Chapter 6- Acellular pathogens Flashcards
1
Q
Who is considered the founder of the field of virology?
A
Dmitri Ivanovski, a Russian botanist. He discovered the source of tobacco mosaic disease (TMD) by using a porcelain filtering device. The device has pores that are small enough to remove small bacteria from an extract from an infected plant. The cause of TMD could not be removed using a filter. It was thought that TMD was caused by a biological poison. Virus is Latin for poison and was used to describe the cause of TMD
2
Q
How can viruses be seen?
A
Using an electron microscope. They are too small to be seen using a light microscope, although their size helps them to infect larger cells
3
Q
Viruses
A
Distinct biological entities, but their evolutionary origin is unclear. They are acellular, so they not included in the tree of life. Viruses are considered obligate intracellular parasites because they have to infect a cellular host to survive and reproduce
4
Q
Virions
A
New virus particles that are formed as viral components like proteins and nucleic acids are produced. These viral components are produced when the viral genome takes over the genome of the host cell. The new virions transport the viral genome to another host cell to carry out another round of infection.
5
Q
Host range
A
The types of hosts a virus is able to infect. Most viruses will only be able to infect the cells of one or a few species, but some viruses have a wider host range
6
Q
Bacteriophages
A
Viruses that infect bacteria
7
Q
Vector
A
An animal that transmits a pathogen from one host to another. Includes mosquitoes, ticks, and flies
8
Q
3 ways that viruses can be transmitted
A
Direct contact, indirect contact with fomites, or through a vector
9
Q
Mechanical transmission
A
When an arthropod carries a viral pathogen on the outside of its body and transmits it to a new host, through physical contact
10
Q
Biological transmission
A
When the arthropod carries the viral pathogen inside its body and transmits it to the new host through a bite
11
Q
Zoonoses
A
When viruses are transmitted from an animal host to a human host and cause disease
12
Q
Reverse zoonoses
A
Caused by an infection of an animal by a virus that originated in a human
13
Q
What size are viruses?
A
Range from 20 nm for small viruses up to 900 nm for typical, large viruses. There are some giant viral species that are closer in size to a bacterial cell
14
Q
Wendell Stanley
A
The first scientist to crystallize the structure of the tobacco mosaic virus in 1935. He discovered that it is composed of RNA and proteins. He isolated the influenza B virus in 1943, which helped with the development of the flu vaccine
15
Q
Capsid
A
A protein coat that surrounds the virus’ nucleic acid genome. A capsid is not filled with cytosol, it is filled with the genome and enzymes that are needed to make new viruses. Capsids are composed of protein subunits called capsomeres. Different types of capsomere proteins interlock to form the capsid
16
Q
Components of a virus (2)
A
- Nucleic acid- DNA or RNA, never both
- A capsid surrounding the nucleic acid
17
Q
Naked (non-enveloped) viruses
A
Viruses formed with only a nucleic acid and a capsid, no envelope
18
Q
Enveloped viruses
A
The capsid is surrounded by a lipid bilayer
19
Q
Viral envelope
A
A small portion of the phospholipid membrane that is obtained as a virion buds from the host cell. The viral envelope can be intracellular or cytoplasmic.
20
Q
Spikes
A
Protein structures that extend from the capsid on enveloped viruses and some naked viruses. The spikes have structures at their tips that help the virus to attach to and enter a cell. One example is the H and N spikes found on influenza viruses
21
Q
How are influenza viruses identified?
A
By their H and N spikes. Hemagglutinin spikes (H) are found in influenza viruses. Influenza viruses also have enzymes like the neuraminidase (N) influenza virus spikes that help the virus to detach from the cell when new virions are released.
22
Q
Shapes of viral capsids (3)
A
Helical, polyhedral, or complex
23
Q
Helical capsids
A
The capsid is cylindrical or rod shaped, and the genome is found inside the capsid. TMV is a naked helical virus and Ebola is an enveloped helical virus
24
Q
Polyhedral capsids
A
Consist of a nucleic acid
surrounded by a polyhedral (many-sided) capsid in the form of an icosahedron. It forms the shape of poliovirus and rhinovirus
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Icosahedral capsid
A three-dimensional, 20-sided structure with 12 vertices. These capsids somewhat resemble a soccer ball
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Complex viruses
Viruses that may have features of both polyhedral and helical viruses. A bacteriophage form is one example. Poxviruses that have complex shapes are often brick shaped, with intricate surface characteristics not seen in the other categories of capsid.
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Bacteriophage structure
A complex virus- one end is helical, the other is polyhedral (the end with the capsid and the genome). The tailed end (tailed fibers and tail pins) helps to insert the viral genome into a cell by making a hole in the membrane. The sheath contracts to insert the genome.
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ICTV's viral classification system
Classifies viruses into families and genera based on viral genetics, chemistry, morphology, and mechanism of multiplication. Using this system, there are 7 orders, 96 families, and 350 genera of viruses
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ICTV's nomenclature
Viral family names end in -viridae (e.g, Parvoviridae) and genus names end in −virus (e.g., Parvovirus). The names of viral orders, families, and genera are all italicized. When referring to a viral species, we often use a genus and species epithet such as Pandoravirus dulcis or Pandoravirus salinus.
30
Baltimore classification system
An alternative to ICTV nomenclature. It classifies viruses according to their genomes (DNA or RNA, single versus double stranded, and mode of replication). With this system, there are 7 groups of viruses that have common genetics and biology
31
IDC classification of viral diseases
The ICD assigns an alphanumeric code of up to six characters to every type of viral infection, as well as all other types of diseases, medical conditions, and causes of death. The code is used to categorize patient conditions for treatment and insurance reimbursement. ICD codes are routinely used by clinicians to order laboratory tests and prescribe treatments specific to the virus suspected of causing the illness. This ICD code is then used by medical laboratories to identify tests that must be performed to confirm the diagnosis.
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Virulent phages
Lead to the death of the cell through cell lysis
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5 stages of the lytic cycle of virulent phage
1. Attachment
2. Penetration
3. Biosynthesis
4. Maturation
5. Lysis
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Temperate phages
Can become part of a host chromosome and are replicated with the cell genome until they are used to make new viruses (progeny viruses)
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Attachment
The first stage of the lytic cycle. The phage interacts with specific receptors on the surface of the host cell (bacteria).
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Penetration
The second stage of the lytic cycle. With a phage, the tail sheath contracts and acts like a needle to inject the viral genome through the membrane and the cell wall.
35
Biosynthesis
The third stage of the lytic cycle. Once it has entered the host cell, the virus synthesizes virus-encoded endonucleases to degrade the bacterial chromosome. Then, it takes over the host cell and uses it to replicate, transcribe, and translate the necessary viral components. This includes capsomeres, viral enzymes, and other components so that new viruses can be assembled
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Maturation
The fourth stage of the lytic cycle. New virions are created.
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Lysis
The fifth and last stage of the lytic cycle. Mature viruses burst out of the host cell, and they can infect new cells
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Lysogenic cycle
In this cycle, the phage genome also enters the cell through attachment and penetration. However, it does not kill the host. It integrates into the bacterial chromosome and becomes part of the host
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Prophage
The integrated phage genome that is formed during the lysogenic cycle
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Lysogen
A bacterial host with a prophage.
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Lysogeny
The process in which a bacterium is infected by a temperate phage. A temperature phage is usually latent or inactive in the cell. When the bacteria replicates its chromosome, it also replicates the phage's DNA and passes it on to daughter cells when it divides.
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Lysogenic/phage conversion
The phage can bring in extra genes, so the presence of the phage virus can change the phenotype of the host bacterium. In the case of bacteria, the extra genes can enhance the bacteria's virulence when they are expressed. In the case of V. cholera, phage encoded toxin can cause severe diarrhea; in C. botulinum, the toxin can cause paralysis.
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Induction
Results in the excision of the viral genome from the host chromosome under stressful conditions. The prophage remains in the host chromosome until this point. After induction, the temperate phage can proceed through a lytic cycle and then undergo lysogeny in a newly infected cell
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Transduction
When a bacteriophage transfers bacterial DNA from one bacterium to another as the bacteria are infected by the virus. During the lytic cycle, the virus takes over the host cell to make more viral genomes. As the genomes are used to make new viruses, there is sometimes a mistake in the genome packaging. A random piece of DNA from the host cell is inserted into the viral capsid. When the virion infects a new host, the former host's DNA will be injected into the new host. This asexual transfer of genetics allows for DNA recombination to occur and gives genes for new traits to be given to the host. Transduction plays an important role in the evolutionary process of bacteria
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Generalized transduction
Occurs when a random piece of bacterial chromosomal DNA is transferred by the phage during the lytic cycle.
46
Specialized transduction
During induction due to stressful conditions, the phage is excised from the host genome. The phage then enters the lytic cycle and produces new phages that will leave the host cell. During the process of excision from the host chromosome, a phage may occasionally remove some bacterial DNA near the site of viral integration. The phage and host DNA from one end or both ends of the integration site are packaged within the capsid and are transferred to the new, infected host. The DNA that is transferred to a new host is from a specific location of the genome rather than a random sequence. The DNA can recombine with the host chromosome. giving it new characteristics
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Tissue tropism
Viruses only infect certain cells within tissues, and they only infect specific hosts. For example, poliovirus exhibits tropism for the tissues of the brain and spinal cord
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How do animal viruses enter the host cell?
Once they bind to host receptors, they can enter the cell through endocytosis or through membrane fusion (viral envelope with the host cell membrane)
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What determines how a viral genome is replicated and expressed?
The nature of the viral genome, since viruses have have genomes that are single stranded or double stranded or RNA or DNA. If a genome is ssDNA, host enzymes will be used to
synthesize a second strand that is complementary to the genome strand, thus producing dsDNA. Therefore, animal viruses express their genes differently than the typical flow of DNA, RNA, and proteins
50
3 types of RNA genome
1. dsRNA (double stranded)
2. Positive (+) single stranded rRNA (+ssRNA)
3. Negative (-) single stranded RNA (-ssRNA).
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What must occur for RNA genomes to be translated into proteins?
+ssRNA is the equivalent of mRNA and can be directly read by the ribosomes. If the genome is -ssRNA, it has to be converted to +ssRNA by a viral RNA dependent RNA polymerase. With dsRNA viruses, an RNA dependent RNA polymerase uses the negative strand of the RNA as a template to make +ssRNA and therefore make proteins
52
Retroviruses
Retroviruses are +ssRNA viruses. They have an enzyme called reverse transcriptase that synthesizes complementary ssDNA, using the +ssRNA genome as a template. Then, the ssDNA is made into dsDNA. The dsDNA can integrate into the host chromosome and become a permanent part of the host
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Provirus
The integrated viral genome that occurs when the dsDNA from a retrovirus genome integrates into the host genome. The virus now can remain in the host for a long time to establish a chronic infection
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Persistent infection
Occurs when a virus is not completely cleared from the system of the host. It stays in certain tissues or organs of the infected person. The virus can remain latent or cause chronic infection
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Latent viruses
Cause latent infections, the viruses are capable of remaining hidden or dormant inside the cell. These viruses can cause an acute infection initially before becoming dormant. One example is the varicella-zoster virus, which causes chickenpox. The virus then foes dormant and lives in the nerve cell ganglia, and can reactivate to cause shingles years later. Epstein-Barr virus and herpes simplex virus are other examples
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How do latent viruses remain dormant?
By existing as circular viral genome molecules outside of the host chromosome. Some become proviruses by integrating into the host genome
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Chronic infection
A disease with symptoms that are recurrent or persistent over a long time. Some infections are chronic if the body is unable to eliminate the virus. HIV maintains chronic infection after a period of latency. It uses mechanisms that interfere with immune function. It prevents expression of viral antigens on the surface of infected cells, alters immune cells themselves, restricts expression of viral genes, and rapidly changes viral antigens through mutation
58
Plant viruses
Can be enveloped or non-enveloped. They can have a DNA or RNA genome, but most of them have a +ssRNA genome. They can have a narrow or broad host range. Most plant viruses are transmitted by contact between plants, or by fungi, nematodes, insects, or other arthropods that act as mechanical vectors. However, some viruses can only be transferred by a specific type of insect vector
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Biotrophic parasites
Parasites that can establish an infection without killing the host, similar to the lysogenic cycle of bacteriophages
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Life cycle of viruses in plants
Infection can be asymptomatic (latent) or can lead to cell death (lytic infection). The virus penetrates the host cell and is uncoated in the cell's cytoplasm when the capsid is removed. Cellular components are used to replicate the viral genome and synthesize viral proteins. To establish a systemic infection, the virus has to enter part of the vascular system of the plant
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Viral titer
The number of virions per unit volume
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Eclipse phase
When viruses bind and penetrate the cells of the host. No virions are detected in the medium. Virions are released from the lysed host cell all at the same in the next phase of their growth cycle, called a burst. This causes a dramatic rise in viral titer
63
Burst size
The number of virions released per bacterium (during a bacteriophage infection)
64
Virus growth curve (4 stages)
1. Inoculation- inoculum of virus binds to cells
2. Eclipse- virions penetrate the cell
3. Burst- host cells release many viral particles
4. Burst size- number of virions released, this causes a plateau in the graph
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Isolation of viruses
Viruses require a living host cell for replication. Infected host cells can be cultured and grown, and the growth medium can be harvested as a source of virus. Virions in the liquid medium can be separated from host cells by centrifugation or filtration
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In vivo
Within a whole living organism, plant, or animal
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In vitro
Outside a living organism in cells in an artificial environment
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How are bacteriophages cultivated?
They can be grown in a dense layer of bacteria in a petri dish or a flask (a bacterial lawn). As the phage kills the bacteria, many plaques are observed among the cloudy bacterial lawn.
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How are animal viruses cultivated?
Animal viruses require cells within a host animal or tissue culture cells derived from an animal or an embryo. For example, influenza vaccines are cultured in hens' eggs for an in vivo host source. Viruses have tissue tropism and have to be introduced into a specific part of the embryo
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Why is animal virus cultivation important? (3)
1. Identification and diagnosis of pathogenic viruses in clinical specimens
2. Production of vaccines
3. Basic research studies
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How are viruses cultivated with in vitro studies?
A primary cell culture can be used with cells that have been extracted from animal organs or tissues. Cells can be extracted through mechanical scraping or by an enzymatic method that breaks up tissue and releases single cells. Primary cell cultures have a limited life span
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Contact inhibition
As cells in a primary culture undergo mitosis, they will eventually come into contact with other cells. This causes mitosis to stop so that cell density won't become too high. To prevent contact inhibition, cells in a primary cell culture have to be transferred to another vessel with fresh medium- this is a secondary cell culture
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Continuous cell lines
If cells in a Petri dish have some cells poured off and fresh growth medium added, contact inhibition will be prevented and the cells can keep growing. HeLa cells are an example
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Cytopathic effects
Distinct observable cell abnormalities due to viral infection. These abnormalities can be observed in in vitro samples observed under a brightfield, fluorescent, or electron microscope. They include loss of adherence to the surface of the container, changes in cell shape (flat to round), shrinkage of the nucleus, vacuoles in the cytoplasm, fusion of cytoplasmic membranes and the formation of multinucleated syncytia, inclusion bodies in the nucleus or cytoplasm, and complete cell lysis. Viruses can also disrupt the cell's genome and cause carcinomas and sarcomas
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Serum
The straw-colored liquid fraction of blood plasma from which clotting factors have been removed. It can be used in a hemagglutination assay
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Hemagglutination
The agglutination (clumping) together of erythrocytes. Many viruses produce surface proteins, like spikes, that can bind to receptors on the membranes of RBCs and cause the cells to clump. Both infectious and noninfectious viral particles can agglutinate erythrocytes
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Hemagglutination inhibition assay
Used to detect specific types of viruses in the patient's sample. Antibodies generated by the immune system can be used to bind to components such a hemagglutinins that are associated with specific types of viruses. The binding of antibodies with the hemagglutinins found on the virus prevent RBCs from interacting with the virus. Therefore, when RBCs are added to the antibody coated viruses, there is no agglutination. It is used to detect the presence of antibodies specific to many types of viruses that have caused or are causing an infection
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Nucleic acid amplification (NAA) tests
Used in molecular biology to detect unique nucleic acid sequences of viruses un patient samples. PCR is an example, which detects the presence of viral DNA in a sample, and reverse transcriptase PCR is another example
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Polymerase chain reaction (PCR)
Used to detect viral DNA in a sample. It amplifies (synthesizes many copies) of a viral DNA segment of interest. Short nucleotide sequences (primers) bind to specific sequences of viral DNA, which enables identification of the virus
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Reverse transcriptase-PCR
Used to detect the presence of RNA viruses. It uses an enzyme called reverse transcriptase to make a complementary DNA from the viral RNA. The cDNA is then amplified by PCR
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Enzyme immunoassay
Uses the ability of antibodies to detect and attach to specific antigens. The antibody that is used for detection attaches to a viral antigen with a high level of specificity. An colorless enzyme is attached to the detecting antibody to tag it, and can interact with a colorless substrate to make a colored end product. Enzyme immunoassays are typically used as preliminary screening tests.
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Viriods
Consist of a short strand of circular RNA that is capable of replicating itself. Unlike like viruses, they don't have a protein coat to protect their genetic information, but they still take over the cell's machinery. Potato tuber spindle disease is an example
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Virusoids
Non-self replicating ssRNAs. RNA replication of virusoids is similar to that of viriods, but virusoids requires that the cell also be infected with a specific helper virus (from the family of Sobemoviruses). In some cases, virusoids remain packaged in the host cell and will only be released when the helper virus enters. Virusoids typically infect crops
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Prions
A misfolded rogue form of a normal protein (PrPc) found in the cell. The rogue prion protein, called PrPsc, can be caused by genetic mutation or spontaneously, and can be infectious. It stimulates other endogenous normal proteins to become misfolded, forming plaques
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Transmissible spongiform encephalopathy
A degenerative disorder that affects the brain and nervous system. Rogue proteins accumulate in these areas, causing the brain tissue to become sponge-like. Brain cells die and form holes in the tissue. This leads to brain damage, loss of coordination, and dementia. The disease is fatal and there is no cure. It is caused by a prion. In humans, Creutzfeldt-Jakob disease is one example of a TSE
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How are TSEs transmitted?
They can be transmitted between animals and from animals to humans by eating contaminated meat or animal feed. Transmission between humans can occur through heredity (which often occurs with CJD) or from contact with contaminated tissue (blood transfusion, organ transplant). There is no evidence for transmission via casual contact with an infected person
