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Viruses: general intro Flashcards

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1
Q

Define a virus

A

Infectious, obligate intracellular parasite
= genetic material surrounded by protein coat/ envelope made from host cell membrane

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2
Q

What is meant by viruses being obligate intracellular parasites?

A

Can only survive + replicate in living cell.
Dependent on host for survival, not considered living if not in host

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3
Q

What is a capsid? Describe its structure

A

it is a symmetric protein shell enclosing genetic material. Composed of capsomeres: composed of aggregates of polypeptide chains

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4
Q

Define a virion

A

Complete infectious virus particle that exists freely outside a host cell. A virus without an envelope is not a virion, but is still infective and virulent.

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5
Q

Define a virus envelope

A

outer coat acquired by some viruses as they penetrate/ bud from nucleus/ cell membrane

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6
Q

What is a peplomer and its function?

A

Surface projections on viral envelope, consist of viral glycoproteins.

Function:
1) Haemagglutinin = Receptor for influenza virus > binds to host cell > causes haemagglutination + antigenic determinant (part that causes immune response)

2) Neuraminindase = enzymatic act. > releases influenza virus from host cell to move on to infect others

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7
Q

What is a pseudovirion?

A

synthetic viruses used to inject genetic material (RNA/DNA) with specific traits into bacterial cells

structure similar to virus but can’t replicate

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8
Q

What are defective interfering viruses?

A

spontaneously generated virus mutants where a critical piece of its genome is lost due to defective replication.

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9
Q

Describe the genome of double-stranded and single-stranded RNA viruses

A

2x: can be segmented

1x:
i) sense/+ strand: resembles mRNA > directly interacts with host’s ribosomes to be translated into virus proteins

ii) anti-sense/- strand: + strand must 1st be made and then translated into proteins [RNA - dependent RNA polymerase used)

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10
Q

Describe the genome DNA viruses

A

1x/2x stranded DNA molecule

Linear/ circular

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11
Q

What is a viroid?

A

= smallest known pathogens

= naked, circular, 1x stranded RNA molecule that doesn’t encode proteins

= replicate autonomously when introduced into host plants (no animal diseases)

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12
Q

What are prions?

A

misfolded proteins with the ability to transmit their misfolded shape into normal variants of the same protein

  • induce conformational changes in normal proteins

= neither bacterial nor fungal nor viral
= no genetic material

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13
Q

What degenerative brain diseases are caused by prions?

A
  • Bovine spongiform encephalopathy (BSE, mad cow disease)
  • Scrapie in sheep
  • Creutzfeldt-Jakob disease (humans)
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14
Q

What is involved in the shadow casting staining method?

A

A heavy metal (like platinum or gold) is sprayed onto a sample from one side only, at an angle.

This creates a “shadow” effect — parts of the sample block the metal, leaving a shadow behind.

The result: the 3D shape and surface details of the sample become more visible under the electron microscope

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15
Q

What is involved in negative staining?

A

A dark stain is applied to the sample.

The stain does not enter the specimen — it only stains the background.

The specimen itself stays unstained and appears light against the dark background.

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16
Q

What is involved in positive staining?

A

A coloured or heavy metal stain is applied to the sample.

The stain soaks into or attaches to the specimen

This makes the specimen appear dark or coloured, while the background stays lighter.

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17
Q

What direct measures are used to visualise viruses?

A

1) Electron microscope
2) Shadow casting
3) Positive staining
4) Negative staining

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18
Q

What indirect measures are used to visualise viruses?

A

Effect on host system:
1) embryonated chicken eggs
2) Lab animals
3) cell cultures
4) serological tests = haemagglutination

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19
Q

Basic morphological forms of viruses and examples of each

A

1) Icosahedral: Bluetongue virus
2) Helical: rabies
3) Complex: pox virus, bacteriophage

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20
Q

Problems with using lab animals

A

= variance in susceptibility between species

= previous infections = immunity

= impractical to accommodate large animals

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21
Q

Disadvantages of using lab animals

A

= cost
= cross infection
= human infections
= previous exposure = immunity

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22
Q

Uses of virus cultivation in embryonated chicken eggs

A

= ID + diagnose viruses in clinical specimens

= vaccine prod.

= research

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23
Q

2 advantages of using embryonated chicken eggs for cell culture

A

= cheap
= easy to handle and infect

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24
Q

What are 4 signs of infection in embryonated chicken eggs?

A

= embryo death
= haemorrhages
= dwarfing/ malformation
= lesions

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25
2 disadvantages of using embryonated chicken eggs for cell culture
= eggs must come from path free flocks > specific pathogen free poultry breeding unit = expensive = susceptible to bacterial contaminants
26
List 3 major observations made by Beijerinck that suggested a virus was the causative agent of Tobacco Mosaic Virus and not bacteria
1) The causative agent is smaller than bacteria 2) The causative agent could not be grown on standard bacterial culture media 3) The causative agent could only reproduce in living plant cells = relies on host to replicate
27
Explain how cell lines are created
Primary cell culture: 1) Cells are extracted from tissues (e.g., animal organs like liver, kidney, etc.). 2) Cells are placed in a culture medium in a petri dish or flask. For anchorage-dependent cells, they need a solid surface to attach and grow. 3) Cells begin to grow and divide (mitosis). 4) Contact inhibition occurs: Cells stop dividing when they form a monolayer and touch each other (normal in healthy cells). To continue growth: i) The culture can be split/diluted by removing some cells and adding fresh medium. ii) Cells can be transferred to a new vessel — this process is called sub-culturing or passaging. ✅ Once cells have been sub-cultured, the culture is called a secondary culture. When cells have been sub-cultured successfully several times it is referred to as a cell line
28
What are continuous cell lines?
Continuous cell lines are cell cultures that are derived from transformed cells/ tumours that may have lost contact inhibition and can grow indefinitely (immortal) and can grow without anchorage.
29
What are transformed cells?
Cells that have been genetically altered naturally (cancer) / artificially (chem./ viruses) to exhibit certain traits: - loss of contact inhibition - immortality - grow without anchorage - rapid growth
30
What % of the karyotype is retained in diploid cell lines?
75% of the number and structure of chromosomes [karyotype] is retained
31
What is the cytopathic effect and what are signs of it?
CE = degeneration and death of cells Signs = - necrosis - cell detachment from surface - Inclusion bodies = small aggregates of viral proteins (cytoplasm or nucleus) - Transformation = integration of viral nucleic acid into cells of monolayer.
32
What type of nucleic acid do viruses contain?
Either DNA or RNA, which can be single-stranded or double-stranded.
33
What is the function of viral nucleic acid?
It encodes the genetic information necessary for viral replication and the production of viral proteins
34
What does the proportion of viral nucleic acid indicate?
It varies (e.g., 1% in influenza, 50% in bacteriophages) and reflects the virus’s genetic complexity
34
How are viral proteins studied?
By separating them using detergents, dissociation, and electrophoresis or chromatography.
35
What are the functions of structural viral proteins?
Protect viral genome from nucleases Aid attachment to host cells Serve as immunological antigens Provide structural symmetry Determine electrophoretic mobility
36
What are internal viral proteins and what do they do?
They perform specialized functions like: Producing enzymes for replication (e.g., reverse transcriptase) Assisting in viral DNA integration into the host genome
37
Where are viral lipids found?
In the viral envelope.
38
What is the role of viral lipids in virus classification and sensitivity?
Viruses are grouped as enveloped or non-enveloped Lipid content makes viruses sensitive to ether and chloroform
39
How are viral lipids added to the virus?
During budding/maturation through the cell or nuclear membrane, incorporating host-derived lipids and proteins
40
What additional structures are added to the viral envelope?
Virus-specific glycoproteins (also called spikes or peplomers)
41
What is the role of viral carbohydrates?
They form part of glycoproteins in the envelope, which are important antigenic determinants
42
Who controls glycoprotein synthesis in viruses?
It is partly controlled by the virus, but largely determined by the host cell genome
43
What are examples of viral enzymes and their functions?
Neuraminidase: helps virus exit infected cells Reverse transcriptase: converts RNA to DNA Polymerases: transcribe DNA/RNA, including: 1) DNA-dependent RNA polymerase 2) RNA-dependent RNA polymerase 3) RNA-dependent DNA polymerase (reverse transcriptase)
44
Why is studying the viral replication cycle important?
To understand and synchronize cellular and viral activity during infection. Synchronization is achieved by infecting all cells in the system with at least one viral particle and removing any unabsorbed viruses.
45
What are the 3 minimum functions viruses must encode proteins for?
Replication of the viral genome Packaging the genome into virions (assembly) Altering the structure and/or function of the infected cell
46
What special ability do some viruses have in the host?
The ability to remain latent (inactive) inside the host, enabled by specific proteins and enzymes encoded by the viral genome.
47
What happens in the initial stage of the one-step growth curve?
The virus inoculum infects the host cells.
47
What is the eclipse phase of viral replication?
The phase where viruses bind and enter cells, but no virions are detectable in the medium yet. period during which infected host cells contain virus particles, but no infectious virions are detectable outside the cell i.e has not been released yet
48
What is the burst phase in viral replication?
All virions are released at once from lysed host cells, causing a sudden spike in viral count
49
What is burst size?
The number of virions released per infected bacterium
50
What is the key difference between viral and bacterial growth curves?
Viruses show a burst release, whereas bacteria multiply continuously
50
What causes the steep rise in viral titer in the growth curve?
The lysis of host cells and release of viral particles into the medium.
51
What happens during the decline of the viral growth curve?
Viral particles degrade if no viable host cells remain for further infection.
52
Briefly explain the 6 steps of influenza virus replication
1) Attachment: Influenza virus (virion) attaches to target epithelial cell receptor (glycoproteins) using haemagglutinin 2) Penetration: Cell engulfs the virus via endocytosis 3) Uncoating: Viral RNA is released into the cytoplasm via lysozymes from host [ beginning of eclipse phase] 4) Biosynthesis [eclipse]: Viral RNA enters the nucleus and is replicated by viral RNA polymerase 5) Assembly: New virions are assembled 6) Release: Viral particles are released into the ECF. The cell continues to make more virus.
53
Can viruses translate their own proteins independently?
No, viruses do not encode a complete translation system and are completely dependent on the host cell’s translation machinery (ribosomes)
54
What is a positive strand in terms of viral genomes?
A strand that has the same sequence as mRNA so they do not need to be transcribed first, they can be translated directly.
55
What is a negative strand in terms of viral genomes?
A strand that is complementary to the mRNA and must be copied into a positive strand (transcribed) before translation.
56
What is the expression strategy of double-stranded DNA viruses?
(+) mRNA is produced from the (-) DNA strand directly. Examples: Adenoviruses, Poxviruses
57
How do single-stranded (+) sense DNA viruses replicate?
First, make a (-) sense DNA strand Then use that as a template to synthesize (+) RNA and (+) DNA Example: Parvoviruses
58
How do double-stranded RNA viruses express their genome?
Each segment of the genome is transcribed separately to produce mRNA. Example: Reoviruses (e.g., bluetongue virus, African horse sickness)
59
What is special about single-stranded (+) sense RNA viruses?
Their RNA genome is the same as mRNA, so it is directly infectious
60
How do single-stranded (-) sense RNA viruses replicate?
Their (-) sense RNA is copied into (+) sense mRNA, which is then translated into proteins.
61
What is unique about single-stranded (+) sense RNA viruses with a DNA intermediate?
Their RNA genome is not used directly as mRNA, but instead is a template for reverse transcription. Example: Retroviruses (use reverse transcriptase)
62
What do retroviruses do with their genome after reverse transcription?
They produce dsDNA that integrates into the host genome as a provirus, becoming a permanent part of the host.
63
How do double-stranded DNA viruses with an RNA intermediate replicate?
Synthesize (+) mRNA after uncoating Translate proteins (enzymes first, then structural) Use post-translational cleavage to produce functional proteins
64
How does RNA synthesis differ between positive and negative sense RNA viruses?
(+) sense RNA acts directly as mRNA (-) sense RNA must first make a (+) sense copy via a replicative intermediate
65
What enzyme do retroviruses carry and why?
Reverse transcriptase, to create a DNA copy from their +ssRNA genome
66
What happens after the synthesis of viral nucleic acid and proteins?
Assembly of new virions Release from the host cell
67
How are capsids of unenveloped viruses formed?
By self-assembly of monomers (structural proteins) into capsomeres in the cytoplasm which is used to build the final capsid
68
Is nucleic acid required for unenveloped capsid formation?
No, empty capsids can form in the cytoplasm without nucleic acid.
69
What are intracellular crystals/inclusion bodies?
Areas where virus particles concentrate at the site of production.
70
How are RNA unenveloped viruses released?
Rapidly and usually with destruction of the host cell.
71
How are icosahedral DNA unenveloped viruses released?
Slowly, after maturation in the nucleus and accompanied by cell autolysis.
72
How do enveloped viruses acquire their envelope?
By budding through the cell membrane or into cytoplasmic vacuoles.
73
Where do herpes viruses assemble and get their envelope?
They assemble in the nucleus and acquire their envelope by passing through the inner nuclear membrane.
74
How are enveloped viruses protected during budding?
They accumulate between nuclear membranes or in vesicles, avoiding exposure to cytoplasm.
75
How does HIV acquire its envelope?
From the plasma membrane during budding at the cell surface.
76
Where do vaccinia viruses derive their envelope from?
The Golgi body.
77
What are conditional lethal mutants?
Viral mutants that only replicate under specific environmental or physiological conditions.
78
What are temperature-sensitive mutants?
Mutants that replicate at normal temperatures but not at elevated temperatures.
79
Why are temperature-sensitive mutants useful?
They help study viral replication by allowing control of replication with temperature changes.
80
What are attenuated viruses?
Viruses that have lost their ability to cause disease but can still infect and trigger immune responses.
81
How are attenuated mutants used?
As live vaccines to produce active immunity without causing disease.
82
What causes viral attenuation?
Passage of the virus in unnatural hosts like embryonated eggs or cell cultures.
83
What is a defective virus?
A virus that cannot replicate or complete its life cycle due to missing components.
84
What can cause a virus to be defective?
A defective host cell (lacking enzymes) or the virus itself being defective.
85
What is a result of infection with many defective viruses?
They may block receptors and cause chronic or latent infections.
86
What are defective interfering particles?
Defective viruses that interfere with normal virus binding and replication.
87
What is viral recombination?
Exchange of genetic material between two co-infecting viruses in the same cell.
88
Why is recombination important in retroviruses?
It allows genetic mixing and diversity of viral strains.
89
What is gene reassortment in viruses?
Exchange of genome segments between viruses with segmented genomes.
90
What is an example of gene reassortment?
Influenza virus combining segments from human and animal strains.
91
What is antigenic shift?
A major genetic reassortment event leading to new viral strains, such as avian-human flu hybrids.
92
What is antigenic drift?
Minor changes in viral genes due to spontaneous point mutations.
93
Why doesn't flu infection lead to long-term immunity?
Because envelope proteins mutate rapidly, changing antigenic properties.
94
What determines the serological properties of a virus?
Structural proteins like capsid proteins (for non-enveloped viruses) or envelope glycoproteins (for enveloped viruses) serve as primary antigens, which affect immune recognition and disease severity.
95
Where do herpes viruses derive their envelope from?
Inner nuclear membrane

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