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
Which viruses cause localized infections of the respiratory tract?
- rhinovirus (PicornaV, common cold)
- respiratory syncytial virus (ParamyxoV)
- influenza cirus (OrthomyxoV)
Which viruses enter the respiratory tract and spread systemically?
- mumps, measles (ParamyxoV)
- rubella virus (TogaV)
- varicella-zoster virus (HerpesV)
What are the most common viral causes of URTI?
- rhinovirus
- coronavirus
- adenovirus
What are the most common viral causes of pharyngitis?
- adenovirus
What are the most common viral causes of influenza-like illness?
- influenza virus
- RSV
What are the most common viral causes of croup (larynx & trachea)?
- parainfluenza
What are the most common viral causes of bronchiolitis?
- RSV
- parainfluenza 3
What are the most common viral causes of pneumonia?
- RSV
- parainfluenza 3
- influenza virus
- adenovirus
Why does rhinovirus cause URTI?
- much more efficient at lower temperatures (33 in URT, 37 in LRT)
What are the common local respiratory tract infections?
- URTI
- pharyngitis
- influenza-like illness
- croup (larynx & trachea)
- bronchiolitis
- pneumonia
Syncitial viruses form
giant cells
e.g. RSV, HIV, measles
Measles replicates in
primary
- epithelial cells of URT
- infects local macrophages, lymphocytes, and DC
secondary
- lymph nodes
- infecting immune cells tf immunosuppressed
enters circulation and –> URT (contagious)
What are Koplick spots?
- diagnostic of measles
- accumulation of lymphocytes
- inside mouth
How is measles transmitted?
- breathing of small particles
- not engulfed in mucous i.e. not coughed or sneezed out
- highly contagious
How do viruses enter the alimentary tract?
- swallowed
- infect oropharnyx –> carried elsewhere
What are the barriers to infection in the alimentary tract?
- sequestration in intestinal contents
- mucous
- stomach acidity (pH = 2)
- intestinal alkalinity to neutralize stomach acids
- pancreatic proteolytic enzymes degrade viral proteins
- lipolytic activity of bile degrades viral envelopes
- IgA
- scavenging macrophages
Viruses that infect the alimentary tract are usually
- hardy
- naked (no envelope)
- icosahedral capsid viruses
- acid and bile resistant
- +/- receptors for epithelial cells (- = abbrasion required)
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
How do viruses enter the alimentary tract?
- infect enterocytes (local)
- infect M cells (can spread to deeper tissues)
How does rotavirus infect the intestinal tract?
- locally
- can withstand stomach acid, alkalinity, bile
- 3 capsids
- can withstand stomach acid, alkalinity, bile
- infects and destroys epithelial cells of the intestinal villi and M cells
- inflammation, diarrhea (gastroenteritis)
- fatal in infants
How does enterovirus infect?
- fecal-oral route
- swallowed in fecal-infected food and water
- aerosol
- replicate in oropharynx then tonsils (URT lymphoid tissue)
- sore throat, confused with resp infection
- swallowed, replicate in Peyer’s Patches (GIT immune tissue)
- shed into faeces
- and/or into blood - viraemia
- further tissue infection can be receptor-dependent
- brain - meningitis
- CNS - polio –> paralysis
- skin - hand foot and mouth disease
- muscle - pericarditis, myocarditis
What is the transcutaneous route of viral infection?
- bypassing skin, e.g.
- minor trauma (papillomavirus: warts)
- injection/needles/piercing (Hep B & C, HIV)
- insect/animal bites (Dengue virus: fever, rash & polyarthritis)
What is the genital route of viral infection?
- via genital tract e.g.
- papillomavirus: warts
- herpes simplex virus
- HIV
- Hep B
What is the conjunctival route of viral infection?
- rare
- specialized mucous membrane
- tend to be adenovirus (swimming pools, optometrist)
- enterovirus
- HSV
How do viruses spread in the body?
- stay local: spread on epithelial surfaces
- subepithelial invasion and lymphatic spread
- viremia
- neural
What is primary viremia?
- virus first enters blood (via lymph nodes, thoracic duct)
- only a little bit
- lasts ~days
What are the two types of viremia?
- virus free in plasma (primary or secondary phase)
- cell-associated (e.g. macrophages, DC, T-cells)
What is secondary viremia?
- When primary viremia reaches target organs
- e.g. liver, BV wall, spleen
- virus grows and replicates there
- released in massive loads
- high viral titre in blood
- to combat immune response so some virus persists
- lasts 1-2 weeks
What are examples of cell-associated viremia?
- monocytes/macrophages:
- measles, dengue
- DCs:
- measles
- T-cells:
- HIV
What is the advantge of cell-associated viremia?
- infects cells that get free passage in blood
- monocytes, macrophages, DCs, T-cells
- can persist for months or years if the genome is latent and can avoid immune attack
- i.e. does not produce proteins that can be expressed on MHC
To infect the fetus, viruses
must cross the placenta
this results in death and abortion if cytocidal (e.g. smallpox)
or
developmental abnormalities if non-cytocidal (e.g. rubella, cytamegalovirus)
Why is rubella dangerous in pregnancy?
- non-cytocidal but can cross the placenta
- replicates and causes developmental abnormalities
- slows down rate of cell division
- small babies, first trimester organ development impaired
- microcephaly, congenital heart defects, cataracts
- rubella rash
- use MMR vaccine
- check levels before pregnancy
- *CMV can do this too
What viruses can infect the baby at birth?
- HSV
- Varicella
- CMV
- coxsackie B (fecal contamination)
What are the determinants of tropism?
- receptor availability
- optimal temperatures
- pH stability
- ability to replicate in macros and lymphos
- polarized release i.e. basal or apical
- presence of activating enzymes
What are the mechanisms of disease production relating to viruses?
- viral-induced damage to tissues and organs
- death as a direct result of replication
- loss of function
- consequences of the immune response
- immunopath
- immunosuppression
- autoimmunitiy
What are examples of viral-induced damage to tissues and organs?
- direct cell death from replication (cytocidal viruses)
- e.g. rotavirus: diarrhea from enterocyte death
- e.g. polio: paralysis from neuronal death in SC
- death from toxicity of viral products
- initiation of cell apoptosis due to loss of function
- loss of function
- e.g. rhinovirus impairs cilia in respiratory epithelium
- predisposes to secondary bacterial infection
- e.g. rhinovirus impairs cilia in respiratory epithelium
How does immunopathology contribute to disease consequences of viral infection?
- powerful immune response
- lympho, macro, cytokines, inflammation
- IL-1, TNFa = fever
- enlargement of lymph nodes = priming of lymphocytes
- can enhance infection
- i.e. viruses that grow in macrophages
- e.g. dengue virus –> haemorrhage fever and shock
- i.e. viruses that grow in macrophages
- persistent infections produce Ab-Ag complexes when Ab cannot clear it
- can go to kidney –> glomerular nephritis
- blood vessel –> vasculitis (bad in HepB carriers)
- CD4 T-cell mediated pathology
- measles rash
- induce eosinophil recruitment by RSV, clogs bronchioles
- CD8 T-cell mediated pathology
- kill hepatocytes in HepB (jaundice)
How does autoimmunity contribute to disease consequences of viral infection?
- Ab response to viral proteins similar to our own leads to autoimmune attack when virus gone
- e.g. myelin basic protein and proteins of influenza cross-react (Guillain-Barre syndrome demyelination, transient paralysis); cocksakie B4 (homology with myocardial cells, myocarditis)
- suspected triggers of autoimmune disease (e.g. diabetes)
How does immunosuppression contribute to disease consequences of viral infection?
- viruses replicating in immune cells can cause immunosuppression
- e.g.
- HIV in CD4 T-cells (kills them), monocytes (inhibits)
- measles (temporary), non-productive replication in T-cells and macrophages, suppress non-infected T-cell proliferation by infected DC displaying measles surface glycoproteins, suppression of IL-12
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
Type 1 interferons
- IFNa & b
- inhibit viral replication
- activate NK cells
- enhance MHC I expression (better targets for cyto-T-cells)
- produced by virus-infected macrophages, DC, and tissue cells, dsRNA
Type 2 interferons
- IFNy
- inhibits viral replication
- activates macros
- enhances MHC I and MHC II expression
- produced by NK cells and T-cells
What type of viruses are adept at immune system evasion?
- large, complexDNA viruses
- e.g. herpesviruses (HSV, VZV, CMV, EBV)
- and poxviruses (vaccinia, myxoma viruses)
What are the two strategies viruses use to evade the immune system?
- not being recognized
- interfering with functioning (e.g. encoding non-structural proteins)
What is antigenic drift?
- mutations generated during RNA replication
- change AA structure of surface glycoproteins
- can be adventagious if in a site where Ab binds
- may confer a selective advantage
- e.g. mechanism of influenza
- can occur on population scale (flu) or within a single patient (HIV)
How is T-cell priming by DCs inhibited?
- blocking of cytokine-induced DC maturation (vaccinia, HCV)
- blocking of signal transduction when pathogens bind TLRs (HSV)
- encoding of homologous proteins e.g. cytoplasmic tail of TLR4 to block signal transduction that initiates maturation (vaccinia)
- blockage of T-cell stimulation (measles, CMV)
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
NK cells are a major source of
IFNy
NK cells are present
in the blood and lymphoid organs of uninfected individuals
NK cells are activated during infection in response to
IL-12 or Type 1 interferons: IFNa & b
NK cells express
FcR receptors
NK cells show spontaneous toxicity to
tumour cells, virus-infected cells
Humans with NK cell deficiency are highly susceptible to
VZV, CMV (both are herpesvirus family)
What are the two receptors of the NK cell, and how do they work?
- Activation receptor
- recognizes molecules on cell surface expressed as a result of viral infection e.g. stress protein, sends a killing signal
- Inhibitory receptor
- binds to MHC I molecules on the target cell, overrides killing signal
**if class I is aberrantly expressed or absent, the inhibitory receptor will not be engaged and the NK cell will kill the target cell**
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
What are interferons?
- soluble factors (cytokines) released from virus-infected cells
- inhibit viral replication in neighbouring cells
- mediated by particular cellular proteins or pathways
- stimulate signalling pathways that upregulate transC and transL of a range of cellular proteins that prime the cell to stop viral infection
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
How do viruses overcome PKR inhibition of translation?
- the first few viruses that enter a cell will replicate RNA withim the capsid to avoid triggering activation of PKR
- production of small stretches of RNA that bind only one monomer of PKR (need two for phosphorylation)
- EBV, adenovirus
- proteins that coat dsRNA so PKR cannot hook on
- vaccinia, reovirus
- encode a homolog of mitochondrial translation factor inactivated by PKR that competes for binding
- vaccinia
What are the genetic factors influencing susceptibility to viral infection?
- inherited defects
- absence of Ig class (can also decrease during pregnancy)
- polymorphisms in genes controlling immune responses (MHC)
- not all MHC are as good at defending viruses, we don’t all have the same ones - they are selcted for on disease exposure
- interferon-inducible genes
- some people lack MxA and MxB, mannose binding lectin, promoters for these molecules - difficulty managing infections
- receptor genes
- don’t express certain receptors e.g. CCR5 and HIV
- CCR5 is chemokine receptor on certain cells
- w/o it seem to not get infected with HIV
- don’t express certain receptors e.g. CCR5 and HIV
What are non-genetic factors influencing susceptibility to viral infection?
- age
- newborns & elderly more susceptible
- young suffer less from immunipathy
- malnutrition
- hormones, pregnancy
- males, pregnant women more susceptible
- dual infections
- two diseases at once, worse symptoms
- immune response might be tailored to only one infection
- secondary bacterial infections can be bad
What are the outcomes of viral infection?
- full recovery (influenza)
- death - usually in immunocompromised hosts, or man is not the natural host (ebola, bird flu pandemics)
- recovery with permanent damage
- tumor formation, cancer
- polio –> paralysis
- persistent infection
