Viral infections & Hypersensitivity reactions Flashcards
What are different ways new infection diseases can emerge in a population?
- Antibiotic resistance
- New clinical presentations
- Changes in geographic regions
- Novel zoonotic infections causing epidemics in human populations (viruses)
What is a virus? what are important features?
Small segments of nucleic acid with a protein or lipoprotein coat
- Some have a lipid bilayer envelope, some don’t
Obligate intracellular parasites → absolutely needs a host cell to undergo replication
Sub-microscopic, filterable → need EM to see it
Unaffected by antibiotics (which target bacteria)
What is Baltimore classification?
It is a viral classification based on genomes
Class I → dsDNA (ex: Herpes, small pox, adenovirus)
Class II → ssDNA (ex: parovirus)
Class III → dsRNA (ex: rotavirus)
Class IV → (+) ssRNA (ex: polio, yellow fever, corona virus)
Class V → (-) ssRNA (ex: rabies, ebola, influenza, LCMV)
Class VI → ssRNA-RT (ex: HIV)
Class VII → dsDNA-RT (ex: Hepatitis B virus)
*RT means they have RNA and convert it to DNA for replication and change it back to RNA or inversly
Which of the following was the first human virus identified:
a. Human immunodeficiency virus
b. Hemophilus influenzae
c. Rabies virus
d. Yellow fever virus
e. Tobacco mosaic virus
b. Hemophilus influenzae → not a virus, its a bacteria
d. Yellow fever virus → YES
e. Tobacco mosaic virus → infects plants, but 1st virus identified
What are important aspects/steps of viral replication and spreading?
- Entry into a susceptible host
- because obligate intracellular pathogens - Replication in cells (cell tropism)
- Tropism = the ability of a virus to infect specific cells but not in other types (need specific cell type)
- most virus use cell machinery for transcription and replication - Spread within host
- local replication (cell-to-cell)
- dissemination to lymph node
- viremia, transport to distal tissue sites (can detect the virus in the blood) - Shedding & transmission to new host: skin lesions, saliva, coughing, urine, feces, semen
What are 3 patterns of viral infections?
Give examples for each.
3 general categories based on levels of infectious virus detectable in organism at various times:
- Acute infection followed by viral clearance by the immune response
Ex: poli, influenza, LCMV Armstrong - Acute infection followed by latent infection and periodic reactivation
Ex: Herpes virus - Acute infection followed by chronic infection
- The immune system is not able to fully clear the virus and gets to an equilibrium with the virus
Ex: LCMV clone 13 (used in model models of chronic infections)
What are the kinetics of the different aspects of host defense against viruses?
- Type 1 IFN and other innate cytokines, NK cells → peak even before the peak of the infection
- Cytotoxic cells, Th1 cytokines, Th2 cytokines → peak a bit after the peak of infection
- Serum Ab → increases slowly and stays high in the blood even after clearance of the virus because of the long-lived cells in the bone marrow still producing Abs
Is it possible to be infected with a virus, but tets negative to it?
YES, different viral loads are seen in different sites/organs
- Nose swab
- Sputum
- Stool
How does Innate immune recognition of virus infection occur?
What does it depends on?
Innate immune receptors triggered depends on viral genome & replication intermediates
TLR9 recognized by + DNA
TLR7 recognized by + RNA
finish… slide 11 L19
Innate receptor leads to transcription of IFN alpha and beta → Type 1 IFN → autocrine signaling (to itself through release and receptor) + act on neighbouring cells
- Type 1 IFN has viral replication suppressive effect
What is Type 1 Interferons? What triggers its synthesis?
Induction of type I interferons: IFNa and IFNb so named because of their ability to interfere with viral replication
Synthesized by many cell types in response to activation of innate sensors: RIG-I, MDA-5 & cGAS/STING
IFNb induces cells to make IFNa, thus amplifying type 1 IFN response
binds to common cell surface receptor known as IFNAR, activating STAT1/STAT2 → production of many interferon stimulated genes (ISGs)
*Induction of antiviral states in neighbouring uninfected cells
What are 2 pathways by which type 1 IFN induce antiviral effects?
Both pathways are triggered by type 1 IFN + dsRNA + ssDNA
- Activated Protein Kinase PKR (ribosome-associated) → phosphorylates initiation factor of translation eIF-2a → preventing mRNA translation shuts down the replication cycle
- Activated Oligoadenylate Synthetase OAS
*Multiple forms: nuclear and cytoplasmic → activates 2’, 5’-Oligo adenylic Acid → activates RNase L → RNA degradation
What are plasmacytoid dendritic cells?
Specialized immune cells which can make 1000x more type I IFN that other cell types
How is type 1 interferons related to SARS-CoV-2 disease burden?
Early robust type 1 interferon response:
- Mild disease
- Viral clearance
- Lower viral load
- Normal T and B cell response
Delayed type 1 interferon response:
- Higher viral load / Severe disease
- Partial viral clearance
- T cell lymphopenia
- Robust B cell response (higher levels of Abs)
Type 1 interferon deficiency:
- Uncontrolled viral replication / Severe disease
- T cell lymphopenia
- Compensatory B cell response (very high Abs)
*T cell lymphopenia = low T cells (type 1 IFN = important survival signal)
What can cause Type 1 inteferon deficiency?
- Genetic mutation in type 1 interferon pathways
- Neutralizing antibodies to type 1 interferons
What are other immunomodulatory functions of IFNa/b?
– changes in cell distribution
– activation of NK cell cytotoxic activity
– regulation of cytokine/cytokineR expression, induction of MHCI to promote CD8 T cell responses
Depending on the context in which type I IFNs are being produced, they can be pro-inflammatory or anti-inflammatory
ex: in HIV, chronic production of type 1 IFN errods immune responses over time
What are important features of NK cells?
When do they come into play in immune responses?
What stimulates their activity?
2nd cell type to after IFN producing cells ~ day 2-5
Lymphoid cells that are a critical first line of defense against infection with intracellular pathogens
- Activity is stimulated by type I IFNs and IL-12
- Produce IFNg
- Express NKRs: NK receptors that can
be activating or inhibitory - They are Cytotoxic, but detection of MHCI leads to downregulation of NK activation
- Missing self model
What is the missing self model? What cell type does it relate to?
The missing self model of natural killer (NK) cells states that NK cells attack cells that lack or have altered MHC class I molecules. This model helps explain how NK cells are part of the immune system’s defense against viruses and tumors.
MHC-I acts as an inhibitor receptor for NK cells, without which NK cells kill their target cell
What are the key steps of a CD8 T cell response in the situation of a viral infection?
- Activation & priming
- Effector differentiation & clonal expansion
- Migration to infected tissue site to deliver effector function (
- Arrive similarly to neutrophils, by the blood, followed by chemokine signals
- Response is mediated by the amount of Ag present
Hi dose of Ag: Expansion → contraction → memory maintenance
Low dose of Ag: → small CD8 T cell response with less memory maintenance and less expansion
What are the 3 phases of CD8+ response?
- Expansion
- Contraction (after antigen clearance)
- Memory maintenance
What is the contraction phase of the CD8 T cell response?
After antigen clearance, we don’t want to keep all these effector CD8 T cells in our lymph nodes:
- Death of >95% of antigen-specific CD8 T cells by apoptosis
- Apoptotic cells are disposed of by specialized
macrophages (CX3CR1+) in the T cell zone
What assay is used to detect antigen-specific T cells? Study Activated CD8 T cells?
Phenotype: expression of cell surface proteins using flow cytometry
- Label different cell phenotype with Ab-florochrome → Flow cytometry
- can identify chainhes in % of cells - Golgi plug + Fix cells + permeabilization + intracellular stain → assess cytokine production by intracellular staining with specific (Anti-cytokine Abs)
Tetramer binding assay:
Tetramer = MHC-I-peptide bound by biotin → 4 of them bound by 1 fluorescetly labelled streptavidin
- requires knowing what is the peptideof interest and MHC allele of the animal model
- Tetramer bidns exclusively to the TCR specific for that antigen → can isolate Antigen=specific cells by FACS
What does the tetramer binding assay reveal on CD8 T cells in the case of Acute vs Chronic infections?
What is this: D^b GP276-286?
D = MHC-I, b = haplotype, 276-286 = specific peptide presented
Lots more tetramer positive cells in acute compared to chronic responses
T cells in acute are much more functional, higher IFNy production
What are TCR transgenic mice?
Mice that all have the same TCR specificity for a specific peptide
OT II CD4 T cells → have specificity for SMARTA peptide
OT I CD8 T cells → have specificity for P14 peptide
*Both from ovalbulmin protein
TCR transgenic mice are created by injecting DNA fragments into fertilized mouse eggs. The DNA fragments contain genes for T cell receptors (TCRs). The mice are then raised by foster mothers.
By having the gene direclty there instead of made by somatic recombination you increase your chances of having this TCR so much that you basically only have that one (allelic exclusion).
What is the role of follicular helper T cells in antibody responses?
T follicular helper cells specialize in promoting germinal center reactions that support: B cell proliferation, somatic hypermutation, class-switch
recombination → afinity maturation
Bi-directional signal exchange:
- TCR interacting with pMHC on B cell provides signal to T cell
- CD40 interacting with CD40L on T cell provides signals to B cell