Module 5

Question 1

Describe the general characteristics of viruses (5)

Answer 1

• Infectious, acellular pathogens
• Obligate intracellular parasites with host and cell-type specificity
• DNA or RNA genome (never both)
• Genome is surrounded by a protein capsid and, in some cases, a phospholipid membrane studded with viral glycoproteins
• Lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce

Question 2

How can viruses be pathogenic

Answer 2

• Cause abnormal growth of cell
• Cause cell death
• Alter cell’s genome
• Cause little noticeable effect in the cell

Question 3

Describe how viruses use genetic information

Question 4

Give examples of how viral genomes are organized at the nucleic acid level

Answer 4

• Double-stranded or single stranded DNA
• Double-stranded or single stranded RNA
• Positive-strand or negative-strand RNA

Question 5

Briefly explain or describe viral life cycles

Answer 5

• Genome of a virus enters a host cell and directs the production of viral components, proteins and nucleic acids, needed to form new virus particles called virions
• New virions are made in the host cell by assembly of viral components
• New virions transport the viral genome to another host cell to carry out another round of infection

Question 6

Distinguish with examples: Bacteriophages

Answer 6

• Viruses that only infect bacteria
• Also called phages

Question 7

Distinguish with examples: plant viruses

Question 8

Distinguish with examples: animal viruses

Question 9

Explain why viruses may be considered obligate intracellular parasites

Answer 9

In order to survive and reproduce, viruses must infect a cellular host making them obligate intracellular parasites

Question 10

What is a vector?

Answer 10

An animals that transmits a pathogen from one host to another

Question 11

Mechanical vs biological vectors

Answer 11

Mechanical vector: Mechanical transmission occurs when the arthropod carries a viral pathogen on the outside of its body and transmits it to a new host by physical contact.

Biological transmission occurs when the arthropod carries the viral pathogen inside its body and transmits it to the new host through biting.

Question 12

In terms of genome what kind of virus is herpes?

Answer 12

• Double stranded enveloped virus

Question 13

In terms of genome what kind of virus is HIV

Answer 13

+ssRNA enveloped DNA

Question 14

Explain the lytic life cycle

Answer 14

1. ATTATCHMENT: The phage attaches to the surface of the host
2. PENETRATION: The viral DNA enters the host cell
3. BIOSYNTHESIS: Phage DNA replicates and phage proteins are made
4. MATURATION: New phage particles are assembled
5. LYSIS: The cell lyses, releasing the newly made phages.

Question 15

Explain the lysogenic viral life cycle

Answer 15

1. The phage infects a cell
2. The phage DNA becomes incorporated into the host genome
3. The cell divides and prophage DNA is passed on to daughter cells
4. Under stressful conditions the prophage DNA is excised from the bacterial chromosome and enters the lytic cycle
5. The cell lyses, releasing the newly made phages
6. New phage particles are assembled
7. Phage DNA replicated and phage proteins are made

Question 16

Explain the process of viral replication as done by animal viruses: DNA

Answer 16

If genome is ssDNA, host enzymes will be used to synthesize a second strand that is complementary to the genome strand, thus producing dsDNA. The dsDNA can now be replicated, transcribed, and translated similar to host DNA.

Question 17

Briefly explain the life cycle of retroviruses

Answer 17

• They are +ssRNA viruses.
• Carry special enzyme called reverse transcriptase within the capsid that synthesizes a complementary ssDNA (cDNA) copy using the +ssRNA genome as a template.
• ssDNA is then made into dsDNA, which can integrate into the host chromosome and become a permanent part of the host.
• Integrated viral genome is called a provirus. The virus can now remain in the host for a long time to establish a chronic infection
• The provirus stage is similar to the prophage stage in a bacterial infection during the lysogenic cycle. However, unlike prophage, the provirus does not undergo excision after splicing into the genome.

Question 18

Briefly explain the life cycle of latent viruses

Answer 18

• Not all animal viruses undergo replication by the lytic cycle. There are viruses that are capable of remaining hidden or dormant inside the cell in a process called latency. These types of viruses are known as latent viruses and may cause latent infections. Viruses capable of latency may initially cause an acute infection before becoming dormant.
• Latent viruses may remain dormant by existing as circular viral genome molecules outside of the host chromosome. Others become proviruses by integrating into the host genome.
• During dormancy, viruses do not cause any symptoms of disease and may be difficult to detect.
• A patient may be unaware that he or she is carrying the virus unless a viral diagnostic test has been performed

Question 19

Use HIV to explain how viruses interact with the human cells

Answer 19

Check retro virus.

• HIV is an example of a virus that produces a chronic infection, often after a long period of latency
• Untreated patients often experience no symptoms for years, but virus maintains chronic persistence through several mechanisms that interfere with immune function, including preventing expression of viral antigens on the surface of infected cells, altering immune cells themselves, restricting expression of viral genes, and rapidly changing viral antigens through mutation.
• Eventually, the damage to the immune system results in progression of the disease leading to acquired immunodeficiency syndrome (AIDS).
• A chronic infection is a disease with symptoms that are recurrent or persistent over a long time

Question 20

Define transduction in the context of viruses

Answer 20

• Occurs when a bacteriophage transfers bacterial DNA from one bacterium to another during sequential infections

Question 21

Compare the life cycle of a typical plant virus with the life cycle of animal viruses

Answer 21

Viral infection can be asymptomatic (latent) or can lead to cell death (lytic infection). The life cycle begins with the penetration of the virus into the host cell. Next, the virus is uncoated within the cytoplasm of the cell when the capsid is removed. Depending on the type of nucleic acid, cellular components are used to replicate the viral genome and synthesize viral proteins for assembly of new virions. To establish a systemic infection, the virus must enter a part of the vascular system of the plant, such as the phloem. The time required for systemic infection may vary from a few days to a few weeks depending on the virus, the plant species, and the environmental conditions. The virus life cycle is complete when it is transmitted from an infected plant to a healthy plant.

• Like animal viruses, plant viruses can have either a DNA or RNA genome and be single stranded or double stranded. However, most plant viruses do not have a DNA genome; the majority have a +ssRNA genome which acts like messenger RNA (mRNA). Only a minority of plant viruses have other types of genomes.

Question 22

Explain the process of viral replication as done by animal viruses: +ssRNA

Answer 22

Translated directly to make viral proteins.
- Viral genomic +ssRNA acts like cellular mRNA

Question 23

Explain the process of viral replication as done by animal viruses: -ssRNA

Answer 23

Host ribosomes cannot translate genome until the -ssRNA is replicated into +ssRNA by viral RNA-dependent RNA polymerase (RdRP)

• RdRP is brought in by the virus and can be used to make +ssRNA from the original -ssRNA genome

Question 24

Explain the process of viral replication as done by animal viruses: dsRNA

Answer 24

• RdRP important enzyme
• RdRP uses the negative strand of the double-stranded genome as a template to create +ssRNA
• Newly synthesized +ssRNA copies can then be translated by cellular ribosomes

Question 25

Define filterable agent

Answer 25

• Capable of passing through the pores of a filter; usually referring to living infectious agents such as viruses that can pass through a filter that retains the usual pathogenic bacteria
• Virions in the liquid medium can be separated from the host cells by either centrifugation or filtration. Filters can physically remove anything present in the solution that is larger than the virions; the viruses can then be collected in the filtrate

Question 26

Why was the term filterable agent used to describe viruses

Answer 26

• Was used to denote a group of disease producing agents, which seemed to differ from other forms of living matter in their ability to pass through earthernware filters having a pore diameter smaller than the smallest bacteria then known.

Question 27

Briefly describe the cultivation of viruses

Answer 27

• Can be grown in vivo or in vitro
• Can be done is flat horizontal cell culture by growing bacteriophages in presence of dense layer of bacteria (phage kills bacteria).

Question 28

Explain how viruses may be identified

Answer 28

• Cytopathic effects (CPEs) are distinct observable cell can include:
  
  • Loss of adherence to the surface of the container
  • Changes in cell shape from flat to round
  • Shrinkage of the nucleus
  • Vacuoles in the cytoplasm
  • Fusion of cytoplasmic membranes
  • Formation of multinucleated syncytia
  • Inclusion bodies in the nucleus or cytoplasm
  • Complete cell lysis

Question 29

What does it mean for viruses to be grown is vivo?

Answer 29

Grown within a whole living organism, plant, or animal

Question 30

What does it mean for viruses to be grown in vitro?

Answer 30

Grown outside a living organism in cells in an artificial environment.

Question 31

In vivo animal studies:

Answer 31

• Animal viruses (in vivo) require cells within a host animal or tissue-culture cells derived from an animals.
• The embryo or host animal serves as an incubator for viral replication.
• Location is important, viruses have a tissue tropism and must be introduced to specific site for growth
• Important for: 1) identification and diagnosis of pathogenic viruses in clinical specimens, 2) production of vaccines, and 3) basic research studies.

Question 32

In vitro studies:

Answer 32

• Various types of cells can be used to support the growth of viruses
• Primary cell culture is freshly prepared from animal organs or tissues
• Cells extracted from tissues by mechanical scraping or mincing to release cells or by an enzymatic method using trypsin or collagenase to break up tissue and release single cells into suspension
• Primary cell cultures require a liquid culture medium in a petri dish or tissue-culture flask so cells have a solid surface such as glass or plastic for attachment and growth
• Have limited life span
• When they undergo mitosis and sufficient density of cells is produced, cells come in contact inhibition and it prevents the density of the cells from becoming too high
• This is called contact inhibition and it prevents the density of the cells from becoming too high. To prevent contact inhibition, cells from the primary cell culture must be transferred to another vessel with fresh growth medium. This is called a secondary cell culture.

Question 33

Hemmagglutination Assay

Answer 33

• A serological assay is used to detect the presence of certain types of viruses in patient serum
• Serum is the straw-colored liquid fraction of blood plasma from which clotting factors have been removed
• Hemaggulation Assay can detect some viruses in patients serum

Question 34

What is hemaggulination? How is it related to viruses?

Answer 34

The aggulatination (clumping) of erythrocytes (red blood cells)

• Many viruses produce surface proteins or spikes called hemagglutinins that can bind to receptors on the membranes of erythrocytes and cause the cells to agglutinate.

Question 35

Pros and cons to Hemaggulination?

Answer 35

• Hemagglutination is observable without using the microscope
• but this method does not always differentiate between infectious and noninfectious viral particles, since both can agglutinate erythrocytes.

Question 36

How do we identify a specific pathogenic virus using hemaggulatination

Answer 36

To identify a specific pathogenic virus using hemagglutination, we must use an indirect approach. Proteins called antibodies, generated by the patient’s immune system to fight a specific virus, can be used to bind to components such as hemagglutinins that are uniquely associated with specific types of viruses. The binding of the antibodies with the hemagglutinins found on the virus subsequently prevent erythrocytes from directly interacting with the virus. So when erythrocytes are added to the antibody-coated viruses, there is no appearance of agglutination; agglutination has been inhibited. We call these types of indirect assays for virus-specific antibodies hemagglutination inhibition (HAI) assays. HAI can be used to detect the presence of antibodies specific to many types of viruses that may be causing or have caused an infection in a patient even months or years after infection

Question 37

Nucleic Acid Amplification Test

Answer 37

• used in molecular biology to detect unique nucleic acid sequences of viruses in patient samples

Ex. PCR - used to detect viral DNA
Reverse transcriptase-PCR used to detect RNA viruses

Question 38

Enzyme Immunoassay

Answer 38

Enzyme immunoassays (EIAs) rely on the ability of antibodies to detect and attach to specific biomolecules called antigens. The detecting antibody attaches to the target antigen with a high degree of specificity in what might be a complex mixture of biomolecules. Also included in this type of assay is a colorless enzyme attached to the detecting antibody. The enzyme acts as a tag on the detecting antibody and can interact with a colorless substrate, leading to the production of a colored end product. EIAs often rely on layers of antibodies to capture and react with antigens, all of which are attached to a membrane filter (see Figure 6.23). EIAs for viral antigens are often used as preliminary screening tests. If the results are positive, further confirmation will require tests with even greater sensitivity, such as a western blot or an NAAT. EIAs

Question 39

Describe virioids and their unique characteristics

Answer 39

• Mean “virus like”
• Consist only of a short strand of circular RNA capable of self-replication
• Do not have a protein coat to protect their genetic information
• Can result in devastating losses of commercially important agricultural food crops grown in fields and orchards
• Can be dispersed mechanically during crop maintenance or harvesting, vegetative reproduction, and possible via seeds and insects, resulting in a severe drop in food availability and devastating economic consequences

Question 40

Describe Virusoids and their unique characteristics

Answer 40

• Pathogenic RNA that can infect commercially important agricultural crops
• Subviral particles best described as non-self-replicating ssRNAs
• Virusoids require that the cell also be infected with a specifc “helper” virus to replicate
• Only 5 described types of virusoids and helper viruses known today
• All helper viruses from family of sobemoeviruses
• Once the helper virus enters the host cell, the virusoids are released and can be found free in plant cell cytoplasm, where they possess ribozyme activity.
• The helper virus undergoes typical viral replication independent of the activity of the virusoid.
• The virusoid genomes are small, only 220 to 388 nucleotides long.
• A virusoid genome does not code for any proteins, but instead serves only to replicate virusoid RNA.
• Virusoids belong to a larger group of infectious agents called satellite RNAs, which are similar pathogenic RNAs found in animals. Unlike the plant virusoids, satellite RNAs may encode for proteins; however, like plant virusoids, satellite RNAs must coinfect with a helper virus to replicate.

Question 41

Describe prions and their unique characteristics

Answer 41

• Proteinaceous infectious particles
• Proteins are acellular and do not contain RNA or DNA, so prions don’t contain RNA or DNA either
• A prion is a misfolded rogue form of a normal protein (PrPc) found in the cell
• May be caused by genetic mutation or occur spontaneously, can be infectious, stimulating other endogenous normal proteins to become misfolded, forming plaques
• Known to cause transmissible spongiform encephalopathy (TSE) in human and animals
• TSE is a rare degenerative disorder that affects the brain and nervous system
• The accumulation of rogue proteins causes the brain tissue to become sponge-like, killing brain cells and forming holes in the tissue, leading to brain damage, loss of motor coordination, and dementia
• Infected individuals are mentally impaired and become unable to move or speak. There is no cure, and the disease progresses rapidly, eventually leading to death within a few months or years.