Viruses Flashcards
What differentiates viral growth from bacterial growth?
- bacteria grow exponentially in culture medium
- viruses have an ‘eclipse period’ where no virus appears to be present
- during this phase it has infected the cell and been broken down into its components
What are the stages of viral replication?
- Attachment to cell surface
- Penetration of the plasma membrane
- Uncoating of the genome protein coat
- 3 phases:
- Genome replication
- mRNA synthesized
- Viral proteins synthesized
- Protein + genome assembly
- Released from cell
How do viruses attach to cell plasma membranes?
- via receptors (normal physiological parts of the PM)
- this defines and limits the host species and type of cell that can be infected
What type of receptors are used by viruses for attachment/adsorption?
- protein
- e.g. ICAM-1 for most rhinoviruses
- carbohydrate
- e.g. sialic acid for influenza virus
- recognition of sugars on carbohydrate side chains of glyoprotiens - very common
How does HIV attach to cells?
- infects CD4 T-cells via CD4 and chemokine (CCR-5) receptors
- gp160 on HIV made up of gp120 and gp41
- on gp41 is a hydrophobic peptide, surrounded by gp120
- CD4 receptor combines with gp120 to capture the HIV
- induces conformational change in gp120 exposing peptide
- recruits CCR-5
- tight binding of HIV to cell in unstable configuration (peptide exposed)
How does viral penetration occur?
Two ways:
- After adsorption, the lipid coat of enveloped viruses fuses with the cell membrane and the nucleocapsid is released into the cytoplasm
- Enveloped and non-enveloped viruses can also stimulate endocytosis on attaching to the PM
What is viral uncoating?
- release of viral genome from its protective capsid
- enables nucleic acid to be transported within the cell for transcription
How does HIV penetrate cells?
- hydrophobic peptide of gp41 insterts into PM
- brings viral membrane in close proximity to cell membrane
- membranes merge, viral contents and genome are emptied into the cell cytoplasm
How does togavirus penetrate cells?
- binding to PM receptor triggers endocytosis
- low pH of endosome can trigger a conformational change in the viral proteins to expose a hydrophobic fusion region to fuse out of the endosome (similar to gp41 peptide)
- or, lysis of endosome releases virus
DNA viruses replicate in
the nucleus*
*exception: pox virus, encodes own machinery, replicates in cytoplasm
RNA viruses replicate in
the cytoplasm*
*exception: influenza, HIV replicate in the nucleus
What occurs during amplification of the viral genome and viral proteins?
- nucleic acid replication to produce new genomes for new virions
- mRNA is produced, codes viral proteins translated by the host cell
- early proteins: non-structural (DNA, RNA polymerases, enzymes or factors to dampen innate immune response)
- late proteins: structural (capsid proteins, virion building blocks)
What are early and late proteins?
- early proteins: non-structural (DNA, RNA polymerases, enzymes or factors to dampen innate immune response)
- late proteins: structural (capsid proteins, virion building blocks)
In order to replicate, RNA viruses require
RNA-dependent RNA polymerase
encoded by the virus
Which sense of RNA can act as mRNA?
+ sense, e.g. poliovirus
How do + sense RNA viruses replicate?
- encodes own RNA-dependent RNA polymerase tf it cannot replicate right away
- must first produce proteins by translating the RNA into a polyprotein
- autocleavage of polyprotein yields polymerase + other encoded proteins
- viral genome can now replicate and produce more polymerases
How do - sense RNA viruses replicate?
they must bring RNA-dependent RNA polymerase with them into the cell
What viruses are examples of Class I and how do they produce mRNA?
Class I: dsDNA
- e.g. adenovirus, herpesvirus, poxvirus
- enters nucleus, uses host cell polymerases
What viruses are examples of Class II and how do they produce mRNA?
Class II: ssDNA, +/- sense
- e.g. parvovirus
- +sense can act as mRNA –> translated to produce its RNA-dep RNA polymerases
- -sense must bring RNA-dep RNA pol into cell
What viruses are examples of Class III and how do they produce mRNA?
Class III: dsRNA
- e.g. reovirus
- replicates in cytoplasm, uses own polymerases
What viruses are examples of Class IV and how do they produce mRNA?
Class IV: +ssRNA
- e.g. picornavirus, togavirus, flavivirus
- +ssRNA can act as mRNA
- replicatres in cytoplasm, encodes polymerase
What viruses are examples of Class V and how do they produce mRNA?
Class V: -ssRNA
- e.g. orthomyxovirus, paramyxovirus, rhabdovirus, filovirus
- -ssRNA must provide its own RNA-dep RNA polymerase
What viruses are examples of Class VI and how do they produce mRNA?
Class VI: +ssRNA that replicates via DNA intermediate
- e.g. retrovirus (HIV)
- carries reverse transcriptase to convert +ssRNA to DNA
- DNA is integrated into the host genome
- DNA is used to create mRNA to create proteins
Translation of structural and non-structural viral proteins is carried out by
ribosomes in the host cell cytoplasm
Post-translational cleavage of viral polyproteins or trimming of structural proteins usually requires
virus-encoded proteases
Glycosylation of viral envelope glycoproteins occurs in the
RER & Golgi vessels, which results in them being deposited into the host cell membrane
How are non-enveloped animal viruses assembled and released?
- icosahedral viruses, structure assembled by:
- spontaneous assembly of the capsid proteins around the nucleic acid genome due to unstable energy state of the original protein
- chaperonin proteins or other mechanisms may assist
- proteolytic cleavage may induce final conformations of capsid proteins
- virions accumulate in the cytoplasm or nucleus until the cell eventually lyses
How are enveloped viruses assembled and released?
budding through the cell surface to obtain envelope of host cell PM:
- patches of viral envelope glycoproteins have accumulated on the PM
- capsid proteins & NA genome condense next to PM and push out
- e.g. influenza, measles - helical genomes covered in spiral protein coats
- some use the cellular secretory pathway to exit the cell
- genome enters vesicle w/structural proteins from RER while in Golgi
- transported to PM where it fuses and releases the virus particles
- e.g. coronavirus
What are the four types of virus-induced changes in cells?
- transformation to tumour cells
- e.g. oncogenic retroviruses
- lytic infection causing cell death and virion release
- enteroviruses, reoviruses
-
chronic infection causing slow virion release (cell lives)*
- e.g. hep C
- persist for years
- do not cause enough damage to trigger a robust immune response
-
latent infection causing no harm to the cell, virus dormant until it emerges later on as a lytic infection*
- converted to a latent form on infection
- e.g. herpesviruses (cold sores)
- latent & chronic infections are persistent infections
What are cytopathic effects?
- morphological changes in virus-infected cells observed in culture on light microscopy
What are inclusion bodies?
- accumulated viral proteins at the site of virus assembly
- i.e. in nucleus or cytoplasm, viral components
How can viruses cause tumour growth?
- cell transformation
- encoding oncogenes that when expressed in an infected cell promote tumour production
- oncogene codes for proteins w/growth promoting properties
- expression leads to uncontrolled proliferation
- likely picked up during evolution through integration of the viral genome into the host DNA
- homologs or variants of cellular genes that promote the cell cycle
- other viruses can cause tumours bc their replication affects the cellular version of an oncogene
What is a quasi-species?
Individual viruses infecting a single person are all slightly different because they are a mix of mutated forms of the virus.
What is the mecahnism of the changing viral genome?
Mutation
RNA-dep RNA pol has no proofreading mechanism, tf errors are not corrected
How does viral genome variation occur as a result of two viruses infecting the same cell?
- rare
- 2 related viruses
- occurs often in flu
- mechanisms:
- recombination - exchange of stretches of NA btw genomes of similar sequemce, especially in DNA viruses
- reassortment - swapping of segments for viruses that have segmented genomes, e.g. influenza and rotavirus
How can the viral infectious process be halted?
- antibodies that block uptake and/or neutrolizes progeny
- very effective
- killing infected cell (cytotoxic T-cells, NK cells, Ab-mediated mechanisms)
- when you don’t have antibodies present initially
- kill cell before virus is released
- interferon
- turns on lots of antiviral molecules
- blocking replication cycle with antiviral drugs
How do antivirals differ from antibiotics?
- Antibiotics can be effective against a spectrum of bacteria (i.e. G+, G-)
- Antivirals target replication, which varies with each virus, tf they are viral specific
- e.g. acyclovir works only on herpesvirus
- want to target only infected cells and leave normal alone - tricky
- still have issue of generating resistance with viruses
What is required for a virus to cause infection?
- entry into the body
- multiplying and spreading
- target of appropriate organ
What is required for a virus to be amintained in nature?
- shed into the environment
- taken up by an arthropod vector or needle
- passed congenitally
Viral replication within the host can be
- local - confined to the organ of entry
- systemic - involving many organs
What is tropism?
- anatomical localization of where the virus can infect
- initally (but not solely) determined by the receptor specificity of the virus
How do viruses enter the body?
- most via mucosal epithelial surfaces
- epidermis of skin is covered in dying cells w/keratin, a hostile environment for viruses which need live cells
- can infect skin at deeper layers via cut, parenteral innoculation (insect bites, IV needle use)
- prefer to be swallowed or breathed in
- conjunctiva
- respiratory tract
- alimentary tract (gut)
- urogenital tract
What is the most important site of viral entry?
Respiratory tract
How are viral infections of the respiratory tract acquired?
- aerosol inhalation of infected nasal secretions
- mechanical transmission of infected nasal secretions via fomites (i.e. sneeze on surface that you touch, then touch your mouth or face)
- then attach to specific epithelial cell receptors
- remain localized (rhinovirus) or spread further (MMR)
What determines the initial site of virus deposition?
- droplet size
- >10microm in nose, 5-10 in airways, less than 5um in alveoli of LRT (more dangerous)
What are the respiratory tract barriers to infection?
- mucous - traps viral particles (innate)
- cilia to move mucous up to be swallowed
- no cilia in alveolar airspaces
- alveolar macrophages instead
- temperature gradient
- 33d in URT (nose), 37 in LRT and lungs
- IgA
What are M cells?
- microfold cells
- found in enterocyte layers
- sample pathogens and lumenal contents
- transocytose pathogens to lymphocytes, DCs, and macrophages underneath M cell
- some viruses can infect the alimentary tract via this route to the basal surface and deeper tissues
cytokines, cells
Virus infection triggers
- Type 1 interferons: TNFa & TNFb
- interacts with macro and DC –> IFNa &b
- produce IL-12, pro-inflam cytokines and chemokines
- IL-12 activates NK cells
- NK cells produce Type 2 interferon: IFNy, kill affected cells
- DC present virus to T-cells
- cytotoxic to kill infected cells
- helper to prime B cells to make Abs
How are viral proteins normally presented on cells?
- viral proteins made in the cytosol are chopped up by the proteosome complex
- into ER via TAP channel
- assembles with newly synthesized MHC I
- transported in vesicle to cell surface for expression
- –> recognition by CD8 T-cells
How does antigenic drift/variation contribute to evasion of CD8 T cell recognition in virus-infected cells?
- the epitopes recognized by CD8s can mutate
- viruses can be selected for because they have mutations in regions associated with MHC I
- can’t interact w/MHC I
- or T cell receptors cannot recognize peptide any more
- e.g. HIV, influenza
How does HIV interfere with MHC Class I receptors?
Nef protein induces endocytosis of Class I such that it is no longer expressed on the surface, and not long enough to be effective
How does HSV disrupt CD8 T-cell recognition?
- encodes a peptide that blocks TAP channel on the cytosolic side
- proteins cannot enter ER to bind to MHC I for expression
How does CMV disrupt CD8 T-cell recognition?
- encodes a protein that binds to the luminal side of the TAP channel to prevent peptides from entering the ER
- cannot bind to MHC I for presentation on cell surface
How does adenovirus disrupt CD8 T-cell recognition?
- encodes a protein that binds to the MHC II, anchoring it to the ER
How does EBV prevent CD8 T-cell recognition?
- EBV = Epstein-Barr virus, form of herpesvirus
- in latently infected B-cells, it inhibits proteosome (viral protein breakdown)
How can replication influence CD8 T-cell recognition?
- viruses can decrease replication of MHC I gene as they replicate
- e.g. HIV, RSV, adenovirus
How do viruses that downregulate MHC I avoid NK cell killing?
- encoding of a protein that keeps ligand for kill+ signal in the ER
- e.g. murine CMV
- encoding of an MHC I-like molecule that sticks on infected cells so that the NK cell things there are normal levels of MHC I
- e.g. human CMV
How do interferons inhibit translation of infected cells?
- IFN binds to receptors on uninfected cells
- +inactive PKR (PKR stops transcription)
- PKR detects the presence of dsRNA
- autophosphorylates to active form
- inactivates ribosome from translating proteins
