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Virology Flashcards

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1
Q

What are viruses?

A

Acellular organisms that are submicroscopic and obligate intracellular parasites.

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2
Q

What are virions?

A

Virus particles that are produced from the assembly of pre-formed components. They do not undergo growth or division.

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3
Q

What is variolation?

A

The inhalation of dried crusts or inoculation of pus from lesions - effective but risky.

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4
Q

What is vaccination?

A

The inoculation of a virus from a material that was safe to those who came in contact with it (e.g. animal disease) and it cannot be contracted by others who it would be a danger to, unlike variolation.

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5
Q

Physical ways to determine virus structure

A

Filtration through membranes of various pore sizes
Sedimentation properties
Spectroscopy: UV light determines nucleic acid, visible light determines light scattering properties
X-ray diffraction determines atomic structure

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6
Q

Chemical ways to determine virus structure

A

Resistance to pH changes

Resistance to protein denaturaing agents

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7
Q

Determining virus structure by EM

A

Transmission and scanning electron microscopes, resolution improved by dropping temperature

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8
Q

Name the three main functions of a virus particle

A

To protect genetic material
To recognise and interact with a host cell
Genome/protein delivery to host cell

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9
Q

Capsid

A

Protective protein coat

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10
Q

Envelope

A

Outer lipoprotein bilayer membrane possessed by many viruses

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11
Q

Genome

A

Nucleic acid comprising genetic material of organism

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12
Q

Helix

A

Cylindrical solid formed by staking repeated subunits

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13
Q

Icosahedron

A

Solid shape with 20 triangular faces around a sphere

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14
Q

Nucleocaspid

A

Ordered complex of proteins and genome

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15
Q

Virion

A

Morphologically complete, mature infectious particle

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16
Q

What are the three major forms seen in viral capsids?

A

Helical, Icosahedral and Enveloped

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17
Q

What is the structure of a helical capsid?

A

Multiple identical protein subunits arranged with rotational symmetry around edge of circle to form a disk. Multiple disks are stacked to form a cylinder. The genome is coated by the protein shell or kept in the hollow part of the cylinder.

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18
Q

What are some examples of viruses with helical capsids?

A

Influenza, mumps, measles, rabies.

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19
Q

What is the structure of an icosahedral capsid?

A

Protein subunits are arranged in a hollow quasi-spherical structure with the genome inside. The simplest ones are built of 3 identical subunits forming one triangular face.

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20
Q

What are some examples of viruses with icosahedral capsids?

A

Picornaviruses, including polio, foot-and-mouth and rhinoviruses.

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21
Q

What are naked virus particles?

A

Viruses without an envelope, leaving the capsid proteins vulnerable to the environment.

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22
Q

How do naked virus particles infect a host cell?

A

They escape at the end of the replication cycle leaving genetic material behind. The cell dies, degrades and lyses which releases virions.

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23
Q

What is the main problem with a naked virus particle mechanism?

A

The host cell dies quickly and prematurely so latent and persistent infections cannot arise.

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24
Q

How does a virus particle exit the host cell without killing it?

A

By extrusion, also known as budding. The particle is coated in a lipid envelope derived from the host cells own membrane, allowing it to slip through the membrane and bud off.

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25
Q

What are the three virus-derived envelope proteins?

A

Matrix proteins, glycoproteins and transmembrane proteins.

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26
Q

Virus Matrix proteins

A

Internal virion proteins that link nucleocapsid assembly to envelope.

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27
Q

Virus Glycoproteins

A

Often antigens anchored to membrane that provide external environment contact.

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28
Q

Virus Transmembrane proteins

A

Form channels through envelope giving virus control over membrane permeability.

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29
Q

How do viruses assemble themelves?

A

A large negative nucleis acid molecule is packaged into a small capsid by using positive molecules, virus or host histone proteins or packaging signals in the viruses own genome.

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30
Q

How many strands does viral RNA have?

A

Can be single stranded or double stranded.

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31
Q

How many strands does viral DNA have?

A

Can be single, double or partially double stranded.

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32
Q

What different structures can a virus genome have?

A

Linear, circular or segmented.

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33
Q

What are the 3 different polarities that single stranded genomes can have?

A

Postive-sense, Negative-sense or ambisense.

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34
Q

Positive-Sense

A

Same polarity or nucleotide sequence as mRNA

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35
Q

Negative-Sense

A

Not the same polarity or nucleotide sequence as mRNA

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36
Q

Ambisense

A

Mixture of positive and negative-sense.

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37
Q

Name 6 areas of a virus genome that have been studied.

A 
Composition
Segment size and number
Nucleotide sequence
Terminal structures
Open Reading Frames
Regulatory signals
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38
Q

What is a virus infection unit?

A

The smallest unit that can cause a detectable effect when added to a susceptible host.

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39
Q

What are the two ways virions can be counted?

A

Directly by electron microscope or indirectly by measuring effects on host.

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40
Q

What is a virus plaque assay?

A

An indirect method of virus quantification using an agar overlay technique.

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41
Q

What are the steps in a virus plaque assay?

A

Dilution of suspension with virus material is mixed with melted agar and host bacteria.
Mixture is poured onto nutrient agar plate.
Host cells grow, viral particles cause cell lysis which spreads to other cells.
Virus replication causes plaques.

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42
Q

What are the three phases of viral replication?

A

Initiation of infection
Replication and expression of virus genome
Release of mature virions from infected cell

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43
Q

Viral replication in the nucleus

A 
Attachment penetration of cell
Genome uncoating
Migration to nucleus
Exiting from nucleus
Assembly maturation
Release from cell
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44
Q

Virus replication in cytoplasm

A 
Attachment penetration of cell
Genome uncoating
Expression
Proteins
Replication
Assembly maturation
Release from cell
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45
Q

What is virus attachment?

A

The specific binding of virus attachment protein to cellular receptor molecule which reside on host cell surfaces.

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46
Q

What is virus tropism and how is it regulated?

A

Virus tropism is the cell type a virus will normally infect and it is regulated by the cellular receptor molecules that bind specific virus attachment proteins.

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47
Q

Which process out of attachment and penetration requires energy?

A

Penetration

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48
Q

What are the three possible mechanisms of viral penetration?

A

Entire virus translocation across membrane of cell
Endocytosis of virus into intracellular vacuoles
Fusion of virus envelope with cell membrane (only for enveloped viruses)

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49
Q

Describe uncoating

A

After virus penetration the virus capsid is removed and the genome is exposed in the form of a nucleoprotein complex.

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50
Q

How does viral translocation penetration work?

A

Viral particle binds cellular receptor molecule
Particle translocation across membrane by receptor
Particle released into cytoplasm
Receptor recycled by cell

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51
Q

How does viral endocytosis penetration work?

A

Viral particle invades clathrin coated pit in membrane
Pit closes and starts to bud off membrane - adherence
Pit joins ends to form a clathrin coated vesicle with viral particles enclosed - joining

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52
Q

How does virus envelope fusion penetration work?

A

Extra cellular virus goes through endocytosis
Acidification of vesicle
Membrane fusion
Genome released

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53
Q

What are the two major tasks a virus must complete when inside a cell?

A

It must make virus proteins by making appropriate mRNA that can interact with host ribosomes to direct protein synthesis
Virus needs to replicate genome

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54
Q

How many classes of viruses are there?

A

Seven

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55
Q

Describe class 1 viruses

A

Double stranded DNA genome e.g. Herpes virus, pox virus
Mechanism of mRNA production and genome replication is the same as the host cell
Can be host factor nucleus replicators or virus factor cytoplasm replicators.

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56
Q

Describe class 2 viruses

A

Single stranded DNA genome e.g. Chicken anaemia virus
Second DNA strand synthesised in nucleus to produce mRNA
dsDNA intermediate formed during replication and used for transcription
One strand becomes viral genome and the other is discarded

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57
Q

Describe class 3 viruses

A

Double stranded RNA genome e.g. Reoviruses
Segmented genomes
Virus transcribes negative sense RNA to make positive sense mRNA which requires RNA dependent RNA polymerase which is part of the virion

58
Q

Describe class 4 viruses

A

Single stranded RNA genome of plus configuration e.g. Poliovirus
Infecting RNA is used directly by the cell as mRNA to easily make virus proteins
Requires virus specific RNA dependent RNA polymerase to make complementary minus strands of RNA then plus strands are made from this
Extra plus strands can be translated as mRNA or packaged as genome into new virions

59
Q

Describe class 5 viruses

A

Single stranded RNA genome of minus configuration e.g. Influenza virus
mRNA synthesised first by virion carried RNA polymerase
Complementary positive sense strand of RNA synthesised by polymerase and used as mRNA
Positive strand used to make more negative strand genomes

60
Q

Describe class 6 viruses

A

Single stranded RNA genome that replicates with DNA intermediate e.g. Retroviruses
Reverse transcriptase carried in virions for later use
Virion ssRNA converted to dsDNA by hybrid RNA DNA intermediate. dsDNA integrated into host genome as template for mRNA synthesis

61
Q

Describe class 7 viruses

A

Double stranded DNA genome that replicates with RNA intermediate e.g. Hepatitis b virus
Virion carried DNA polymerase completes DNA replication
Transcription by host RNA polymerase in nucleus
Viral reverse transcriptase copies to DNA to be packaged into new virions

62
Q

What is the seven class virus classification system called?

A

The Baltimore system

63
Q

When does the virus become infectious?

A

At the maturation stage

64
Q

How are mature viruses released?

A

Non enveloped viruses are released by lysis of the host cell

Enveloped viruses bud from the cell

65
Q

Why can some viruses spread via cell to cell contact?

A

They can avoid release into the external environment offering more protection.

66
Q

Why is he rate of spontaneous mutation in some viruses e.g. HIV?

A

Because there are high error rates in RNA dependant RNA polymerases.

67
Q

What is a quasispecies?

A

A mixture of molecular variants due to high spontaneous mutation rates.

68
Q

Name 4 types of viral mutations

A

Biochemical markers, deletions, plaque morphology, revertant

69
Q

What is a biochemical marker mutation?

A

A change in the chemistry of the virus e.g. Drug resistance mutation or altered virulence

70
Q

What is a deletion mutation?

A

One or more virus genes removed which can only revert to wild type via recombination.

71
Q

What is a plaque morphology mutation?

A

When the plaque is larger than normal the virus replicates quicker than wild type, when smaller it replicates more slowly

72
Q

What is revertant mutation?

A

Involves reverse mutation by correction of original mutation or second site compensatory mutations which involve a separate gene from the original.

73
Q

What is the most significant response to virus infection in animals?

A

The activation of the immune system.

74
Q

What is the humoral immune response?

A

Production of antibodies

Clears virus and stops it spreading to uninflected cells

75
Q

Name all the main virus entering sites to the human body

A

Eyes, mouth, respiratory tract, skin abrasions, anus, urogenital tract, alimentary canal

76
Q

Name 3 things that can infect a viral infection course

A

Biology of virus
Response to infection by host
Site at which virus enters body

77
Q

Why can’t viruses infect the skin without injury?

A

Because the outer layer is made of dead cells which cannot be infected.

78
Q

Describe 3 ways viruses can breach the skin by injection and give examples.

A

Biting Arthropods by taking blood meals e.g. Arboviruses
Biting animals e.g. Rabies
Contaminated needles or blood to blood contact e.g. Hepatitis and HIV

79
Q

Why are STIs and eye infections common?

A

Because the methods of infection are through mucosal membranes which are easier to penetrate than other barriers e.g. The skin

80
Q

Name 3 types of viruses that infect through the genitourinary tract.

A

Herpesviruses, papillomaviruses, retroviruses

81
Q

Name 2 types of viruses that infect through the conjunctiva.

A

Adenoviruses, Picornaviruses

82
Q

What are 3 reasons the GI tract is a favourable site of infection?

A

Intestinal epithelium has fast replication rate
Lots of lymphoid tissue
Constant stream of food and fluids make it easy for viruses to travel

83
Q

Name 3 ways the body can counteract viruses infecting the GI tract via the oral route.

A

Low pH in stomach
Many digestive enzymes
Specific defense mechanisms

84
Q

Name a virus that infects the mouth or oropharynx via the GI tract

A

Herpesvirus

85
Q

Name 5 viruses that infect the intestinal tract.

A

Adenoviruses, Coronaviruses, Reoviruses, Picornaviruses (enteroviruses) and Caliciviruses

86
Q

Why is the respiratory tract a favourable site of viral infection?

A

Constant contact with the external environment by respiration makes it easy for viruses to travel directly to the site.

87
Q

How are respiratory viruses normally transmitted to a new host?

A

Via the respiratory tracts of other hosts i.e. breathing in close proximity.

88
Q

Name 2 defenses that the body has to protect the respiratory tract from viruses.

A

Filtering and cells/antibodies from the immune system.

89
Q

Name 4 viruses that locally infect the upper respiratory tract.

A

Orthomyxoviruses, Picornaviruses, Adenoviruses, Coronaviruses

90
Q

Name 2 viruses that locally infect the lower respiratory tract.

A

Parainfluenza, Respiratory syncytial viruses (both paramyxoviruses)

91
Q

Name 4 viruses that systemically infect the body via the respiratory tract.

A

Herpesviruses, Paramyxoviruses, Poxviruses, Togaviruses

92
Q

What does herpes virus cause when systemic infection via the respiratory system occurs?

A

Varicella-Zoster (chicken pox)

93
Q

What does paramyxovirus cause when systemic infection via the respiratory system occurs?

A

Mumps and Measles

94
Q

What does poxvirus cause when systemic infection via the respiratory system occurs?

A

Smallpox

95
Q

What does togavirus cause when systemic infection via the respiratory system occurs?

A

Rubella

96
Q

What is Horizontal transmission?

A

Direct host to host transmission of the virus.

97
Q

What is vertical transmission?

A

Transmission of a virus from one generation of hosts to the next, could be via the fetus, breastfeeding after birth or the germline itself.

98
Q

Name 3 ways a virus can spread through a host system.

A

Direct cell to cell contact
Via the bloodstream
Via the nervous system

99
Q

Describe polio dissemination.

A 
Virus ingested
Gut associated lymphoid tissues
Regional lymph nodes
Blood
Blood brain barrier
Spinal cord
Gut
100
Q

Describe rabies dissemination

A 
Virus entry
Striated muscle
Peripheral Nerves
Central Nervous System
Peripheral Nerves
Salivary gland
101
Q

What is local spread?

A

The infection of contiguous cells resulting in lesions or sores.

102
Q

What is viremia?

A

The dissemination of a virus through the hosts bloodstream. The virus may be free in the plasma of the blood or be cell associated.

103
Q

What is the difference between primary and secondary viremia?

A

Primary viremia is when the virus enters the blood after local replication whereas secondary viremia is when the virus enters the blood from widely dispersed sites of replication.

104
Q

What is an acute infection and give examples.

A

An infection that is quickly cleared by the immune system and immunity is required. May be local (rhinovirus) or disseminated (measles).

105
Q

What is a persistent infection and name the 3 categories.

A

The virus can stay in the host for a long time so that new susceptible individuals can enter into the population. Can be slow, latent or chronic.

106
Q

What is a slow infection and give an example

A

The infection progresses slowly and inevitably towards death and the virus can be taken from all stages of infection e.g. HIV.

107
Q

What is a chronic infection and give and example

A

An infection that has constantly high rates of replication and viremia. Can be absent, late to develop or chronic but doesn’t always lead to death e.g. Hepatitis B.

108
Q

What is a latent infection and give an example

A

An infection that has an acute stage with symptoms, the immune system attacks and the virus will go into asymptomatic latency. The genome of the virus remains in the host cell and sometimes can be reactivated e.g. herpes.

109
Q

Name 4 types of viral immune evasion

A

Counteraction of host cytokines
Inhibition of antigen presentation
Evasion of complement mediated defence
Antibody avoidance

110
Q

How do viruses counter host cytokines?

A

Encode soluble homologues of cytokine receptors as decoys
Encode cytokine homologues as antagonists
Block activities of cytokine induced effectors
Produce neutralizing cytokine binding proteins
Directly inhibit cytokine induced gene expression

111
Q

How do viruses inhibit antigen presentation?

A

Down-regulation of gene expression of MHC class 1 receptors on molecules of infected cells e.g. HIV

112
Q

How do viruses evade complement mediated defence?

A

Incorporation of host cells into envelope especially host derived proteins that protect healthy host cells from complement immune attacks and by secreting proteins that accelerate C4 breakdown.

113
Q

How do viruses avoid antibodies?

A

Antigenic variation e.g. spontaneous mutation
Inherently poor antigens e.g. in HIV
Replication in immunopriviledged sites e.g. CNS
Establishing a latent infection so viral proteins not expressed

114
Q

Name 5 types of vaccines

A

Recombinant, DNA, live-attenuated, subunit and inactivated

115
Q

What is a DNA vaccine?

A

Fragments of a harmful virus’s genome encoding immunogenic proteins are inserted into the host so that it will be translated and become immunized.

116
Q

What is a recombinant vaccine?

A

A harmless or attenuated virus gets part of a harmful virus’s genome incorporated into it and then carries it to the host which recombines in the host cell to produce an immunogenic protein.

117
Q

What is a live attenuated vaccine?

A

A virus with a reduced pathogenicity is introduced to the host to elicit an immune response. This can be dangerous - may be biochemically or genetically unstable.

118
Q

What is a subunit vaccine?

A

A specific virus protein (often coat protein) is brought into the host in a high dosage which elicits a rapid and high level of immunity.

119
Q

What is an inactivated vaccine?

A

The virus is exposed to a denaturing agent to lose infectivity and keep antigenicity

120
Q

Name 4 chemotherapy methods used in virology.

A

Nucleoside analogues, fusion inhibitors, protease inhibitors, influenza antiviral agents

121
Q

Describe nucleoside analogues

A

Azidothymidine (AZT) inhibits retroviruses by inhibiting reverse transcription and production of virally encoded DNA intermediate

122
Q

Describe fusion inhibitors

A

Enfuvirtide binds gp41 membrane protein of HIV which stops conformational changes that lead to HIV and T lymphocytes fusing

123
Q

Describe protease inhibitors

A

Prevent viral replication by binding active site of HIV protease which stops large viral proteins being processed into individual components

124
Q

Describe influenza antiviral agents

A

Adamantanes interfere with influenza A ion transport proteins which inhibits virus uncoating.
Neuraminidase inhibitors block active site of neuraminidase in influenza A and B.

125
Q

What is the incubation period for hand, foot and mouth disease?

A

3 - 5 days

126
Q

What are the symptoms of hand, foot and mouth disease?

A 
Fever
Sore throat
Swollen lymph nodes
Diarrhoea
Rash
Blisters
Ulcerations
Dehydration
Aseptic meningitis and encephalitis
127
Q

How is hand, foot and mouth disease transmitted?

A

Contact with saliva, blister fluids and faeces
Aerosol
Fomites

128
Q

Virology of hand, foot and mouth disease

A 
Caused by enterovirus of picornavirus family
ssRNA positive sense
Small capsid virus
Moderate divergence
Rencombination
129
Q

Diagnosis of hand, foot and mouth disease

A 
Swab and vesicle in VTM
Cell culture (cytopathic effect)
Neutralisation tests
Molecular testing
Co-incidental detection
130
Q

What are the symptoms of Norovirus?

A

Nausea
Vomiting
Diarrhoea
Abdominal Pain

131
Q

How is Norovirus transmistted?

A

Faecal-oral route
Aerosol transmission of vomitus
Contamination of water

132
Q

Norovirus Virology

A 
Caused by enterovirus (picornavirus)
ssRNA positive sense
Small capsid virus
Unculturable
5 genogroups
Low infectious dose
High shedding rate
Short term immunity
Immune against alcohol disinfectants
133
Q

Norovirus Diagnosis

A

Not able to be cultured

RT-PCR

134
Q

Norovirus Epidemiology

A

Main cause of acute non-bacterial gastroenteritis
Seasonal
Animal reservoirs (shellfish)

135
Q

Molluscum Contagiousum Symptoms

A

Common skin and mucosal disease
Small white/pink lesions
Waxy core
Itchy but painless

136
Q

MCV Transmission

A

Direct and fomites

137
Q

MCV Epidemiology

A 
Worldwide (122m)
Common in humid and crowded areas
Common in children
Adult STI
Immunocompromised people
138
Q

MCV Clinical Management

A 
Cryotherapy
Laser
Salicylic acid
Imiquimod
Anti-retroviral drugs
Personal Hygiene
139
Q

Describe Roche Sequencing Platform

A

Longer reads up to 1000bp
Scalable
Capable of sequencing 1/4 of human genome in one run

140
Q

Describe Illumina Sequencing Platform

A

Shorter reads up to 250bp
Scalable
Caable of sequencing 150 genomes in one run

141
Q

Describe Ion torrent Sequencing platform

A

Shorter reads up to 200bp
Fast
Can sequence 1/4 genome in one run

Microbiology (6 decks)

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