make and release new viruses

What are the two classifications of viruses that are used?

1) Informal classification system 2) formal classification system

3 principle purposes for cultivating animal viruses

1) Isolate and identify viruses in clinical specimens. 2) Prepare viruses for vaccines. 3) Do detailed research on viral structure, multiplication cycles, genetics, and effects on host cells.

Describe the primary purposes of viral cultivation.@

1) Isolate and identify viruses in clinical specimens. 2) Prepare viruses for vaccines. 3) Do detailed research on viral structure, multiplication cycles, genetics, and effects on host cells.

What are the two possible bacteriophage life cycles?

1) Lytic phase/lytic cycle - life cycle of bacteriophage that ends in destruction of the bacterial cell. 2) Lysogenic cycle - bacteriophage DNA becomes incorporated into the host cell DNA and then not undergo replication or release immediately.

3 early discoveries of elusive viruses

1) Pasteur developed a vaccine for rabies - Coined the term "virus" (Latin for poison) 2) Ivanovski and Beijernick: tobacco disease caused by a virus 3) Loeffler and Frosch: foot-and-mouth disease caused by a virus

What are the two types of RNAs found in viruses?

1) Positive-sense RNA: Single-stranded RNA genomes that are ready for immediate translation into proteins (not all single-stranded RNA genomes) > parvovirus 2) Negative-sense RNA: RNA genomes that need to be converted into the proper form to be made into proteins > influenza virus is segmented (genes exist on separate RNAs), so they are cannot be translated immediately.

What are the three phases of temperate phage lifecycle?

1) Prophage 2) induction 3) Lysogenic conversion

Two types of a carrier relationship between the virus and the host cell. Give examples.

1) Provirus: viral DNA incorporated into the DNA of the host > Measles virus. Remain hidden in brain cells for many years, causing progressive damage and loss of function. 2) Chronic latent state: periodic activation after a period of viral inactivity > Herpes zoster viruses (chicken pox and shingles) and herpes zoster simplex (cold sores and genital herpes). Latency in nerve cells and emerge later.

What are the two ways in which transformation (cancer/tumors due to infections by oncogenic viruses) could occur?

1) Virus carries genes that directly cause cancer - Viral genes directly produce proteins that lead to uncontrolled cell growth 2) Virus produces proteins that induce a loss of growth regulation in the cell - Viral genes affect expression of host oncogene leading to uncontrolled cell growth (oncogenes are [3) Altered host's DNA produces proteins that lead to uncontrolled cell growth]

Discuss the predominant view among scientists as to the nature of viruses.@

1) Viruses are not organisms but infectious particles 2) They are inactive 3) Obligate intracellular parasites

How do viruses compared to "cells"? List 2 major differences.

1) Viruses bear no resemblance to cells - Lack protein-synthesizing machinery 2) Need only those parts required to invade and control a host cell: - External coating (protein sell, a.k.a. capsid in all; and envelope in some) - Core containing nucleic acids (DNA or RNA)

What are 3 other noncellular infectious agents besides viruses?

1) prions 2) satellite viruses 3) viroids

List and describe the 6 steps of animal virus replication @

1. Adsorption 2. Penetration 3. Uncoating 4. Synthesis 5. Assembly 6. Release from host (lysis/exocytosis)

General phases in the life cycle of animal viruses (6 steps)

1. Adsorption 2. Penetration 3. Uncoating 4. Synthesis 5. Assembly 6. Release from the host cell

What percentage of the bacterial chromosome is composed of viral genes?@

10-20%

[How and where viruses can dock can have medical consequences. What is the example given in the class?]

1918 Spanish Flu. The surface proteins of influenza viruses, hemagglutinin and neuraminidase, play important roles in virulence, host specificity, and the human immune response. Influenza RNA fragments were isolated from lung tissue of three victims of the 1918 flu. The 1918 neuraminidase shares many sequence and structural characteristics with avian strains... Phylogenetically, the 1918 neuraminidase gene appears to be intermediate between mammals and birds, suggesting that it was introduced into mammals just before the 1918 pandemic. How did they get that info? 1) isolated RNAs from formalin fixed paraffin embedded slide section and sample of lung tissue from autopsy; 2) from a victim buried frozen in permafrost in 1918.

Experts estimate that up to ______ of human cancers are caused by viruses

20%

Creutzfeldt-Jakob Disease (CJD) Give two disease examples

A type of spongiform encephalopathies caused by abnormal form of prion proteins - Affects the central nervous system of humans - Causes gradual degeneration and death - Transmissible by an unknown mechanism - Several animals are victims of similar diseases a) Scrapie: Sheep, mink elk b) Bovine spongiform encephalopathy (mad cow disease): cows

What is a "host range"? What are the three host ranges of the viruses?

A virus can invade its host cell only through making an exact fit with a specific host molecule - Restricted host range: hepatitis B only infects liver cells of humans - Intermediate host range: poliovirus infects intestinal and nerve cells of primates - Broad host range: rabies virus infects various cells of all mammals

What occurs in prophage?

After adsorption to the host cell and penetrating its cell membrane, a temperate phage enters an inactive state in which phage DNA is inserted into the host chromosome

Criteria of an informal classification system:

Animal, plant, or bacterial viruses DNA or RNA viruses Helical or icosahedral

[What virus is being studied as a possible treatment for CF?]

Bacteriophage The mucus-filled lungs harbor Pseudomonas aeruginosa, bacteria that normally lives in soil and water and harmless to healthy people but causes persistent lung infections in CF patients. A research in research showed that a combinations of two bacteriophages reduced the number of P. aeruginosa from 10 million to a thousand in 6 hrs.

Why is it difficult to treat viral infections?

Because the nature of viruses makes it difficult to design effective therapies against them. Viruses mutate at a rapid rate.

a. Live animal inoculation; list injection sites for viral exposure

Brain Muscle Body cavity Skin Footpads

[factoid: Streptococcus pyogenes]

Causes "strep throat," fresh-eating disease, and serious bloodstream infections. When it carries genes from bacteriophage, lysogenized S. pyrogenes carries genes coding for erythrogenic toxin, which lead to postinfection problems such as scarlet fever (skin rash & high fever). Gram-positive, aerotolerant bacterium in the genus Streptococcus. These bacteria are extracellular, and made up of non-motile and non-sporing cocci. It is clinically important for humans. It is an infrequent, but usually pathogenic, part of the skin microbiota

Naked viruses

Consist only of a nucleocapsid

What is the virus-induced damage to the cell that alters its microscopic appearance called?

Cytopathic Effects (CPEs) - Virus-induced damage to the cell that alters its microscopic appearance - Cells can become disoriented, undergo major changes in shape or size, or develop intracellular damage

Viruses lack enzymes for most metabolic processes and synthesizing proteins. However, they possess some enzymes for ____ (3 possible types).

DNA/RNA synthesis. 1) Polymerases: synthesize DNA and RNA 2) Replicases: copy RNA 3) Reverse transcriptase: synthesizes DNA from RNA. e.g., HIV

Standard virus classification systems use all of the following except:@ Genetic makeup Structure Disease caused Chemical composition

Disease caused. Formal classification doesn't include disease caused.

Virus Life Cycle Step 2. Penetration. What is the mechanism by which a virus enters the host cell? Two styles of penetration.

Endocytosis: entire virus is engulfed by the cell and enclosed in a vacuole or vesicle. 1) The virus fuses with the wall of vesicle, and the whole virus penetrates the cell membrane. 2) The viral envelope directly fuses with the cell membrane (so the envelope and spikes become part of the host's cell membrane). The nucleocapsid penetrates the cell membrane.

DNA virus multiplication processes

Example: dsDNA 1) viral DNA enters the host nucleus 2) transcriptions in 2 phases: a) early phase: viral DNA that codes for enzymes needed to replicate DNA is transcribed b) late phase: viral DNA that codes for structural viral proteins is transcribed 3) viral mRNA moves to the cytoplasm 4) viral mRAN translated into structural proteins; viral proteins enter the host nucleus 5) viral DNA is replicated repeatedly in the nucleus 6) viral DNA and proteins are then assembled in the nucleus 7) viral DNA can insert itself into host DNA as it is double-stranded (latency)* 8) These new virions bud off the membrane (if enveloped/lyse if nonenveloped) and are ready to infect other cells. *Note: This latency may lead to the transformation of the cell (cancer, tumor).

RNA virus multiplication processes

Example: ssRNA with spikes 1) Adsorption: The virus attaches to host cell's receptors 2 Penetration: the virus is engulfed into a vesicle 3) Uncoating: viral envelope is uncoated, freeing its viral RNA into the cell's cytoplasm. 4) Synthesis (replication & transcription) Viral proteins are synthesized for new viruses (RNA molecules, capsomeres & spikes) 5) Assembly: viral spike proteins are inserted into the cell membrane for the viral envelope. Nucleoplasid is formed from RNA and capsomeres. 6) Release: Enveloped viruses bud off the host cell membrane (if enveloped), carrying away an envelope with the spikes. 8) These new virions bud off the membrane (if enveloped/lyse if nonenveloped) and are ready to infect other cells.

3) viroids

Extremely small, viruslike agents that cause disease in several economically viable plants. - About one-tenth the size of an average virus - Composed only of naked strands of RNA - lack a capsid or other type of coating

True/False: Viral mutation rates are low and viruses are easy to track in a population.@

False

True/False. Bacteriophage takes shapes that are symmetrical

False.

True/False: The term plaques is only used to describe the effects of bacteriophage on cell cultures.@

False. Could be human type viruses. Can be clearings on other cell cultures. The ability to form plaques is not restricted to phages only since animal and plant viruses also form plaques and lesions on cell cultures, host tissues, or leaf surfaces (BMC Microbiology)

True/False: Viruses that infect animal cells can never infect human cells.@

False. Rabies can infect various mammals, including humans. H1N1 swine flu crossed from pigs to people.

True/False. All viruses have "spikes."

False. Some, but not all, viruses have spikes on them. ... Spikes are found on both naked and enveloped viruses. - The enveloped viruses with membranes have glycoprotein spikes protruding from the capsid. - On naked viruses, they project from the nucleocapsid.

True/False: Viruses are alive.@

False. They are infectious particles.

A virus name ending in -viridae denotes a viral: @ - Genus - Family

Family

Virion What is its structural components?

Fully formed virus able to establish infection in a host Virion has a core of DNA or RNA and a capsid.

spongiform encephalopathies

Implicated in chronic, persistent disease in humans and animals Brain tissue removed from affected animals resembles a sponge

Which naturally occurring human cell product is used as antiviral drug?

Interferon (IFN): Used with some success in preventing and treating viral infections FYI: Cells that have been infected with viruses or other germs give off interferon-alpha and interferon-beta as a warning signal to your immune system. That triggers immune cells called white blood cells to release interferon-gamma to fight the germs.

Virus Life Cycle Step 1. Adsorption

Invasion begins when the virus encounters a susceptible host and adsorbs specifically to receptor sites on the cell membrane. Adsorb: to attach (like a virus) Absorb: to soak in (like a paper towel)

What is the difference between DNA virus replication and RNA virus replication?@

Locations of protein synthesis differs. DNA virus needs to get into the host nucleus. 1) DNA virus: - transcription occurs in the host nucleus - translation occurs in the host cytosol - most viral components assembly occurs in the host nucleus 2) RNA virus: > transcription & translation occur in cytosol > most viral components assembly occurs in cytosol

Virus Life Cycle Step 6. [Nonenveloped and complex viruses] are released from host cell via cell ____________

Lysis (or ruptures) pp. 153

What is the acquisition of a new trait by the infected bacterium from a temperate phage called? [Give examples of such traits]

Lysogenic conversion - diphtheria toxin: difficulty breathing, heart failure, paralysis, and even death - cholera toxin: massive, watery diarrhea - botulism toxin: neurotoxin that causes difficulty breathing, muscle paralysis, and even death

Describe the differences between the lytic and lysogenic phase of viral replication.@

Lysogenic: inactive "prophage" phase - bacteriophage DNA becomes incorporated into the host cell DNA and then not undergo replication or release immediately. - When phages in the lysogenic cycle are induced, they are activated and progress into viral replication (the lytic cycle) and end in the destruction of the bacterial cell. Lytic: - life cycle of bacteriophage that ends in destruction of the bacterial cell.

Is it possible to measure the number of viral infections worldwide?

No. a) Most common cause of acute infections that do not result in hospitalization: colds, chickenpox, influenza, herpes, warts b) Viral infections that only occur in certain regions: Dengue fever, Rift Valley fever, Yellow fever* *Note: regions may expand with air travel, global climate change, etc.

True/False: Viruses can be cultured using the same methods as bacteria and fungi.@

No. A virus needs a host. Needs to be cultured, if anything, with a living tissue, etc.

True/False: Viruses can be seen with a light microscope.@

No. Need electron microscopes mostly. However, some can be seen under the light microscopes (at least around 200 nm in size to be visible) e.g., pandoravirous (1000 nm) But can't see: influenza A virus is around 80-120nm, the HIV virus around 120nm and the rhinovirus which causes the common cold around 30nm.

List and describe 5 unique properties of viruses.@

Not cells Need a host (obligate intracellular parasites) Inactive macromolecules outside the host; active only inside host cells Protein shell (capsid) surrounding nucleic acid core Some have envelope (more fragile with cleaning products) made of modified piece of the host PM Ultramicroscopic in size (20 nm to 450 nm) Can have either DNA or RNA but not both dsDNA, ssDNA, ssRNA, or dsRNA Carry molecules on surface that determine specificity for attachment to host cell (spikes)

[antigenic drift and H1N1 virus]

One way influenza viruses change is called "antigenic drift." These are small changes (or mutations) in the genes of influenza viruses that can lead to changes in the surface proteins of the virus: HA (hemagglutinin) and NA (neuraminidase). The HA and NA surface proteins of influenza viruses are "antigens," which means they are recognized by the immune system and are capable of triggering an immune response... Such a "shift" occurred in the spring of 2009, when an H1N1 virus with genes from North American Swine, Eurasian Swine, humans and birds emerged to infect people and quickly spread, causing a pandemic. When shift happens, most people have little or no immunity against the new virus.

Describe the difference between primary and continuous cell lines.@

Primary: cells go through mitotic division, generally short-lived. Continuous: altered chromosomes, grow fast, show changes in morphology, can be cultured continuously if given proper nutrients

1) prions What they do, a type of disease that they cause, and how they infect cells

Prions deposit distinct protein fibers in the brain tissue - Common cause of various types of spongiform encephalopathies - Prions infect and convert normal version of prion protein into abnormal version

What is viral capsid? What is it made of?

Protective outer shell Capsomeres: Identical protein subunits that spontaneously self assemble to form the capsid

Prions are composed of: @ DNA RNA Protein Polysaccharide

Protein (misfolded protein)

Capsids

Protein shell surrounds the nucleic acid

What is the significance of viruses being recognized as "filtrable"?

Realization that something smaller than bacteria was causing the disease. After infectious fluids were passed through filters designed to trap bacteria, the cell-free filtered fluid remained infectious. This proved that something smaller than bacteria was the cause of the disease!

List the key strategy for addressing viral infections

Scientists focus on developing vaccines against viruses since so few antiviral drugs are available and antibiotics do not work on viruses.

What types of diseases do viroids cause?

Significant pathogens in economically important plants: tomatoes, potatoes, cucumbers, citrus trees, and chrysanthemums

How do some viral infections lead to certain cancer? What are these viruses called?

Some animal viruses enter their host cell and permanently alter its genetic material, leading to cancer Oncogenic viruses

Severe effects of viral infections Give examples.

Some have high mortality rates: Rabies, Ebola Other viral infections lead to long-term disability: Polio, Neonatal rubella

a. Live animal inoculation. List examples.

Specially bred strains of animals used for animal cultivation of viruses: White mice Rats Hamsters Guinea pigs Rabbits

Spikes What are they made of?

Spikes are found on both naked and enveloped viruses. - Protruding glycoproteins on the enveloped viruses essential for attachment to the host cell - On the naked viruses, they project from the nucleocapsid

Criteria of a formal classification system

Structure Chemical composition Similarities in genetic makeup

What is genome? Do viruses have a genome although they are not cells? Compare and contrast viral genomes to "cells."

The full complement of DNA and RNA carried by a cell. Although viruses are not cells, this apply to viruses. - Viruses contain either DNA or RNA but not both. - The number of viral genes is small compared to that of a cell > Possess only the genes necessary to invade host cells and redirect their activity

What are the simplest way to detect viral growth in cell culture?

To observe degeneration and lysis of infected cells - Plaques: > Clear, well-defined patches in the cell sheet > Develops when viruses released from an infected cell radiate out to surrounding cells and infect them > Infection spreads gradually and symmetrically from the original point of infection

What is the effect of oncogenic viruses on the cell called?

Transformation Notes: = cancer/tumor caused by infections by oncogenic viruses

True/False. Most viruses are propagated through cell culture.

True

True/False: Viral infections are more common than bacterial infections.@

True

True/False. Viruses are either "naked viruses" or enveloped viruses.

True. Naked viruses = capsid (protein shell) + nucleic acid Enveloped viruses = naked viruses + envelope

c. Using "cell/tissue culture" techniques

Uses in vitro cultivation system: a simple, effective way to grow populations of isolated animal cells in culture dishes for virus cultivation - Much of a virologist's work involves developing and maintaining cultures

Envelope

Usually a modified piece of the host cell membrane

Virus Life Cycle Step 4. Synthesis

Viral nucleic acid takes control over the host's synthetic and metabolic machinery. - Mechanism varies depending on whether the virus is a DNA or RNA virus - RNA viruses replicate in the cytoplasm - DNA viruses replicate in the nucleus

How do you name viruses? Examples.

Virus families: Suffix -viridae Virus genera: Suffix -virus Fam: Filoviridae / Genus: Ebola virus Fam: Herpesviridae / Genus: Simplexvirus

What are the two types of animal cell cultures?

a) Primary cell culture b) Continuous cell culture

Two disease examples caused by satellite viruses [PPT lists only the first one]

a) adeno-associated virus (AAV). first found in cells infected by adeno virus but actually AAV can infect any cells infected by other viruses or had their DNA disrupted thru other means b) delta agent: a naked circle of RNA (no capsid, envelope) expressed only in the presence of hep B virus. Causes even more severe liver damage.

What occurs in induction?

activation of a "prophage" in a lysogenic cell to undergo the lytic cycle

Viruses were discovered by filtering infectious fluid through a filter designed to trap ________.@

bacteria

Virus Life Cycle Step 6. [Enveloped viruses are] released from host cell via ______ or ______.

budding or exocytosis: - Nucleocapsid binds to the membrane - A small pouch is formed - Pinching off of the pouch releases the virus with its envelope - Viruses are shed gradually without destruction of the cell

Nucleocapsid

capsid and nucleic acid together

Viral capsids are constructed from ________ subunits.@

capsomere

Accumulated damage from a virus infection kills most host cells, but some cells maintain a _______ relationship, in which the cell harbors the virus is not immediately lysed.

carrier

The influenza virus has traditionally been cultured in ________.@

chicken embryo. Before the development of cell culture, many viruses were propagated in embryonated chicken eggs. Since 2009, scientists are using both chicken embryos and a continuous cell line derived from animal kidney cells to produce flu vaccines.

Types of nucleic acids in viruses

dsDNA, ssDNA, dsRNA or ssRNA

Virus Life Cycle Step 3. Uncoating

enzymes in the vacuole dissolve the envelope and capsid, releasing the virus (free DNA/RNA) into the cytoplasm.

Viruses can infect ________.

every type of cell: bacteria, algae, fungi, protozoa, plants, animals

Enveloped viruses

naked viruses (capsid + nucleic acid) + envelope

Satellite viruses require ________ in order to multiply.@

other viruses

Pasteur developed a vaccine for the _______ virus@

rabies

What are temperate phages?

special DNA phages that have the ability to undergo adsorption and penetration but do not immediately undergo replication or release

List three unique forms of viral nucleic acid.@

ssRNA -- positive-sense RNA & negative-sense RNA dsRNA ssDNA Special RNA types: retrovirus, segmented,

Occasionally, phage genes in the bacterial chromosome cause the production of _____ or _____ that cause pathology in the human

toxins, enzymes

Doctors and scientists most often rely on _________ to treat or prevent viral infections: @ Antibiotics Antiviral drugs Vaccines Herbal remedies

vaccines

_________ infect plants.@

viroids