Unit 2 Flashcards
Virus Spread and Entry Virus Replication (76 cards)
1
Q
Where do viruses typically reside?
A
Reservoirs
2
Q
How do viruses get from a reservoir to a host?
A
Transmission
3
Q
Name the factors that can affect virus stability in the environment.
A
- Virus composition (envelope/naked)
- Temperature
- pH
- Humidity
- Presence of organic matter
4
Q
What are the non-living reservoirs for viruses?
A
soil, air, water
5
Q
What are the living reservoirs for viruses?
A
human, animal, vector
6
Q
What is horizontal transmission and what are the types?
A
Virus is transferred from a reservoir/host to another host.
Direct and indirect contact.
7
Q
What is vertical transmission and what are the types?
A
Virus is transferred from host to offspring.
- Transplacental
- Perinatal: virus in mother’s blood or vaginal secretions and spreads to newborn during birth.
- Post natal: through breast milk
8
Q
Where do bacteriophages encounter their host?
A
Non-Living: water and soil.
All bacteriophage are transferred via horizontal transmission but some can perform vertical transmission.
9
Q
Where do plant viruses encounter their host?
A
Can be difficult due to the cell walls present in plants. Some plant viruses reside in soil and water and can get to the plant through abrasions.
But living vector reservoirs are the most common source for transmission.
10
Q
Plant or animal viruses in their insect vector can be 1 of 3 things?
A
- non circulative
- circulative but non propagative
- circulative and propagative
11
Q
Where do animal/human viruses encounter their hosts?
A
Air and water are common non living reservoirs for human viruses.
Example: Hantavirus (air) and Rotavirus (water)
Human and insect vectors also play a role too.
Example: Herpes simplex viruses (human) and Zika (insect)
But animals are the most common for humans . 80% of viruses for humans are zoonotic.
Example: MERS-CoV (camels), SARS-CoV (palm civets) and Ebola (African bushmeat.
12
Q
What are the routes of entry into the human body?
A
- Respiratory Tract
- Gastrointestinal Tract
- Urogenital Tract
- Conjunctiva Tract
- Skin
13
Q
What is the most common route of entry and why?
A
Respiratory Tract.
Humans breath about 5-8 L of gas per minute.
14
Q
What immune defenses does the respiratory tract contain?
A
Nasal cavity and upper resp. tract (Tonsillar lymphoid organs and esophagus): Mucus and ciliated cells
Lower resp. tract (Trachea, bronchial lymph node, bronchus): mucus and ciliated cells
Alveoli: alveolar macrophages
15
Q
How do viruses fight the respiratory tract immune defenses?
A
They can attach to and enter into ciliated epithelial cells.
16
Q
What immune defenses does the fecal/oral route contain?
A
Stomach: acidic pH, digestive enzymes and bile detergents
Small and Large Intestines: mucus layer (lined with phagocytic cells and perstalsis)
17
Q
How do viruses fight the fecal/oral route immune defenses?
A
Because the small intestines have villi and microvilli to increase surface area, they are able to attach/enter into intestinal epithelial cells or be transcytosed through M cells into deeper intestinal tissues.
18
Q
What immune defenses does the urogenital tract contain?
A
Mucus, low vaginal pH.
19
Q
How do viruses fight the urogenital tract immune defenses?
A
Some can enter directly enter uroepithelial cells while most take advantage of the small cuts that occur during sex to get into deeper tissues or even use the immune cells that are recruited to the site of damage.
Example: Human papillomavirus
20
Q
What immune defenses does the conjunctiva contain?
A
Constant movement of eyelid baths conjunctiva in secretions that flush out foreign particles. RARE route of entry. Invasion occurs after minor abrasions
21
Q
What immune defenses does the skin contain?
A
Extremely effective barrier. Why?
The top layers of skin are dead and viruses require living cells in order to replicate.
But viruses can wait for a breach in the barrier which is very common.
22
Q
What is a localized infection and two examples of it?
A
The infections remain at the primary site.
Rhinovirus (respiratory tract)
Norovirus (gastrointestinal tract)
23
Q
What is a systemic infection and two examples of it?
A
The infections disseminate from primary site.
Measles (respiratory)
Polio (gastrointestinal)
24
Q
How does a virus spread?
A
- Simple diffusion - great distances but encounter many barriers and cell defenses.
- Direct Cell to Cell Contact (HTLV-1 and HIV) - virus particles can stick to an infected cell and wait for another susceptible cell to brush up by; viral proteins can stick to an infected cell until it brushes up another susceptible cell to perform syncytia.
- Direct Polarized Cell to Cell Contact (VSV) - where viral proteins are expressed on one end of the cell and brought to another susceptible cell.
- Hematogenous Spread - spread through the bloodstream by using the lymphatic system.
- Neural Spread - spread through PNS/CNS through the lymphatic system and through neurons.
25
What is the order a virus moves in the lymphatic system?
1. Primary site to lymphatic capillaries (very permeable).
2. Capillaries to lymphatic vessels
3. Vessels to the regional lymph node where the virus replicates
26
How can viruses gain access the CNS through viremia?
3 ways for a virus to cross the blood brain barrier
1. From capillaries into choroid plexus and cerebral spinal fluid
2. From capillaries directly across into brain tissue
3. From infected immune cells in blood that cross capillary walls
27
What are the types of viral infections?
1. Acute Viral Infections - rapid and self-limiting (Rhinovirus)
2. Chronic/Persistent - continuously produced (hepatitis C)
3. Latent - lays dormant with occasional reactivations (herpes simplex virus)
4. Transforming/Oncogenic - carries viral oncogenes (human papilloma virus is associated with 6 different types of cancer)
28
What are the steps for a virus to enter and replicate in a host?
1. Attachment
2. Entry
3. Uncoating
4. Biosynthesis
5. Assembly
6. Maturation and Release
29
What type of bonds are being held in the attachment stage?
Electrostatic interactions.
Initially the attachment between the virus and hose cell is reversible but as more receptors bind, the attachment becomes irreversible.
30
What virus parts are attaching to the host cell parts?
Virus glycoprotein spikes/protein fibers are attaching to host cell receptors
31
What is tropism?
where a virus can only infect a particular cell
32
What is broad host range and what are some examples?
A virus can bind to a cellular receptor that is present on cells found in a wide variety of animals.
Rabies (-ssRNA helical) can infect bats, raccoons, dogs and humans.
Flu (-ssRNA icosahedral) can infect birds, ferrets, pigs and humans.
33
What is restricted host range and what are some examples?
Virus can bind to a cellular receptor that is present on cells found in one particular cell type.
Hepatitis B (an enveloped gapped DNA icosahedral virus)
HIV (an enveloped +ssRNA icosahedral retrovirus)
34
Coreceptors are what?
a second cellular receptor that must also interact with the virus particle in order to promote viral entry.
Example: HIV requires a coreceptor along with the normal CD4 receptor that the gp120 attaches to.
35
How do you identify the cellular receptor(s) a virus usurps?
1. Biochemical Methods (traditional/nonspecific) - treat cells with a wide range of enzymes that cleave surface moieties and reassess virus binding. Influenza is treated with neuraminidase which removes sialic acid residues rendering the virus unable to attach to the host cells.
2. Immunological Methods (newer/specific but requires appropriate reagents) - incubate cells with monoclonal antibodies against cell surface molecules and reassess virus binding. Rhinovirus is incubated with antibodies against surface intercellular adhesion molecule 1 (ICAM1).
3. Genetic Methods (newer/specific and requires 2 critical reagents) - Requires a susceptible cell that can be infected by the virus along with a resistant cell that cannot be infected. With polio, they transfered dna fragments from the positive cell into the negative cell and then assess the negative cell for virus binding.
4. High Throughput Methods (latest shit) - cells grown on slides and receptor/target is discovered by assessing "gain of binding" using a fluorescent detection antibody.
36
What is membrane fusion (pH independent fusion)?
Only enveloped viruses that possess specific fusion proteins on the surface of the viral envelope can perform membrane fusion where the membrane of the envelope fuses with the cell membrane. (HIV)
37
What is endocytosis?
Phagocytosis: Not all cells can perform phagocytosis and only a few viral species appear to enter via this pathway. Creates a phagosome.
Pinocytosis: Occurs constitutively in all cells. Macropinocytosis is used by larger enveloped viruses which trigger membrane ruffling. Caveolar endocytosis create small lipid raft microdomains "pitted" internally with caveolin proteins. Cellular GTPase dynamin required for invagination.
Receptor Mediated Endocytosis: Used by naked and enveloped viruses that create clathrin coated pits. Cellular GTPase dynamin required for invagination.
38
What host cell cues are used for virus uncoating?
1. receptor
2. chemical
3. enzymatic
4. mechanical
39
How do viruses that require nuclear replication get to the nucleus?
Dynein walk the cargo to the nucleus on microtubules to the nuclear pore complex.
Others use importin to transport the protein to the nucleus. The cargo has nuclear localizations signals that alert the importin to the protein.
Some wait til the cell goes into mitosis and wait for the envelope to break down for them to insert themselves in.
40
What are the 3 bang for bucks that viruses take advantage of?
Alternative Splicing
Ribosomal Frameshifting
Leaky Scanning
41
What is constitutive splicing?
Occurs in the nucleus and requires snRNPs that form a spliceosome. Removes intronic sequences and ligates exons together.
42
What is alternative splicing?
Similar to constitutive splicing.
Occurs in the nucleus and requires snRNPs.
BUT one pre-mrna can yield multiple different mRNA and therefore multiple different proteins.
1. Exon Skipping
2. Intron Retention
3. Mutually Exclusive Exon
4. Alternative 5' Splice Site
5. Alternative 3' Splice Site
43
What are ribosomal frameshifts?
-1 Ribosomal Frameshift:
Requires a slippery sequence (X XXY YYZ) and a downstream RNA structure. Ribosome stalls and then backtracks 1 nucleotide before restarting.
+1 Ribosomal Frameshifts
Requires a slippery sequence and a rare codon for which few tRNAs are available. Ribosome stalls and to avoid the long pause it moves forward 1 nucleotide before restarting.
44
What is leaky scanning?
When you have ACG or AUG with a weak Kozak consensus. The first site is passed over and scans/starts at the next AUG which is in a different frame -> new protein.
45
What is a neurotropic virus?
One that invades the CNS
46
How does a neurotropic virus gain access to the nervous system?
Some can gain access through olfactory nerves or through the PNS to CNS.
Other neuroinvasive viruses can gain access to the CNS through viremia. 3 Ways to cross blood-brain barrier.
1. From capillaries into choroid plexus and cerebral spinal fluid.
2. From capillaries directly across brain tissue
3. From infected immune cells in blood that cross capillary walls.
47
What is the goal and hurdle of entry?
to get to the virus particle into the cell cytoplasm
getting through the actin cortex
48
How does the virus leave and endosome?
The change to a low pH and activation of host cell proteases trigger a conformational change and membrane fusion for enveloped viruses. For naked viruses they have a conformational change thus being able to penetrate the membrane.
49
What happens if the viral capsid is too big for the NPC?
The capsid proteins bind to nucleoporin proteins at opening of NPC and docks.
50
What happens if the viral capsid is small enough to go through the first barrier of the NPC but not the second?
They capsid is stuck and will release the genome from the end of the NPC.
51
What is required to be added to the mRNA strand for nuclear export?
5' cap and 3' poly A tail
52
What obstacles do dsDNA viruses have when they replicate in the nucleus?
Nuclear replication dsDNA:
1. Viral origin of replication is not recognized by polymerases.
2. The 5' end problem
3. DNA synthesis is regulated in host cells so the replication cellular machinery may not be present.
53
What solution do dsDNA viruses have when they replicate in the nucleus?
1. All DNA viruses require at least one viral origin recognition protein (ORP) to initiate DNA replication. Then transcription and translation are the first things to occur. where the viral ORPs are made with the NLS so they are transported back to the nucleus.
2. The 5' end problem is solved by circularizing the genome. no end!
3. The virus genomes encode viral cyclin like proteins that can modulate the normal cell cycle.
54
What obstacles do dsDNA viruses have when they replicate in the cytoplasm?
1. They do not have access to all the proteins and enzymes needed for replication or transcription.
2. The cell signals the host of a foreign presence.
55
What solutions do dsDNA viruses have when they replicate in the cytoplasm?
1. BYOP&E (that's why they have large genomes.
| 2. Creation of viral factories stolen from organelles to hid the process.
56
What obstacles do +ssDNA viruses have when they replicate in the nucleus?
All human +ss DNA viruses replicate in the nucleus
1. Host cell does not possess DdRp capable of converting ssDNA to mRNA
2. Hurdles of dsDNA
57
What solutions do +ssDNA viruses have when they replicate in the nucleus?
1. They hijack cellular DdDps to create a ds DNA intermediate then perform rolling circle replication
58
What obstacles do dsRNA viruses have when they replicate in the cytoplasm?
1. No access to host cell transcriptional machinery
2. Lack of RdRps
3. Host cell quickly detects and degrades cytoplasmic dsRNA (foreign invader)
59
What solution do dsRNA viruses have when they replicate in the cytoplasm?
1/2. BYOP&E including RdRp
3a. Some are concealed within two capsids and therefore only shed one when entering and uncoating within the host. Therefore the mRNA is released from the inner capsid.
3b. Viral factories
60
What obstacles do +ssRNA viruses have when they replicate in the cytoplasm?
All human +ssRNA viruses replicate in the cytoplasm.
1. viral mRNA genomes are not capped
2. lack of RdRp
61
What solutions do +ssRNA viruses have when they replicate in the cytoplasm?
1. viral mRNA have secondary structures that allow the polymerase to cap on. The structure creates an Internal Ribosome Entry Site
2. RdRp is within the genome so it's transcribed for replication
62
What obstacles do -ssRNA viruses have when they replicate in the cytoplasm?
All are cytoplasmic except for human flu.
1. must convert the - sense RNA to + sense. Lack of RdRp
2. + sense mRNA cannot be capped. Translational issues
63
What solutions do -ssRNA viruses have when they replicate in the cytoplasm?
1. BYOP&E including RdRp. But this is a special RdRp.
| 2. The special RdRp can both steal host mRNA caps and stutter at the end of strands to create a polyA tail.
64
What obstacles do +ssRNA-RT viruses have when they replicate in the cytoplasm?
Rely on RT to integrate the genome into the chromosomes. Has to use viral RT to create an RNA/DNA hybrid that is then integrated into the host.
65
What obstacles do gapped dsDND viruses have when they replicate in the nucleus?
Rely on RT to integrate the genome into the chromosomes. Has to use viral RT to create an RNA/DNA hybrid that is then integrated into the host.
66
What is the goal of assembly?
To put together the virus capsid and package the viral genome and any essential viral proteins within the viral capsid to generate a virus particle.
67
What are the stages of assembly?
1. Individual capsid proteins produced
2. Capsid protein fold into structural units
3. Viral genome and proteins packaged into capsid
68
What are the 2 general methods of virus assembly?
1. Concerted - the virus particle assembles only in association with the genome
2. Sequential - The virus capsid components are 1st assembled and then the genome packaged within the capsid.
69
What are assembly hurdles?
1. Getting all the viral components to the correct location for assembly
2. Selectively packing the viral genome and not host cell genome
70
What are assembly work arounds?
For location:
1. localization or signal sequences contained within many viral proteins are recognized by host cells and allow nuclear import/export, membrane targeting, or membrane retention of viral proteins.
2. Viral factories are built to hold the shit. Microtubules are used to travel to the factories.
3. Many viral components, nucleocapsids can associate within kinesin thereby hijacking the cell's transportation system to allow cytoplasmic movement towards the factories.
For selective packaging:
1. specific packaging signals in the viral DNA/RNA sequence are recognized by specific viral proteins
71
What is virus maturation?
In order to produce an infectious virus particle, many viruses require conformational changes, rearrangement and/or cleavage or viral proteins once the viral capsid has been sealed or the virus particle released from the host cell. (HIV and Dengue)
72
What are 3 general methods of animal virus release?
1. Lysis (naked)
2. Exocytosis (naked or enveloped)
3. Budding (enveloped)
73
Describe Lysis release.
There is a disruption in the host cell membranes which lead to cell death.
One mechanism of viral induced lysis is through the creation of viroporins (small hydrophobic viral proteins that oligomerize to form pores in host cell membranes)
This can affect ionic homeostasis and cause membrane depolarization.
74
Describe Exocytosis release.
Since it's a normal cellular process that allows the secretion of cargo through its release from intracellular vesicles via budding.
Naked viruses can hijack the pathway and bud from the closest cellular organelle.
Certain enveloped viruses can also hijack the pathway along with stealing organelle membrane itself.
Other enveloped viruses can steal the plasma membrane itself while also inserting viral proteins into the host cell plasma membrane.
75
How do virus particles get into the host cell plasma membrane?
1. Microtubule transport
| 2. Actin comet tails
76
What is ESCRT
proteins that facilitate plasma membrane invagination, vesicle maturation and subsequent vesicle scission. For enveloped viruses that initiate budding by hijacking ESCRT that is normally used during daughter cell separation after cell division.
