Definition of a Virus

• filterable (small)
• supermolecular biochemical complex (can be crystallized)
• DNA or RNA genome
• genome surrounded by protein or membrane shell
• cannot make energy
• replicate by assembly, not binary fission
• virion is genome + package
• package is protein shell (capsid) or membrane bag (envelope)

DNA Virus Properties

• permanent
• Nuclear (exceptions exist)
• virus may manipulate cell growth to promote replication
• utilizes host machinery for transcription
• microinjection of genome will infect the cell
• DNA dependent RNA polymerase?

RNA Virus Genomes

• transient
• Cytoplasmic (exceptions exist)
• Must ENCODE RNA dependent RNA polymerase
• solves problems for mRNA and protein production
• Microinjection of +RNA genome will infect the cell
• non +RNA viruses must carry a polymerase into the cell

Naked Capsid

Viral Structure

• protein components
• basic structures: helical (nucleocapsid) or Icosahedral (icosadeltahedral)
• viral attachment structure: surface unit of capsid, specific protein of capsid (VAP)
•  stable to detergents (hard to disinfect), drying, temperature, acid (can go thorugh GI system), proteases (fecal oral transmission

Envelope

Viral Structure

• components consist of membrane, lipids, proteins, glycoproteins (viral attachment protein), ect
• amorphous: influenza
• nucleocapsid in A Bag: herpes
• defined structure: rabies is like a bullet and pox a boxcar
• labile to acid, detergent, drying and heat
• viral glycoproteins modify cell membranes
• released by budding and cell lysis (do not have to kill cell to exit)

Virus Genomic Replication

DNA

• in nucleus except pox and hepadna
• semi-conservative, requires a primer, infections genome
• ssDNA in nucleus
• dsDNA in nucleus: small viruses (PPP) the cell provides DNA pol and large viruses are encoded by virus 
• thymidine is the limiting reagent in large viruses
• error prone: mutations (virus polymerase)  
• Hepadna: longer than genome, +RNA template made in nucleaus. viral reverse transcriptase converts RNA to DNA

Virus Genomic Replication

RNA

• in cytoplasm, except retro and orthomyxo
• determined by genome structure
• must generate full length template
• generates double stranded RNA (interferon inducer)
• very error prone: MUTATIONS (no error checking)
• +RNA: template is neg RNA
• - RNA: template is a pos RNA
• dsRNA: pos strand = template for dsRNA
• Retro: full lungth mRNA transcribed from DNA= genome

Envolped Viruses

Assembly

• components include: nucleocapsid, matrix protein, glycoprotein modified membrane
• site of envelopment: plasma membrane, intracellular membrane
• budding: either buds out of the cell into the interstitial fluid or into the cytoplasm from an intracellular membrane
• poxvirus is the exception**

Small DNA virus

Polyoma virus as example

• small circular DNA genome
• early and late genes
• depends on host for DNA and mRNA production
• stimulates cell growth to promotoe DNA synthesis
• early genes in one direction of DNA and late genes in the other direction
• has introns
• has T angigens that inhibit p53 and RB proteins that normally slow down growth of cell (early gene action)
• late genes than do viral capsule

Large DNA Viruses

Herpesviruses

• Large virus; ds DNA; enveloped icosadeltahedral capsid
• immediate Early (take over), Early (enzymatic), and Late genes (structural)
• encodes pol, scavenging enzymes, cell manipulation, immune escape, etc
• do not encode an DNA dep RNA polymerase (dont need too)
• latent/recurrent infections: determined by viral/host control of transcriptions (hides in cells)

Huge DNA Virus

Pox

• large virus; ds DNA; enveloped, complex internal structure
• complex mode of replication
• replicates in cytoplasm
• encodes many proteins including DNA and RNA polymerases
• loses membrane when entering cell and leaves core

RNA Genome Replication

• requires a full length template
• uses viral polymerase
• occurs in cytoplasm:
• +RNA viruses create a scaffold or vesicle for replication and transcription(rnavironucleus)
• exceptions are orthomyxoviruses and retro viruses
• make many mistakes (mutations)
• ALL negative RNA virues are enveloped

T cell receptors

• CD2 is an adhesion molecule and CD3 is the activation complex ass w/ TCR (CD3 is only on T cells)
• T Cell Receptor: specifically binds antigen 
• Most Tcell Rec are αβ
• 5% of T cell receptors are γδ: invariant, may be triggered by alarm signals (HSP) ect
• Subset Co-receptorsL CD4: bind to MHCII and CD8 bind to MHC I

Natural Killer T Cells

• restricted diversity of TCR (<5% of total)
• invariant TCR responsive to CD1 presentation of glycolipids
• facilitates innate responses (anti-mycobacterial response)

T Cell Markers

•  regulatory: CD28 (activates) and CTLA4 (inhibition) effect APC by binding to B7
• CD40L for activation of B cell, DC, or macrophage
• adhesion molecules:  LFA-1, CD2 (adhesion and activation; SLAM)
• SLAM stands for signaling lymphocyting activation molecule
• Effector functions: Fas and FasL (Fas ligand) (promotes killing)(both TNF family
• MHC molecules and chemokine receptors

CD4 T Cells: Helpers

• TCR: extracellular interactions with MHC + antigen; membrane interaction w/ CD3 (delivers TCR signal)
• CD4 molecule: interactions w/ MHC II and than sends intracellular signal throuhg Lck
• Naive CD4 tcells move around looking for stimulation
• they are initiated by dendritic cells
• promote cell-cell activation: CD40L and cytokines
• change chemokine receptors (wander)
• killing: induction of apoptosis: Fas ligand on T cell binding to Fas on target cell to promotoe apoptosis 
• causes "clean death"

CD8 T cells: Killers, suppressors

and some help

• TCR: TCR signals
• CD8 molecule: interacts w/ MHC 1 on other cells and activates the T cells internal Lck
• initiated by dendritic cells
• killing: induction of apoptosis in target: binding and release of perforina nd granzyme or FasL binding to Fas
• suppression: cessation of ongoing resposne by killing excess effector cells (B cells, T cells, etc)
• cytokine production: consistent w/ nature of the response per DC instructions (IFN gamma for Th1) 

Thymus

• cortex: TCR recombination; 5% pre t cells grow and move to medulla
• Medulla: antigen selection
• AIRE: generic transcription activation
• education by DCs and macrophages through MHC I and II
• maturation through cytokines form thymic stromal (epithelial ) cells

The Goldilokcs Phenomenon

CD4+CD8+T Cell Selection

• TCR does not form properly: No Stimulation; Apoptosis
• TCR binds too loosely or not at all to anything: No stimulation: N growth: NO CELLS: No response
• TCR binds too Tighly to MHC and self peptides: Over timulation: Burnout: Apoptosis; NO CELLS: No response
• TCR Binds just right to MHC: stimulation: T cells grow mature

Consequences of Th1 Response   

• cytokine production: IL-2, IFN gamma, TNFbeta (LT)
• expansion of lymphocyte numbers
• activation of CD4 and CD8 T cells
• polarization of response of APCs to inflammation and attack
• B cell class switch to IgG

IFN gamma

• epitomizes Th1 response
• promotes cell-mediated responses
• promotes Ig class switch to IgG
• promotes anti-microbial responses: B cell help for IgG subtype that fixes C' and promotes CD8 CTL development
• ACtivates macrophages (M1 macrophage): promotes intracellular killing
• enhances dendritic cell function
• promotes IL-12 production by DC and macrophages
• prevents Th2 responses: prevents IL-4 production

LT (TNFbeta) Mediated Responses

• activates and recruits neutrophils
• macrophages: activates NO production
• ETC: kills some tumor cells and fibroblasts

Negative Consequences of Th1 Responses

• excessive inflammtion
• DTH responses: poison Ivy
• Autoimmune cycle of stimulation: multiple sclerosis, psoriasis, chron's disease

IL-4 Mediated Response 

• epitomizes Th2 response
• promotes growth: T cells and B cells, Mast Cells
• Inhibits Th1 Response
• alternative macrophage activation (M2): wound healing

IL-10 Mediated Responses

• inhibits Th1 responses
• inhibits T cell proliferation
• inhibits macrophage/DC proudction of Th1 cytokines (IFNg) 
• Promotes B Cell growth (enhances Th2 response): promotes systemic clean up of proteins in body
• promotes tolerance/suppression (Treg cells)

TGFbeta

• Treg response
• blocks T cell activation
• blocks monocyte to macrophage activation
• released in large quantities in the eye
• enhances wound healing
• part of signal: w/ IL-1 for Th17 response, For IgA class switching

Hygiene hypothesis

• absence of early expose to microbes allows for development of Th2 type responses to antigen but fewer Tregs
• lack of IL-12 stimulation of Th1 responses
• enhances Th2 responses promote allergic responses
• increased numbers of allergy prone individuals in developed countries

Viral Recombination

• exchange of genes: may be cross over of closely related genes via breakage and relinking or may be via copy choice mechanism
• Reassortment: a special form of recombination where segmented viral genomes swith (exchange) gene segments to create new genomes
• Integration: viral genome cross over and insertion into host cell chromosomes

CD40 and CD40L

• CD40L expressed on activated CD4 T Cells
• CD40 other cells
• On B Cells, DC, macrophage and endothelial cells
• TNF receptor family
• binding=clustering=TNF receptor associated factors (TRAF) bind and deliver response
• actiavtion of NFkB, API, etc
• Actiavtion of cell
• increased expresssion B7 

Delayed Type Hypersensitivity (DTH Reaction)

• Type IV Hypersensitivity
• Huge number of CD4 T cells made for an antigen
• PPD is shot into intradermal area
• T Cells wander make a defense against it, causing skin reaction (granuloma usually)

Chronic Granulomatous Disease

• Disease has Multiple Granulomas
• neutrophils and macrophages lack ROS ability and cannot effectively kill the phagocytized bacteria
• macrophages containing the bacteria stimulate T Cells
• T cells convert macrophages into epitheliod cells that surround the infection
• with CGD can happen with even strep or staph
• granuloma

Immunoglobulin Class Switching

• B Cell binds protein w/ surface Ig
• internalizes and processes protein
• presents peptide on MHC II
• TCR and CD4 bind to MHC II
• B7 binds to CD28 to activate T Cell
• T Cell activates B Cell w/ CD40L: CD40
• T cell directs outcome w/ cytokine: IFNgamma: IgG
• T cell directs outcome: IL4, IL5: IgG or IgE or IgA

Natural Killer Cells

• innate
• lack TCR and CD3
• activated by target cell
• Not MHC restricted (your NK cells kill my viral infected targets)
• MHC receptor inhibits killing
• generic response
• kills w/ perforin/granzymes
• no memory
• NKT cells have a TCR but resemble NK cells
• also contains FasL (just like CD4 and CD8 T cells)

T Regulators

• CD4 and CD25 Cells
• CD25 means activated cells (it is the alpha subunit of IL-2
• produce TGFbeta and IL-10 to calm cytokines
• CD8 suppressor cells

Resolving an Infection

• prevent initiation (binding)
• prevent replication of the virus: inhibit viral protein synthesis, promote mutation
• eliminate the free virus: mop up action by antibody
• eliminate the virus factories: kill the cells: lytic virus kills the cells, induce apoptosis, immune cytolysis (tissue damage)

Interferons

• Alpha: many subypes, acid stable, produced by most cells and INDUCED BY VIRUSES,etc
• Beta: one sub type, acid stable, induced by viruses and produced mainly by fibroblasts
• Gamma: macrophage activation factor and produced by NK and T cells as part of Th1 responses
• Alpha and Beta are Early interferons
• only one molecule is needed per cell for these to activate
• dying cells can release Alpha and beta to warn other cells

Cell Antiviral State

• initiated by alpha and beta interferon
• activated only if cell is infected (need dsRNA)
• protein Kinase (PKR) for eLF-2alpha of ribosome: activated by double stranded RNA
• eLF-2alpha prevents translation of capped mRNA, including virus capped ones
• 2-5'A Synthetase: makes a 2, 5 polyadenosine that activates RNAse L to degrade mRNA
• Mx protein: anti-influenza

NK Cells

• important for LOCAL CONTROL of enveloped/non-cytolytic virus infections
• acts as local militia (bully squad)
• activated by interferon alpha or IL-12
• targeted by reduced MHC expression due to virus
• IFN and NK cell response may be sufficient to cont rol virus infection preventing disease!!!
• overzealous NK cell response in adults may result in more problemsome disease

Anti-viral Antibody 

• neutralizes extracellular virus: blocks virus attachment and destabilizes structure
• Opsonizes Virus for phagocytosis: promotes clearance (but can facilitate infection of macrophage)
• blocks viremic spread to target tissue!!!!
• initiates complement cascade
• ADCC (antibody dependent cytotoxicity) 

Immunopathology

• lymphokine and interferon effects: fever and flu like
• tissue damage (esp enveloped): inflammation, DTH and CTLs
• Rash: T cells or immune complexes
• immune complex disease (HBV)
• Autoimmune reactions? (MS)
• immunosuppression (HIV, EBV, CMV, MEASLES)

Evasion of Immune Responses 

(Viruses)

• Humoral (antibody): latency, cell-cell transmission and change antigens
• Humoral (complement): inactivate C3 or other
• Interferon
• Antigen Presentation to T cells
• Immune Ce  ll Function: infect cell; encode lymphokina analogue
• inflammation (inhibit)

Potential outcomes Virus Infection

• Inapparent: -> Subclinical or Latent
• Immortalizing -> oncogenic
• Apparent: -> Acute or chronic

Steps in Viral Infection of Body

• Entry: mucuc m., skin, UG tract, placenta, blood
• Initiation: replication and local spread
• Incubation period: amplification and viremia
• Prodrome (early non spec symptomes): amplification, viremia and cytokine actions
• pathogensis: virus and host related pathogensis
• Resolution: interferon, NK, cell med, and antibody
• Convalescence:tissue repair and immune memory

Disinfection

• evneloped viruses (except corona and Hep B) are inactivated by soap solvents and dryness
• capsid viruses require .5% hypochlorite (bleach), 1% glutaraldhyde or 70% ethanol
• autoclaving and dry heat will kill vyruses
• for Hep, HIV and other blood borne viruses: universal blood and body fluid precautions, disinfection of HBV requires use of a 10% bleach solution 

Human Papillomavirus

Diseases

• genital Tract: condyloma acuminata and genital malignancies
• Respiratory Tract: respiratory papillomas
• Mouth: oral papillomas
• skin: common hand wart and plantar foot wart

Progressive Multifocal Leukoencephalopathy (PML) 

• polyomavirus
• PML-1:
• demyelination disease of CNS caused by JC virus infection of oligodendrocytes
• viral infection is lytic and destructive
• PML2: patients have previous impaired cell-mediated immunity (JCV is opportunistic)
• patients suffering from AIDS at increased risk for PML (1-4% develop disease)
• disease, when clinically apparent, is rapidly progressive with death w/i a year

BK Polyomavirus

• human one is widespread aprox 90% of young children are infected
• a mjor cause of kidney transplant dysfunction and rejection
• factors for virus reactivation not understood at this time
• Polyomavirus allograft nephropathy (PVAN): mononuclear inflam cells and tubulitis mimics graft rejection and important to distinguish from immune rejection since treatment is different