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MOD 1 Flashcards

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1
Q

What are viruses?

A

Viruses are microscopic infectious agents that can reproduce only inside a cell they infect.

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2
Q

Why are viruses considered non-living obligate intracellular parasites?

A

Because they lack ribosomes, mitochondria, and cannot generate ATP.

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3
Q

What does the ‘viruses first’ hypothesis suggest?

A

It suggests that viruses predate cellular hosts.

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4
Q

What does the progressive hypothesis suggest about the evolution of viruses?

A

It suggests viruses evolved from genetic elements that gained the ability to move between cells.

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5
Q

What does the regressive hypothesis propose about viruses?

A

It suggests viruses are remnants of cellular organisms that lost metabolic organelles.

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6
Q

What do giant viruses encode?

A

encode metabolic enzymes, translational components, products of RNA maturation

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7
Q

What led to the discovery of viruses?

A

The Chamberland-Pasteur porcelain filter identified filterable pathogens.

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8
Q

How is virus quantification enabled?

A

By the principle that each plaque or lesion is formed by one virus particle.

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9
Q

What are some virus culturing methods?

A

Embryonated chicken eggs and human cell cultures.

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10
Q

What does ultracentrifugation allow for?

A

Highly purified and concentrated virus preparations.

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11
Q

What does electron microscopy enable?

A

Visualisation of virus structure.

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12
Q

What is required for crystallography in virus study?

A

Purified virions or viral proteins to be crystallised for X-ray diffraction analysis.

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13
Q

What is a key feature of cryo-electron microscopy?

A

It does not require crystallisation of viruses.

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14
Q

What revolutionised viral genome sequencing?

A

Maxam-Gilbert and Sanger methods.

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15
Q

What do RT-PCR and RT-qPCR enable?

A

Quantitative detection of viral RNA.

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16
Q

What does next generation sequencing enable?

A

Parallel sequencing of millions of DNA fragments from total nucleic acid of infected cells.

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17
Q

What do immunofluorescence, ELISA, and Western blot rely on?

A

Antigen-antibody interactions.

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18
Q

How is virus taxonomy organised?

A

Family → Subfamily → Genus → Subgenus → Species.

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19
Q

On what basis are viruses classified?

A
  1. nucleic acid type
  2. capsid symmetry
  3. presence/absence of lipid membrane
  4. particle dimensions
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20
Q

What are the seven stages of the virus life cycle?

A

Attachment, Penetration, Uncoating, Transcription/Translation, Genome replication, Assembly, Release.

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21
Q

What are the criteria for defining cellular receptors?

A
  1. Virus binds receptor
  2. Antibody to receptor blocks infection
  3. Expression of receptor gene confers susceptibility
  4. Disruption blocks infection
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22
Q

What receptor is used by influenza viruses?

A

Sialic acid receptor, differing by species with α(2,6) for human and α(2,3) for avian strains.

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23
Q

How do enveloped viruses fuse at the cell surface?

A

pH-independent

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24
Q

What characterises Class I fusion proteins?

A

α-helical
spikes
trimers in pre-fusion state

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25
What characterises Class II fusion proteins?
They are β-sheet dimers that become trimers during endosomal pH-triggered conformational change.
26
How do non-enveloped viruses like poliovirus enter cells?
By pore formation, inserting VP1 hydrophobic region into the membrane.
27
How does adenovirus enter cells?
By endocytosis, then endosomal lysis via penton base release.
28
How does reovirus become infectious?
It uses lysosomal proteolytic uncoating to become infectious subviral particles (ISVPs).
29
What is the basis of Baltimore classification?
Nucleic acid type and replication strategy.
30
What characterises Class I viruses?
They are dsDNA and replicate using host DNA and RNA polymerases.
31
What characterises Class II viruses?
They are ssDNA and replicate through a dsDNA intermediate using host polymerases.
32
What characterises Class III viruses?
They are dsRNA and transcribe mRNAs using viral RNA-dependent RNA polymerase.
33
What characterises Class IV viruses?
+ssRNA that can be directly translated into polyproteins.
34
What characterises Class V viruses?
-ssRNA that must carry viral RdRp in virion to produce mRNA.
35
What characterises Class VI viruses?
+RNA with DNA intermediate (retroviruses) that use reverse transcriptase.
36
What characterises Class VII viruses?
They have gapped dsDNA and replicate via RNA intermediate to form cccDNA.
37
What is required for virus assembly?
Compartmentalisation and intracellular trafficking of viral components.
38
How is poliovirus capsid stabilised during assembly?
By glutathione binding.
39
How does herpesvirus nucleocapsid accommodate the genome?
By protein scaffold cleavage by viral protease.
40
What does RNA genome packaging involve?
Secondary structure motifs and packaging of two RNA copies.
41
How many RNA segments does influenza virus package?
8 RNA segments with bipartite signals.
42
How does HIV assemble and bud?
At and buds through the plasma membrane, using Gag and ESCRT complex.
43
Where does coronavirus bud?
Into the ERGIC, and virions are released via membrane vesicle fusion.
44
How do flaviviruses mature?
Via furin cleavage of prM in the trans Golgi network.
45
How are non-enveloped viruses released?
By cell lysis, involving membrane rupture or apoptosis.
46
How can gene therapy be delivered?
Ex vivo or in vivo using viral vectors.
47
What do retroviral vectors allow?
Sustained expression of therapeutic gene by integrating into the host genome.
48
What are adenovirus vectors used for?
Vaccines, offering high transduction efficiency, but are highly immunogenic.
49
Where do adeno-associated viruses integrate?
At a specific site in the host genome, useful for sustained expression.
50
What is the benefit of saRNA vaccines
Much lower doses to induce effective immune response due to self-amplification.
51
What is CPER?
A bacteria-free method to generate viruses from viral RNA or synthetic DNA.
52
What is CPER useful for?
Identifying virulence factors and making viral chimeras like Binjari virus.
53
How does SV40 replicate?
Via semiconservative fork replication, using short RNA primers and host machinery.
54
How does adenovirus replicate?
Via strand displacement, initiated by terminal protein recruiting viral DNA polymerase.
55
How do parvoviruses replicate?
Using self-hybridised terminal repeat DNA as primer and host DNA polymerase complex.
56
Where do poxviruses replicate?
In the cytoplasm, encoding all proteins required for RNA transcription and DNA replication.
57
What do reoviruses have?
Segmented dsRNA and transcribe mRNAs using viral RNA-dependent RNA polymerase in core.
58
How do Class IV viruses produce proteins?
Via translation of polycistronic mRNA and replicate through -RNA intermediates.
59
What does complex Class IV transcription include?
Production of subgenomic mRNA for translation of structural proteins like C, p62, E2.
60
What do non-segmented Class V viruses show?
Transcription gradient from 3’ to 5’, due to ~30% drop-off at each gene junction.
61
Where do segmented Class V viruses replicate?
In the nucleus and use host mRNA 5’ caps as primers.
62
How do retroviruses produce dsDNA?
By using reverse transcription, which is integrated and transcribed by host RNA pol II.
63
How do hepadnaviruses convert rcDNA?
To cccDNA in the nucleus, serving as a template for transcription of core and HBx mRNAs.
64
Where are packaging signals in DNA viruses usually found?
In non-coding regions, while in RNA viruses they involve secondary structure motifs.
65
What do segmented RNA virus genomes have?
Bipartite packaging signals that ensure specificity and orientation in virion.
66
What does virus maturation involve?
Conformational changes or cleavage to produce infectious particles.
67
Where do flavivirus particles mature?
In the trans Golgi network, where furin cleaves prM and pr dissociates from E.
68
How can non-enveloped viruses be released?
Via cell lysis, apoptosis, or inhibition of host protein synthesis.
69
What is gene therapy used for?
To correct dysfunctional genes due to mutation or deletion, using viral vectors for delivery.
70
What does ex vivo gene therapy involve?
Modifying cells outside the body and reintroducing them into the patient.
71
How do retrovirus and lentivirus vectors integrate?
Into the host genome non-specifically, allowing sustained gene expression.
72
How was X-CGD treated?
Using a retrovirus vector delivering NADPH gene into myeloid phagocytes.
73
What are the limitations of adenovirus vectors?
They are highly immunogenic, with limitations due to pre-existing immunity and vector clearance.
74
What do next-gen adenovirus vectors do?
Remove inflammatory genes to improve safety and reduce immune response.
75
What characterises adeno-associated viruses?
They integrate at a specific site in the host genome and are non-pathogenic, stable, and non-immunogenic.
76
How was Leber’s Congenital Amaurosis treated?
Using AAV injected into the subretinal space.
77
Why do saRNA vectors require lower doses?
Because they self-replicate and amplify antigen expression.
78
What do modified nucleotides in saRNA vaccines do?
Increase stability and decrease host immune response.
79
What do lipid nanoparticle (LNP) formulations help with?
Deliver RNA efficiently in vivo without VLP generation.
80
What instability do conventional +RNA virus manipulations face?
Due to toxic full-length cDNA clones in bacteria.
81
What methods can overcome instability in RNA virus manipulation?
Low-copy plasmids, intron insertion, in vitro ligation, assembly in BAC/YAC.
82
What does CPER avoid?
Cloning by using circular polymerase extension reaction to assemble full-length viral genomes from DNA fragments.
83
What is CPER ideal for?
Rapid generation of viruses and swapping gene regions to test virulence.
84
What is an example of CPER application?
Binjari virus chimeras generated for WNV studies.
85
How do enveloped viruses fuse at the endosome?
pH-dependent
86

MICR3002 (6 decks)

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