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Viruses Flashcards

1
Q

What types of genomes do viruses have?

A 
dsDNA
ssDNA
dsRNA
ssRNA
Circular
Linear
Non-segmented
Segmented
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2
Q

How are viruses classified?

A

Baltimore classification - how they replicate genome and produce mRNA

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3
Q

Do viruses generally insert their genome into the host cell genome?

A

No - only retroviruses do

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4
Q

What does reverse transcriptase do?

A

Makes DNA from RNA

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5
Q

How do DNA viruses express their genome?

A

Same flow of info as cell: DNA -> RNA -> Protein

Make use of cell transcription and translation machinery

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6
Q

How do RNA viruses express their genome?

A

Eukaryotic cells don’t have RNA dependent RNA polymerase
Eukaryotic cells don’t often encode for more than one protein on each mRNA
All encode RNA dependent RNA polymerase

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7
Q

How do +ve strand RNA viruses replicate?

A

Genomic RNA acts as mRNA on cell entry

Translated to produce polymerase

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8
Q

How do -ve strand RNA viruses replicate?

A

Need to carry polymerase in virion

Required to convert -ve RNA to +ve RNA after entry

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9
Q

How does dsRNA replicate?

A

Have segmented genomes
+ mRNA produced
Produces proteins and +/- RNA

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10
Q

How does ssRNA replicate?

A

+ve sense produces protein, a -ve RNA to produce a +ve mRNA or genomic RNA packaged into virion

-ve sense produces +ve mRNA to produce protein or +ve RNA to produce -ve RNA

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11
Q

What are some +ve stranded RNA viruses?

A 
Picornaviridae
Coronaviridae
Flaviviridae
Alphaviridae
Calciviridae
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12
Q

What are Picornaviruses?

A

Non-enveloped
Icosahedral
Diverse - over 200 serotypes

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13
Q

What are the groups of picornaviruses?

A

Enteroviruses
Eg. Poliovirus
Faecal-oral transmission
Poliovirus can cause paralysis in most virulent strains

Rhinovirus
Many serotypes
One cause of the ‘common cold’

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14
Q

What does the picornavirus genome look like?

A

Small section of ssRNA, +ve sense - 7.2-8.5 kb
Has virus protein at 5’ end - caps it
Long UTR at 5’ end
3’ end polyadenylated
Encodes single polyprotein in one reading frame

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15
Q

How does viral receptor binding occur?

A

Binds to specific receptor - CD155 in polivirus
Endocytosis to uptake virus
Loss of VP4 allows RNA to exit plasmid and enter cytoplasm

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16
Q

How long does gene expression take for +ve sense RNA viruses?

A

Picornavirus very rapid - 5-10 hours
Genomic RNA directly translated by ribosomes
~30 min after infection, cellular protein synthesis declines sharply - ‘Shutoff’

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17
Q

What is ‘Shutoff’?

A

Cleavage of ‘cap-binding’ complex’ (CBC)
Involved in binding the m7G cap structure at the 5’ end of all eukaryotic mRNAs during initiation of translation
CBC cleaved by poliovirus protein 2A

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18
Q

How is viral RNA recognised and translated after Shutoff?

A

5’ UTR contains IRES: Internal Ribosome Entry Site
Overcomes need for 5’ cap
Allows translation of viral mRNA

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19
Q

What happens to the polyprotein?

A

Proteases encoded within the polyprotein which cleaves itself to produce smaller proteins

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20
Q

Why is the Vpg protein important?

A

Acts as a primer for complimentary strand synthesis
2 uracils attached to Vpg by viral RNA polymerase 3D
Base pair with Adenosines in polyA tail

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21
Q

How are virus particles assembled for Picornavirus?

A

Capsids preform and RNA packaged in

Formation of capsid - polyprotein cleaved to form VP0, VP3, VP1 complex
As matures virus cleaves VP0 to VP2 and VP4 which seal the capsid

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22
Q

What are some examples of -ve RNA viruses?

A

Orthomyxoviruses - influenza
Rhabdoviruses - rabies
Paramyxoviruses - mumps, measles, RSV
Filoviruses - ebola

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23
Q

What are the different types of influenza?

A

Influenza A - infect wide variety of hosts, epidemics and pandemics
Influenza B - not as severe as type A, seasonal epidemics
Influenza C
Influenza D

A and B have annual vaccines

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24
Q

What is the structure of -ve RNA viruses?

A

Pleiomorphic - mostly spherical
Lipid envelope and glycoprotein spikes - haemaglutinin trimer (HA) for receptor binding and entry, neuraminidase tetramer for exit cell efficiently
Inner side of envelope lined by matrix protein M1
8 genome segments packaged into core
‘RNP’ (RNA and nucleoprotein) in helical form

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25
How does attachment occur for -ve RNA viruses?
HA spikes bond to mucoproteins with terminal sialic acid HA monomers have 2 disulphide linked domains, HA1 and HA2 Interaction can be reversed by polysaccharide cleavage by NA spikes
26
How does entry occur for -ve RNA viruses?
Particle engulfed by endocytosis Endocytic vesicles acidified by cell - M2 protein Low pH results in conformational change in HA Activates membrane-fusion function in HA2 Fusion of viral envelope with endosomal membrane - releases RNA genomic segments into cytoplasm
27
How does gene expression and genome replication occur?
Nuclear targeting sequences in NP protein - translocates into nucleus through a nuclear pore -ve sense genomic segment can be used as a template for mRNA or a cRNA intermediate to make more copies of genomic RNA
28
How does host protein 'Shutoff' occur for -ve sense RNA viruses?
Steal cellular mRNA caps for their own protein synthesis PA, PB1, and PB2 bind to cap and cleave it, added to viral -ve RNA segments Uses cap as a primer and encoded a polyA tail Destroys cellular mRNA
29
How does viral assembly occur for -ve RNA viruses?
Nucleoprotein (NP) migrates back into nucleus Associated with newly-synthesised vRNA to form nucleocapsids Migrate back out into the cytoplasm and towards cell membrane - higher level of free NP = more cRNA synthesis
30
What are some viruses with dsDNA genome?
Papillomaviridae, Adenoviridae, Herpesviridae, Polyomaviridae, Poxviridae
31
How do dsDNA viruses replicate?
+/- DNA can be transcribed to mRNA for translation of proteins to make capsid OR Can be replicated to produce more dsDNA
32
What are some examples of ssDNA viruses?
Circoviridae, Parvoviridae
33
How so ssDNA viruses replicate?
DNA used as template to produce dsDNA dsDNA used to produce mRNA to make proteins OR Split in to + and - DNA, + strand packaged in to virion
34
What do all DNA viruses have?
Origin of replication: Hairpin structures eg. parvovirus Multiple origins in some eg. herpesvirus Can be at the end and use a terminal protein to initiate replication eg. adenovirus Can have a looped DNA structure that initiates replication eg. poxvirus
35
What are the 2 mechanisms of DNA synthesis?
Replication fork - RNA primers | Strand displacement - never RNA primed
36
Which viruses use a replication fork for DNA synthesis?
Papillomaviruses, Polyomaviruses, Herpesviruses, Retroviral proviruses
37
Which viruses use a strand displacement for DNA synthesis?
Adenoviruses, Parvoviruses, Poxviruses
38
How does the replication fork mechanism work?
Leading and lagging strands as can only synthesise in 5'-3' direction Produced replication bubble as in bacteria
39
How does strand displacement work?
Template strand copied by polymerase Non-template strand displaced and coated in ssDBP When DNA sythesis of template stand complete displaced strand circularises as it base pairs with itself This is then bound by a polymerase and DNA synthesis occurs, removing ssDBP
40
How does parvovirus prime itself for replication?
Self base-pairing loop acts as a primer for DNA replication
41
What are papovaviruses?
2 genera of oncogenic viruses: Papillomaviruses - eg. HPV Polyomaviruses - eg. SV40
42
What is HPV?
Human Papillomavirus >160 types Ubiquitous - infection can be completely asymptomatic BUT Some can cause benign skin warts - papillomas Others cause cervical cancer - HPV16 and HPV18
43
What is the structure of HPV?
Non-enveloped DNA genome in icosahedral capsid L1 makes up capsid as well as varying amounts of L2 Current vaccine targets L1
44
What is the genome structure of HPV?
8 kb Circular dsDNA, persists as an episome ie. doesn't normally integrate into host DNA Genome divided to late and early regions Late - capsid genes: virion formation, genome encapsidation, membrane penetration, post-entry trafficking
45
Which are the oncogenes?
E6 and E7 Immortalise the cell and prime it for viral DNA replication by disrupting the cell cycle Mediate inhibition of p53 and pRB tumor-supressor genes that block cell cycle from G phase to S phase
46
What are the other functions of E6 and E7?
E6: activates telomerase E7: triggers chromosomal instability - could be why HPV can integrate into genome Both essential for maintenance of HPV-transformed cells
47
What's the function of E1?
Helicase starts replication fork/bubble, recruits cellular DNA polymerase to Ori
48
What's the function of E2?
Transcriptional regulation Recruit E1 to Ori Tethers viral DNA to chromosomes during cell division
49
What is the HPV lifecycle?
Needs access to basal layer | Expression changes as the host cells replicate and move further to the upper layers of cells
50
Is HPV enough to cause cancer?
No, probably requires co-factors High infection rate but only a small % progress to invasive cancer Long latency period
51
What is required for cervical carcinoma?
HPV DNA integration is required in most When genome integrates often a part of the HPV E2 protein deleted - regulates expression of E6 and E7 Leads to overexpression resulting in unregulated cell cycling
52
What are the 3 sub-families of herpesvirus?
Alphaherpesvirinae - HSV-1, HSV-1, VZV Betaherpesvirinae - CMV, HHP-6, HHP-7 Gammaherpesvirinae - EBV, KSHV All associated with long latency period
53
What's the structure of herpesviruses?
Large DNA genome Icosahedral capsid Protein tegument surround the capsid Envelope contains many glycoproteins
54
What's the genome structure of herpesviruses?
Unique long (UL) and unique short (US) regions bounded by inverted repeats
55
How does cellular entry occur for herpesviruses?
HSV envelope contains at least 9 glycoproteins Some initiate attachment and others the process of fusion Capsid migrates to the nucleus - enters via nuclear pore, genome is circularised
56
How does herpesvirus latency occur?
Viral genome exists as episome in circular form and produces very few if any proteins No antigens for cell to recognise Only starts producing proteins when activated
57
How does gene expression occur in herpesviruses?
3 classes of mRNA made: Alpha - immediate early (IE) mRNAs Regulators of virus transcription Beta - (delayed) early mRNAs Non-structural regulatory proteins and minor structural proteins DNA replication enzymes Gamma - late mRNAs Major structural proteins
58
How does genome replication occur for herpesvirus?
In nucleus Virus-encoded DNA-dependent DNA polymerase and DNA-binding protein involved Rolling circle replication - nick introduced, replication starts and strand displacement which is replicated, produces genome lengths which are cleaved and circularised
59
What are retroviruses?
``` Enveloped viruses ssRNA genome 2 copes of genome - diploid viruses Replication involves: reverse transcription of RNA genome into DNA integration of DNA into host chromosome ```
60
How do retroviruses replicate?
RNA to -DNA to dsDNA - integrates into host genome +mRNA produced to make proteins OR Genomic +RNA produced packaged into virion
61
What is the structure of retroviruses?
Host-derived lipid bilayer envelope Surface glycoproteins Matrix Capsid containing RNA in nucleocapsid, protease, integrase, and reverse transcriptase
62
What is retroviral genome structure?
RNA 5' Cap structure 3' polyA tail Protein coding region with: gag, pro, pol, env Always in that order Encapsidation signal shows which RNA should be packaged into capsid DNA Long terminal repeats at either end containing promoter and enhancer elements
63
What are the retroviral proteins?
Gag - structural components eg. capsid proteins Pro - protease important for maturation of virus Pol - reverse transcriptase, Rnase H, and integrase Env - envelope proteins
64
How does reverse transcriptase occur?
tRNA binds at a PBS near 5' end This primes the start of reverse-transcription, which proceeds through a unique sequence and then repeat to 5' end on RNA template Repeat sequence of new DNA can now bind 3' end of RNA Primes continued reverse transcription through whole TE transcript RNA template degraded by RNAse H leaving a fragment that primes 2nd strand DNA synthesis Synthesis moves through 3' unique sequence, the repeat and 5' unique sequence This fragment primes from 5' end Synthesis completes in both directions Resulting dsDNA enters nucleus with viral integrase allows 3' OH of each strand to attack target at sites a few bps apart - short target site duplication
65
How does HIV attachment and entry occur?
SU protein attaches to CD4 on target cell - expressed on CD4 T-lymphocytes and macrophages CD4 not sufficient, co-receptor required, chemokine receptors Conformational change causes membrane fusion
66
How does HIV get a range of proteins from one transcript?
Alternative splicing using host cell machinery
67
How does HIV maturation occur?
``` Driven by viral protease Cleaves nucleocapsid matrix proteins to rearrange and form final structure Immature -> mature virus particles Essential for HIV to be infectious Target for anti retroviral drugs ```
68
What are the three types of retroviral transformation?
Acutely transforming Viral oncogenes Growth factors, transcription factors, kinases Eg. Rous Sarcoma Virus Insertional mutagenesis Viral integration near cellular proto oncogene - myc Eg. avian leukosis viruses Transacting functions Transactivation of cellular genes - HTLV-1 Tax gene
69
What are oncogenes?
Several protein families involved in regulation of cell growth and replication Growth factors and receptors Signal transduction pathways Transcription factors
70
What are cancer associated features of retrovirus replication?
Reverse transcription of diploid RNA genome to dsDNA genome - recombination Integration into target cell DNA Transcription of viral genes controlled by promoter and enhancer elements in LTR
71
How do acutely transforming retroviruses cause oncogenesis?
Cause tumours rapidly Carry cellular oncogene in genome - captured Almost all defective and require helper virus Tumours polyclonal
72
How does oncogenic capture occur?
Integration adjacent to proto-oncogene Read-through transcription Co-packaging Recombination during reverse transcription Integration of resulting DNA genome containing onc Transcription of viral RNA containing onc controlled by viral LTR
73
How do insertional mutagenesis retroviruses cause oncogenesis?
Activate cellular oncogene by provirus insertion Non-acute-transforming retroviruses Tumours develop slowly No cellular oncogene Replication-competent Tumours monoclonal Transform cells by insertional mutagenesis
74
How do transacting functions retroviruses cause oncogenesis?
Encode viral oncogene with no cellular homologue Can activate cellular gene transcription OR Directly oncogenic
75
What are the human retroviruses that cause cancer?
HLV1 HLV2 HIV1 HIV2
76
What is HLV1?
Deltaretrovirus Complex genome Lacks classical oncogene Tax protein involved in oncogenesis - causes ATLL Also trans-activates expression of cellular genes Lead to T-cell activation and proliferation
77
How can HIV 1 lead to oncogenesis?
NO direct cause but immunodeficiency can leave person susceptible to other oncogenic viruses

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