Viral Pathogenesis Lecture 6 PDF

Lecture 6: Viral Pathogenesis ● ● ● ● ● Viral Pathogenesis - how a virus causes a disease Disease symptoms can result in tissue damage Terminologies ○ Viral disease- some harmful abnormality that results from a viral infection of the host organism ○ Clinical disease - when a host consists of over...

Lecture 6: Viral Pathogenesis ● ● ● ● ● Viral Pathogenesis - how a virus causes a disease Disease symptoms can result in tissue damage Terminologies ○ Viral disease- some harmful abnormality that results from a viral infection of the host organism ○ Clinical disease - when a host consists of overt signs and symptoms. ○ A virus is pathogenic for a particular host if it can infect and cause signs of disease in that host. ○ A strain of a certain virus is more virulent than another strain if it commonly produces more severe disease in a susceptible host ○ Viral virulence in intact animals should not be confused with cytopathogenicity for cultured cells (e.g. in vitro); In some cases, virus can lyse the cell in vitro but not in ex vivo. ○ Viruses highly cytocidal in vitro may be harmless in vivo, and, conversely, noncytocidal viruses may cause severe disease. Steps in Viral Pathogenesis ○ Entry and primary replication ○ Viral Spread ○ Cellular injury ○ Host immune response ○ Viral clearance or establishment of persistent infection Viral shedding ○ pertains to the shedding of infectious virus into the environment last stage in viral pathogenesis ○ Shedding usually occurs from the body surfaces involved in viral entry and occurs at different stages of disease depending on the particular agent involved. ○ It represents the time at which an infected individual is infectious to contacts. ○ In some viral infections, such as rabies, humans represent dead-end infections, and shedding does not occur. ○ Modes of transmission: ■ Direct transmission: - transfer of the virus by direct contact or droplet spread - direct contact: may include skin-to-skin contact, sexual intercourse, or kissing droplet spread: includes the transmission of virions in respiratory droplets that are sneezed or coughed out of one person and immediately enter the respiratory tract of another person ■ Indirect transmission: - requires the presence of an intermediary between hosts - airborne transmission: carried by dust or aerosolized particles that remain suspended in the air for long periods of time - fomites: nonliving physical substances that can indirectly transmit virions - Transmission via vectors - living intermediaries that can also transmit viruses (e.g. mosquitoes, ticks). Since these are arthropods, the terms arbovirus is used to denote arthropod-borne viruses. ENTRY AND PRIMARY INFECTION ● ● For host infection to occur, a virus must first attach to and enter cells of one of the body surfaces—skin, respiratory tract, gastrointestinal tract, urogenital tract o There are various points of entry RESPIRATORY TRACT Most common portal of entry for viruses into the human body. The mucosal surfaces of the respiratory tract translate to a very large surface area with which viruses can interact. A resting human inhales around 2 gallons of air every minute, and within each breath are aerosolized droplets and particles that could contain viruses, such as from a cough or sneeze of an infected individual. Example of virus that enters via respiratory tract: Influenza virus (cause flu) - overtime, virus developed ways to overcome the host’s defenses. As a response, host will also change its defenses and the cycle repeats; like a chess game. It has neuraminidase, which cleaves sialic acid, allowing the virus to exit. Aside from this, it can also cleave sialic acid in the proteoglycans, located in the mucus. Thus, it won’t be trapped and can enter the epithelium of the URT ● Upper respiratory tract (URT) ○ The epithelium contains abundant goblet cells that produce mucus, a thick fluid that traps inhaled particulate matter. ○ Mucus serves as physical and chemical barrier. Chemically, it contains enzymes, immune cells, which can engulf the virus. Physically, it traps the virus. ○ Majority is lined with cilia, small hairlike structures that move together like oars to push the mucus and its trapped contents to the throat, where it is swallowed or spit out. ● Lower respiratory tract (LRT) ○ Within the lungs, the two bronchi branch into bronchioles that lead to an estimated 300 million alveoli where gas exchange occurs ○ Smaller aerosolized particles or liquids are able to travel into the lower respiratory tract (larger droplets are deposited in the URT). ○ Mucus-secreting goblet cells are less abundant. ○ Ciliated cells are present at the beginning of the lower respiratory tract but are absent in the alveoli of the lungs. ○ Less ciliated as you go lower ○ In cigarette smokers, cilia becomes less mobile in a cold environment. Thus, mucus does not move, ○ ○ making them more susceptible to virus during cold season. In the alveoli, physical barrier becomes more permissive for the gas exchange occur. However there are numerous macrophages. Hence, still protected. Within the alveoli of the lung are found many alveolar macrophages GASTROINTESTINAL TRACT A hollow tube that stretches from the oral cavity (mouth) to the anus. The small intestine is composed of fingerlike projections called villi that increase the surface area of the epithelium. Under the epithelium of the small intestine, lymph node– like masses called Peyer’s patches contain millions of antibody - secreting lymphocytes, macrophages, and other immune system cells. Interspersed within the epithelial layer are M (microfold) cells, specialized epithelial cells that constantly survey the contents of the small intestine lumen. These cells transfer the molecules from the lumen to the immune system cells found in the lymphoid tissue below (Peyer’s patch). Paneth cells- produce mucus, the fluid lining of small intestine. It release fluid that contains defensins, which can inactivate bacteria’s peptidoglycan and prevent the virus to enter M cells engulf different contents of small intestine à gives it to macrophages and other immune cells à immune cells will now have a sample, allowing the immune cells build the immune system It is also a good point of entry for virus because if viruses replicate in the immune cells, it is an easy entry. Viruses that enter via the gastrointestinal tract must be able to survive its hostile environment. Successful viruses must be resistant to the low pH and the detergent qualities of bile Must also be resistant to peptidase and lipases There are many compounds that provide protection for the host, such as saliva, which contains enzyme, that can breakdown carbohydrate (e.g. amylase), and antibodies, causing the cell to agglutinate. There’s also stomach acid (~1.5-3 pH), which denatures protein. Bile is also present, which breakdowns fats. The membrane envelopes of most enveloped viruses are disintegrated by bile. Hence, most virus that enter through this tract is nonenveloped Acid-labile viruses (viruses that are easily destroyed in acidic environment) are unable to withstand the low pH - of the stomach, while acid-resistant viruses contain capsid proteins that are not denatured by low pH (or their protein denaturation is reversible). Within the Picornaviridae family, Rhinoviruses are acid labile, whereas Poliovirus is acid resistant. Poliovirus, reovirus, and HIV are thought to exploit M cells to gain entry past the epithelium UROGENITAL TRACT The genital tract refers to the organs that are involved in reproduction Viruses that are transmitted via the genital tract as a result of sexual activity are sexually transmitted diseases. abrasion during sex allowing virus to interact to inner part. Transmitted through fluid, such as semen HIV is more likely to be transmitted in male-female than male-male. Thus, male-to-male transmission of HIV is commonly through GIT (e.g. anal) Cells can be infected, exhibited by the tropism of human papillomavirus (HPV) for the epithelium of the cervix or penis, or viruses can gain entry into the body through breaks in the genital epithelium or by binding local cell receptors, as occurs with hepatitis B virus (HBV) or human immunodeficiency virus (HIV) SKIN Largest organ Composed of two layers of tissue: the outermost epidermis and the underlying dermis Viruses that replicate in the epidermis, such as HPV, gain access through small cuts or abrasions in the skin that allow access to the lower, dividing layers of skin where viral replication can occur - Epidermis are dead cells and so virus cant replicate in dead cells. Hence, a good barrier. Bites of insect vectors (mosquitoes, ticks, mites) can introduce viruses into the dermis, and the subcutaneous tissue can be accessed by viruses through animal bites, needle punctures, or improperly sterilized tattooing or piercing equipment VIRAL SPREAD - - PLACENTA ● Congenital Infections: ○ occur when a mother infects a fetus before its birth ○ occur via vertical transmission (generational transmission of viruses from parents to their offspring) ○ Vertical transmission often leads to long-term persistence of the virus within the child. ○ can occur when a virus crosses the placenta during pregnancy. The blood of the mother is not mixed with the blood of the fetus; instead, the placenta is the interface between the mother and developing fetus, allowing oxygen, waste products, and nutrients to pass between mother and fetus ● Transplacental Infection vs Perinatal Infection ○ Transplacental- placenta has a very selective membrane (e.g. does not permit blood à diff blood type) but still allows oxygen, waste, etc. Thus, virus use this system to enter the fetus. ○ Perinatal- during delivery, babies and mothers fluid are mixed, allowing virus to infect babies. C-section minimizes perinatal infection. Thus, this procedure is recommended to mothers that has disease (e.g. HIV positive); this is used by virus that cant bypass the placenta. ● Virus moves from the point of entry to different parts of the organ Tropism determines the pattern of systemic illness produced during a viral infection. Ex. hepatitis B virus has a tropism for hepatocytes, where disease is caused by the virus. There are 4 factors that affect Viral Tropism: is the cell susceptible? (host has receptors) is the cell permissive? (cells have machineries for the virus to replicate such as Transcription Factor); TF is cell-specific (Susceptibility does not mean permissive) absence of immune cells/defense mechanism (if there are few immune cells, virus can enter) accessibility of tissue (e.g. some cells in placenta are susceptible and permissive but inaccessible) Many viruses produce disease at sites distant from their point of entry. After primary replication at the site of entry, these viruses then disseminate within the host Can be through just locally or can move towards different organs and thus, local and systemic infection, respectively. FIRST MECHANISM: via the bloodstream or lymphatics ○ The presence of virus in the blood is called viremia. ○ Types/Characteristics of Viremia ■ Passive viremia- virus enters the circulatory system for the first time ■ Primary viremia- infection re-occur, infecting 1-2 cells, then replication happens (parang local lang). Eventually, progeny viruses exit the cells after infection. ■ Secondary viremia- if more virus enters, it will infect other cells/organs. ○ ● This is how infection in the blood is determined (by checking the concentration of virus in blood) ○ Virions may be free in the plasma (eg, enteroviruses, togaviruses) or associated with particular cell types. SECOND MECHANISM: Neural Spread ○ Muscle- has muscle neurons ○ Skin- sensory nerve endings, which can serve as point of entry for some viruses ○ After entering, it can infect the neurons and can travel long distances because neurons innervate different parts of the body. ○ Since it is present in the cell and not in blood, it is difficult for the immune cells to detect it. ○ ○ ○ ○ ○ Retrograde- from a nerve ending to the soma (cell body) Anterograde- from the soma to the nerve endings Neurons are polarized cells Dendrites -> axons -> release of neurotransmitter sa cell na naka synapse; opposite direction pag retrograde. SUMMARY: when viruses travel long distances they can go from point of infection to other organs through neurons or blood (more common); because not all virus can infect neurons ENTRY TO ORGAN Organs are lines with capillaries for waste and gas exchange to occur. Capillaries have epithelial cells that have sinusoid/fenestrations, which can be used by the virus to enter the organ through transcytosis (caveolin-dependent) or virus can also replicate inside the cells. These sinusoids are covered with immune cells (e.g. Kupffer cells in liver) Some virus don’t event enter the immune cells, they just stick to the receptors on its surface. It is hard to infect the brain through the blood due to BBB, which is very selective. Typically, those that can enter the CNS moves retrogradely (e.g. rabiesvirus) Diapedesis/Trojan Horse Approach- virus infects immune cells and these cells will enter the BBB upon activation Directional release- for epithelial cells (polarized release), to the outer surface allow evasion of the immune response Apical release- remains in the outer, allowing it to evade immune system. Uses local infection because only infect neighboring cells Basolateral-allows virus to be released and spread. Thus, use systemic infection. HOST DEFENSE/RECOVERY FROM INFECTION ● ● ● Viral Spread Once virus infected the host (in the cells where it can replicate), there are two cycles during replication: Lytic response- if there’s enough number of them, they will be released, breaking the PM Lysogenic response- replicating inside, and not released but genomic materials are still expressed. Eventually, a gene is detected, allowing it to enter the lytic cycle. Pwedeng lysogenic -> lytic or lytic -> lysogenic ● ● ● ● Defense mechanisms inhibit replication of virus For most organisms have immune systems: ○ Innate (nonspecific) immune response ■ Already in place. Regardless of the virus’ species, it will act against it if it infects the host. ■ Physical barriers (e.g. tight junctions in the skin, epithelial and mucous membrane surfaces, mucus itself) ■ Anatomical barriers (e.g. eyes- tears; skinsweat, desquamation, flushing; blood-brain barrier, gastrointestinal tract- gut flora, digestive enzymes) Epithelial and phagocytic enzymes (e.g. lysozymes) ■ Phagocytes (neutrophils, monocytes, macrophages) ■ Inflammation-related serum proteins - Cells that release cytokines and inflammatory mediators (i.e., macrophages, mast cells, natural-killer cells) ○ Adaptive immune response (acquired/specific) ■ Specific for a particular virus, immunological memory ■ Carried out by lymphocytes (B cells,T cells) two types of immunity: ● Humoral immunity: B cells differentiate into plasma B cells that can produce antibodies against a specific antigen. ● cell-mediated immunity: primarily directed at intracellular infectious agents Viral spread from an organism to another organisms, horizontally; different from placenta because placenta is vertical transfer Occurs various ways such as via fluid (urine/viruria, semen, blood/viremia), feces (via anal -oral tract, due to poor sanitation in food) pertains to the shedding of infectious virus into the environment last stage in viral pathogenesis ○ apical exit through respiratory tract (e.g. coughing is good for the host and virus, because it expels virus particles (less virus in the system) and it is also being released to environment (will infect other organisms) Shedding usually occurs from the body surfaces involved in viral entry and occurs at different stages of disease depending on the particular agent involved. It represents the time at which an infected individual is infectious to contacts. ● ● In some viral infections, such as rabies, humans represent dead -end infections, and shedding does not occur. Environment affect viral transmission ○ Example: after sneezing, big particles settle on the ground and less likely to infect, but small particles stays on the air, causing more infection. In humid environment, particle stays shorter in the atmosphere because it gets heavy. In dry, viral transmission is more likely, particles stays longer. In hotter environment, virus denature. In cold environment (may vary ), people tend to stay indoors, and so, easier transmission. ● ● ● Lecture 7: Host Immune Response – Intrinsic, Innate and Adaptive PRRs ○ Host receptors that recognizes MAMPs, may be located on the host cell surface, endosomal membranes, cytoplasmic, or secreted ○ Examples of PRRs include the membrane-bound Tolllike receptors (TLRs) and cytoplasmic NOD-like receptors (NLRs), RIG-1-like receptors (RLRs), and protein kinase R MAMP (PKR) MAMP (PKR)-PRR engagement generally leads to signaling events that ultimately activate transcription factors such as NFkB & the Interferon regulatory factors IRFs (i.e. IRF3, IRF7), promoting the expression of IFNs and inflammatory cytokines IRFs - a type of chemokines that are more specific to viruses; they interfere viruses Coordinated host response to infection Types of PRR: Tall-like Receptors (TLR) - Intrinsic and innate are non specific Intrinsic immune response: response of an infected cell to a pathogen without the reliance of transcription; in the cell, it has proteins that can detect pathogens and eliminate them or induce transcription of genes; when genes are transcribed, this is innate immune response ● ● ● ● Can be found in plasma membrane or endosomal membrane since they have integrin Has cytosolic region that recruits and activates Myd88 and Trif Recognize MAMPs which can be dsDNA, ssRNA, siRNA, or CpG motifs (can be methylated) -> Once activated by MAMPs, they homodimerize (same type of TLR) or heterodimerize (diff type) -> TLR then activate and recruit adaptor proteins: Myd88 and Trif which activate NFkb and IRF (interferon regulatory factor) -> IRF bind to gene or DNA (IRF response element) and will induce transcription of interferons (alpha 1) Specific TLRs recognize specific MAMPs; they recognize each other Two TLRs that are present in the cytoplasm: RIG-1 & MDA5 INTRINSIC CELL RESPONSE ● MAMPs ○ Macromolecules that are shared among groups of microorganisms & recognized as foreign to the host. ○ Examples of MAMPs include (but are not limited to) dsRNA, peptidoglycan, LPS, flagellin, viral proteins RIG1 & MDA5 Cytoplasmic RNA helicases that function as RNA sensors ● RIG-1 ○ Detects 5’ triphosphate RNA (without 5’ cap) ● MDA5 ○ Detects long dsRNA (and RNA without 5’ cap) ● Protein kinase R (PKR) ○ Sensor for viral dsRNA, inhibits cap-dependent translation by eIF2α ● cGAS ○ Cyclic GMP-AMP synthase (cGAS) binds to viral dsDNA in the cytoplasm Types of PRR: Protein Kinase R (PKR) Process: 1. RIG-1 and MDA5 have CARD domains which are phosphorylated when inactive 2. When they recognize specific MAMPS, the card domain undergoes confomational change where the Phosphate group becomes exposed and is dephosphorylated by phosphatase (PP1a) 3. CARD domains become ubiquitinated by TRIM25 and Riplet particularly in their lysine residues 68 (they can now activate other proteins) 4. Ubiquitinated card domains then bind to the proteins present in the mitochondria which are MAVS (mitochondrial antiviral signalling proteins); they aggregate with one another; ubiquitinated site becomes a platform for activation of IKK (inhibitory kappa B kinase)-TBK complex 5. IKK homodimerize and phosphorylate IKB which inhibits kappa B kaya nadisinhibit si kappa B/NFKB 6. When IKK associate with TBK (TANK binding kinase), TBK phosphorylate IRF, stabilizing them, IRF induce transcription of interferons How viruses evade RIG-1 & MDA5 responses? ● Sequestration or modification of viral RNA ligands ○ capping ● Manipulation of posttranslational modifications on RIG-1, MDA5, MAVS ● Cleavage of RIG-1, MDA5, MAVS ● Sequestration (of CARD domains) or relocalization of RIG-1, MDA5 ● ● ● Inhibits eiF2 Once it recognizes dsRNA, it phosphorylates eiF2-GDP but not where it is supposed to be. This inhibits GDP to become GTP. This inhibits translation Becomes active when associated with MAMPs through autophosphorylation How Virus Responds to PKR: There are viruses that inhibits PKR directly There are some that promotes inhibition of PKR via RAS pathway which normally induces cell proliferation There are some that activates phosphatase that dephosphorylates eiF2 GTP Interferons when transcribed and released, they bind to interferon receptors which induce transcription of PKR; positive feedback Types of PRR: cGAS (cyclic GMP–AMP synthase) ● Takes ATP and GTP monophosphorylated and cyclic and make them Type I IFNs ● Summary: RIG1, MDA5, cGAS, TLR, TRIF, and Myd88 activate NFKB and IRF which induce expression of interferons (type I) which will act in autocrine or paracrine fashion How viruses evade cGAS responses? Viral manipulation of STING post-translational modifications Cleavage of STING Prevent/limit cGAS sensing of nucleic acid ligand - Viruses (or viral components) bound by PRRs trigger downstream signalling events that lead to the production of Type I IFNs α/β). These cytokines are released from the cell and then bind to IFNAR receptors on the surface of adjacent cells to stimulate synthesis of IFN-responsive genes Additional Info ● ● Cytokines ○ small signalling proteins that are secreted by specific immune cells. Cytokines mediate cell-cell communication to regulate a range of immune responses. Interferons (IFNs) ○ a group of cytokines that are generated in response to several pathogens (‘interfere’ with viral infection). ○ There are 3 types of IFNs: ■ Type I (α/β) - released through intrinsic, induce local signalling system; induced following PRR signalling and bind to IFNAR receptors on target cells – help to establish antiviral response. ■ Type II (ϒ) ■ Type III (λ1, 2, 3) Process 1. When interferons are released, they bind to IFNAR receptors which will activate JAK-STAT pathway 2. Jak and Tyk can autophosphorylate each other’s tyrosines 3. They phosphorylate and activate Stat protein which activates IRF 4. IRF binds to ISRE (IFN-sensitive response element) that will induce expression of more interferons or other genes like PKR ● 2’,5’-oligo A synthetase ○ Activated by dsRNA, promotes production of oligo A which, in turn, activates RNase L. RNase L then cleaves a bunch of RNA (poly U region); kaya maraming RNA without 5’ cap; hence they can activate MDA5 and RIG-1 ● Mx GTPases ○ GTPase with diverse roles in the inhibition of virion assembly ○ ○ Effects of the inflammatory cytokines IL-1, IL-6, TNF-α in response to viral infection ○ At the site of infection, cells get infected and they release chemokines and interferons, chemokines signal sentinel cells to go to the site of infection Have receptors for chemokines (g protein coupled receptors); upon binding, they trigger the cytoskeletal system to initiate cell movement towards direction where there is a high concentration of chemokines When they go to the site of infection, they engulf pathogens and apoptotic bodies and process them and take the foreign antigen present in these Natural Killer (NK) cells INNATE CELL RESPONSE ● When NKFB and IRF induce expression of interferons, this is already part of innate cell response kasi may change ng regular gene expression of the cell ● ● ● ● ● ● ● Part of innate immune response and activate adaptive immune response: macrophages, dendritic cells, natural killer cells Part of adaptive immune response: T cells, B cells Sentinel Cells ● Sentinel cells (i.e. macrophages, dendritic cells) ○ Phagocytes ○ can monitor the presence of viral infection via uptake of apoptotic bodies of infected cells Intended to kill infected cells Have 2 receptors: inhibitory & activating receptors MHC1 = major histocompatibility complex Normal cell ○ MHC I on normal cell is recognized by NK inhibitory receptor inducing a signalling cascade that will inhibit NK cells from killing normal cells; no cell death Infected cell ○ Lack of MHC I on infected cell can’t stimulate an inhibitory signal which leads to NK cells release enzymes that will induce a caspase signalling cascade and induce cell death to target cell Virus-encoded mechanisms for modulation of NK cell activity ● Expression of viral protein with similar homology as cellular MHC I ● Release of viral-encoded activating receptor antagonist ● Downregulation of activating ligand on infected cell ● Sequestration of Chemokines or blocking Chemokine receptors ● Newly produced virus particle (virion) may engage the inhibitory receptor or infect NK cell ● ● B lymphocytes - mediates humoral immunity; focuses on eradicating virus particles via neutralization, release antibodies T lymphocytes - cell mediated immunity; focuses on directly eliminating the pathogens or infected cells ADAPTIVE IMMUNE RESPONSE ● ● Innate: The Complement System ● ● ● ● Composed of serum proteins that form a cascade ultimately resulting to the enhancement of immune response; complement proteins circulate in the blood in their inactive forms; typically activated by presence of microbes or pathogens or signals induced by infection 3 pathways activating complement system: classical, lactin, and alternative pathway These 3 pathways converge on the activation of C3 C5 convertase which converts C3 and C5 to their active form; C3 - opsinin; C5 - complex with C9 to form pores C3 and C5 can work together to induce inflammation which is due to release of cytokines and recruitment of immune cells into a specific region Innate & adaptive immune responses against viruses Major cells: B cells and T cells ○ have receptors, which recognize foreign antigens – pathogen-specific ○ (aka ‘lymphocytes’) – major effector cells of the adaptive response (specific to an infection) ○ differentiate from lymphoid progenators Dendritic cells ○ ‘bridge’ of the innate and adaptive immune response. Also called ‘antigen-presenting cells (APCs)’ ○ Sentinel cells phagocytose pathogens or apoptotice bodies, processes them and takes foreign antigen and takes it to the surface, it then activates B and T cells ● ● ● Each lymphocyte has a unique antigen receptor, meaning that they each recognize a specific antigen. Interaction of antigen with its corresponding antigen receptor initiates signalling cascades within the lymphocyte, that promotes cell proliferation, differentiation and activation of effector functions of the lymphocyte in order to defend against the foreign invader. When these receptors are activated, they promote proliferation, differentiation and activation. ● Antigen presentation to T cells by antigen-presenting cells (dendritic cells, macrophages, B cells) ● Class I MHC pathway ○ Antigen peptides found in the cytosol of the APC (or other infected cell) bind to MHC class I molecules ○ Peptide-MHC class I complexes are recognized by antigen receptors on the CD8+ T cell ○ Proteosome degrades proteins to peptides, they enter the endoplasmic reticulum via tap receptors ○ Peptides, acting as antigens, get loaded to MHC Class I receptors and are exocytosed out for CD8 to recognize them ○ MHC I is activated – cytocollic virus – CD8 T cells Class II MHC pathway ○ Antigen peptides found within intracellular vesicles of the APC bind to MHC class II molecules ○ Peptide-MHC class II complexes are recognized by antigen receptors on the CD4+ T cell ○ Peptides are processed and loaded to MHC Class II receptors and are recognized by CD4 T cells ○ MHCII is endocytoses – CD4+ T cells Examples of viral evasion of antigen processing and MHC presentation ● ● ● When a pathogen enters a dendritic cell, chemokines are released in order to alarm neighboring cells. Specialized antigen presenting cells (APC) ○ When a pathogen enters the cytosol, they process these pathogens and take peptides from their proteins now acting as antigens, and load to the MHC receptors. They are then sent to the surface via endomembrane system and the dendritic cells travel to the lymph nodes where they present these antigens to the naive lymphocytes, allowing them to activate Mature dendritic cells are no longer phagocytic ● When dendritic cells stop presenting MHC class receptors, they may be a target for NK cells ○ Humoral vs Cell-mediated Immunity ● ● ● Identified by the presence of a c cellular protein called CD4 embedded in the plasma membrane and are called CD4+TH cells ○ Activates phagocytes to kill microbes ○ Secrete cytokines which enhance the activity of macrophages, NK cells, B cells, other helper T cells, cytotoxic T cells, and suppressor T cells Cytotoxic T cells ○ CD8 + T cells ○ Directly responsible for cell-mediated immune response ○ Kills parasite-infected cells, even cancer cells Humoral Immunity ○ Mediated by antibodies produced by B lymphocytes (B cells) ○ Functions to defend against & eliminate extracellular pathogens ○ Antibodies bind & neutralize pathogens or target pathogens for phagocytosis Cell-mediated Immunity ○ Mediated by effector functions of T lymphocytes (T cells) ○ Largely functions to defend against & eliminate intracellular pathogens ○ Specific types of T cells can activate macrophages to kill phagocytosed microbes or can directly destroy infected cells Humoral Adaptive Immune Response (B-Cells) ● ● ● ● B cells do not require antigen presentation via MHC molecules; once activated, they release antibodies B cells activation requires cytokine signals generated by CD4 T cells Naïve T cells undergo development in the thymus (no interaction with foreign antigen yet) Interaction with APC triggers proliferation & differentiation of T cells in the lymph node (interaction with foreign antigen) Cell-mediated Adaptive Immune Response (T-Cells) 2 Types of T cells ● T-helper (TH) cells ○ CD4 + T cells ● ● Complement system Sensitizes of NK cells, and macrophages IgG & antibody-dependent cell-mediated cytotoxicity (ADCC) ● ● ● ● ● Different antibody ‘isotypes’ serve different roles in the humoral immune response When B cells are activated, they release antibodies that are specific to infections Target may be a virus-infected cell The cytoplasmic granules contain perforin & granzymes – mediates killing in a similar manner to cytotoxic T cell Infected cells that produces viral proteins in the plasma membrane – target of antibodies that recruit NK cells Lecture 8: Virus-Host Interaction: Patterns of Infection Functions of Antibodies ● Neutralization ○ ● Block attachment of viral receptor to host receptor, prevent uncoating, promote agglutination ○ Agglutination: clump together; agglutinated viruses make an easier target for immune cells than single viral particles Opsonization ○ Activation of phagocytes: virus-bound antibodies and antibodies bound to virus-infected cells bind to receptors called Fc receptors, on the surface of phagocytic cells and triggers phagocytosis ● Lytic Cycle ○ After replication, gene expression and assembly, virions are released through lysis of the host cell. (usually nonenveloped, more virulent, cytopathic). ○ Cytopathic to the cell ● Lysogenic Cycle ○ Associated with latent or temparate infections ○ The virus genome and protein are replicated and translated ○ Non cytophatic to the cells Viral Pathogenesis ● ● Adverse physiological consequences that occur as a result of viral infection of the host organism The pathogenesis that may follow a viral infection relies on several parameters in addition to its impact on infected cells Acute Infection ● Pattern of infection whereby virus particles produce rapidly & infection is resolved quickly by the immune system (short-term infection). Survivors are usually immune to subsequent infections. ● virus first enters host entry site and then viral replication happens -> innate immune response becomes activated -> virions keep going up until it is detected by adaptive immune response -> virus then goes down in numbers Intrinsic and innate immune response usually act locally Symptoms result from late innate immune response There is a threshold level of virus required for you to have symptoms or to activate adaptive immune response kasi pag onti lang siya, pwedeng yung intrinsic lang mag-act and there will be no symptoms Lastly, immunologic memory is established, meaning may mga immune cells or lymphocytes equipped to battling against a specific pathogen (little to no symptoms pag nainfect uli) Patterns of Viral Infection ● ● ● ● ● ● Acute Infection ○ Virus undergo viral replication cycle ○ Virus particles produced, symptoms appear, infection is cleared (7-10 days) Persistent Infection ○ Latent: periodic episodes of acute infections followed by quiescent phase (little or no detection of viral particles); reactivation stimulated throughout host life (may result in virus particle production) ○ Asymptomatic: virus productin continues for the life of the host or in tissues where immune cells do not often patrol (symptoms may or may not be apparent) ○ Pathogenic: Period of years separates primary infection and fatal appearance of symptoms; production of virus particles may be continuous or not detectable throughout life Additional Info: ● Although acute infections may be resolved within a few days, some viral progeny may be shed and transmitted to other hosts before the infection can be contained ● Acute infections may also be inapparent (asymptomatic) whereby limited or no clinical symptoms may be detected. In these cases, virus replication occurs to levels that facilitate transmission, but may not damage host… well-adapted pathogens (i.e. poliovirus) Antigenic variation infections may facilitate repeated acute Incubation Period ● ● The period of time before symptoms of disease appear following initial infection. During this period, viral genomes may be replicated & intrinsic/innate immune responses initiate the production of cytokines (i.e. type I interferons). During this, viral genomes may be replicated and intrinsic/innate immune responses initiates production of cytokines (type I interferons) ● Influenza virus can undergo a lot of mutation which can lead to nonfunctional proteins, when a mutation happens to the hemagglutinin or antigen, the antibodies can no longer recognize them and will allow the influenza virus to infect the host again ● ● Antigenic Drift: accumulated mutation in the viral genome that results on a substantial change in genetic makeup; can result in a new strain or evasion of the adaptive immune response Antigenic Shift: there are multiple segments of influenza virus, for it to be functional, it needs all the 8 segments (it needs to package it), if you get infected with at least 2 segments, there could be reassortment. If these would infect a host, it will be a different protein that won't be recognized by the antibodies Persistent Infection ● ● while there is no single mechanism responsible for establishing a persistent infection, when viral cytopathic effects are minimized and host defenses are suppressed, persistent infection may be likely As you may therefore expect, a feature of establishing persistent infection is the reduction of host defenses. In fact, modulation of the adaptive immune response may perpetuate a persistent infection Persistent Latent Infection 3 properties: ● Viral gene products that promote virus reproduction are not synthesized (or in small quantities) ● Cells that contain the viral genome are poorly recognized by the immune system ● The viral genome persists intact within the infected cell to ensure productive infection may be initiated at a later time. Ensures that virus progeny may be transmitted to new hosts Example: Herpes simplex virus (HSV-1) ● Enveloped viruses | Group I: dsDNA genome ● Transmission: HHV-1: Saliva; HHV-2: sexual contact, maternal-neonatal ● Infection: Primary site of infection – epithelial mucosal cells; Latency established in sensory ganglia ● Associated diseases: Skin vesicles or mucosal ulcers Viral proteins may block the adaptive immune response Primary Infection Of Sensory Neurons & Reactivation ● ● Viral gene products may block presentation of viral peptides within MHC I complexes at several steps within the pathway (i.e. lowering expression of MHC I genes, blocking production of proteasome-derived viral peptides, interfering with MHC I biogenesis & transport to cell surface) This type of immune modulation may prevent or delay elimination of virus by cytotoxic T cells General patterns of viral infection ● LAT (latency-associated transcripts) ○ Parts of the viral genome that induce latency by inhibiting translation of other viral genomes ○ Normally not translated ○ Remain in RNA form ○ Can inhibit other RNAs; preventing translation ○ suppresses apoptosis so that latently infected host cells stay alive for the reservoir, and suppresses the expression of lytic genes during latent infection. Persistent Asymptomatic Infection ● Lymphocytic Choriomeningitis Virus ● After infecting a host cell, the dengue virus hijacks the host cell's machinery to replicate the viral RNA genome and viral proteins. After maturing, the newly synthesized dengue viruses are released and go on to infect other host cells. Symptoms: Agonizing limb pain (‘break bone”), fever, bleeding gums, rash, vomiting Lecture 9: Viral Vaccines and Antivirals ● ● ● ● ● Non-cytophatic nature creates carriers If introduced congenitally or immediately after birth, viral peptides cannot be recognized as foreign. If introduced later in life, mice dies of encephalitis and edema Though noncytophatic behavioral and learning assessment revealed that persistently infected mice as smart as their uninfected peers When a virus infects a fetus congenitally, it is recognized as “self” kaya di narerecognize ng lymphocytes kaya no symptoms Not lethal ● ● Adaptive immunity makes the success of vaccines possible B cells are activated by helper T cells and dendritic cells but they do not require them Persistent Pathogenic Infection HIV ● Since nalessen CD4 T cells, people with HIV or AIDS do not die because of the virus, but another infection since walang CD4 T cells na magfifight off ng infection na yon Immunopathology ● ● Clinical signs of viral disease (fever, aches, tissue damage, nausea) largely stem from the host’s immune response to infection This damage is referred to as ‘immunopathology’ (may be the price to pay by the host to eliminate infection!) Dengue Fever ● Called breakbone fever; a mosquito-borne viral disease that occurs in tropical and subtropical areas of the world ● Symptoms appear up to two weeks after infection ● Not contagious ● Those who become infected a second time are at an extreme risk of sever disease ● 4 serotypes of dengue virus – antibodies to any 1 serotype do not efficiently protect against infection by another* ● ● T cells and B cells are effector cells of the adaptive immune response. These cells are required for recognition of foreign antigens Following initial encounter with pathogen, memory T and B cells are established. -> Re-exposure to the same pathogen reactivates memory cells to control the secondary infection quickly & prevent disease. Vaccines ● Vaccines induce the production of memory cells (B cells and T cells) without the actual disease ● The goal of vaccination is to trigger an immune response more rapidly and with less harm than a natural infection: In essence, to avoid the disease (symptoms) that often accompanies the first exposure (and preferably establish a long lasting immunological memory) Passive Immunization ● ● ● ● ● ● ● The first encounter with an antigen produces a primary response. Antigen A introduced at time zero encounters little specific antibody in the serum. After a lag phase, antibody against antigen A appears; its concentration rises to a plateau & gradually declines. When later challenged with a mixture of antigens A and B, a very rapid and intense antibody secondary response to A occurs, illustrating immunological memory. The goal of vaccination is to trigger an immune response more rapidly and with less harm than a natural infection: in essence, to avoid the disease (symptoms) that often accompanies the first exposure (and preferably establish a long-lasting immunological memory) Several Criteria for an effective vaccine: ● Safety - Vaccines are administered to large numbers of people, relatively few of which are likely to die or even catch the disease that the vaccine is designed to prevent. Even low toxicity is unacceptable. ● Protection - vaccine must be able to produce protective immunity in a very high proportion of the people to whom it is given. Vaccine must be able to generate long-lived immunological memory – important in poorer countries where it is impracticable to give regular ‘booster’ shots. ● Cost - The vaccine must be relatively cheap if they are to be administered to large populations. Delivery methods must also be quick & easy and there should be few associated side-effects. ● Biological stability & route of administration are also important to consider ● ● ● Direct administration of the products of the immune response (i.e. antibodies or stimulated immune cells) obtained from an appropriate donor to a patient. Short-term effects Naturally acquired passive immunization: neonates and infants acquire passive immunization from the mother. Antibodies are passed through the placenta (for the developing fetus) or from breastmilk (for newborns). This provides transient protection to the immunologically naive newborn Artificially acquired passive immunity: immunoglobulins (or activated lymphocytes, Adoptive transfer) acquired from immunized donors or donors recovering from the disease are administered intravenously. This provides a short-term (weeks/months) protection, but does not develop immunological memory Why? Passive immunization provides immediate protection and does not require the host to mount an effective memory response Example: protection against rabies. Preparation of human immunoglobulin is delivered asap to the site of animal contact – this serves to contain virus before it can be disseminated throughout the body. Active Immunization ● ● The process of inducing an immune response by exposure to attenuated or killed virus preparations or with purified viral proteins. Long-term effects. Each of these methods uses components of the pathogenic virus that the vaccine is intended to target. Several ways it can be acquried: ● Inactivated killed vaccine: ○ Virulent virus particles are isolated and are inactivated by procedures such as treatment with formaldehyde, UV irradiation, or extraction of enveloped viruses with detergents ○ Immune responses plotted against time after injection of an inactivated virus vaccine. Often requires multiple doses (first dose often not sufficient to produce effective response). ● Subunit vaccine: ○ vaccines formulated with purified conpinents of viruses rather than intact virus particles (e.g. protein subunit, nucleic acid) Antigenicity ● Can be improved by mixing them with a substance that stimulated the early inflammatory response. These ‘immunostimulants’ are called ‘adjuvants’ (adjuvare is Latin for ‘to help’). ● Adjuvants ○ compound or mixture that stimulates immune responses to an antigen. Researchers can optimize a vaccine by using different combinations of adjuvant and immunogen to induce a protective immune response. ○ Help localize antigen at inoculation site ○ Can stimulate the innate immune response (i.e. act as ligands for pattern recognition receptors like TLRs) **Advantage and disadvantage: ○ Safe for immunodeficient individuals as the treated virus cannot reproduce ○ Often requires multiple doses as the first dose may not be sufficient to produce effective response ○ Inactivation methods may have negative effects on antigenicity ● ● Replication-competent attenuated vaccine ○ Results after injection with attenuated virus. A single dose is administered at the start of experiment. Filled histogram under the curve indicates the titer of infectious attenuated virus. Limited virus reproduction stimulates potent & lasting immune response. Recombinant vaccine ○ Can be constructed by recombinant DNA technology/cloning: ○ Once genome of pathogenic virus is cloned in a suitable system, point mutations, insertions, deletions can be introduced bstandard recombinant DNA techniques ○ Virulence gene can be isolated and mutated and the attenuated virus can be constructed ○ Note that multiple point mutations or deletions are preferred to reduce or eliminate the probability of reversion to virulence ● ● ● ● They help to localize antigen at the inoculation site They can stimulate the innate immune response (i.e. act as ligands for pattern recognition receptors like TLRs) target mechanisms involved in viral entry, reproduction, and exit Major limitation: high degree of safety, potency Antivirals ● ● Antivirals target mechanisms involved in viral entry, reproduction, and exit Major Limitation: High degree of Safety, Potency Maraviroc ● For HIV ● Inhibition of entry: Binds to CCR5 and inhibits SU from binding to it ● Inhibition of genome replication: ● Inhibition of exit: inhibits neuraminidase (allows separation of viral particle) Introduction to Viral Epidemiology ● Epi + demos + ology = upon + people + study = study of distribution and determinants of diseases or health outcomes in a specific population Patterns of Disease ● Endemic ○ Stable pattern of disease occurrence ○ Predictable, native ○ Example: flu, chickenpox ● Epidemic ○ Aka “outbreak” ○ Unexpected increase in the number of cases in the population at a given time and place ○ 1 case may be considered an outbreak (e.g. the plague) ○ Examples: measles outbreak (caused by vaccine hesitancy), smallpox ● Pandemic ○ Epidemic spread to a much larger area ○ Examples: COVID-19 (caused by SARS-CoV-2), influenza after World War I Epidemiologic Triad ● Agent: Virus ○ 3 important properties: ■ Infectivity - ability to infect ■ Pathogenicity - ability to cause disease ■ Virulence - ability to cause severe disease or death Measures of Disease Frequency ● Incidence ○ Denominator (S): number of disease-free individuals in a population at a given time ○ Numerator: number of new cases at a given time ○ Related to the pathogenicity of the agent - Attack rate ○ Studies about the new cases in a disease-free population through the SIR Model (susceptible-infected-recovered/removed) ● Secondary Attack Rate ○ Denominator: number of persons in contact with an index case ○ Numerator: number of persons who become infected ○ Related to the infectivity of the agent ● Cause-specific Mortality Rate ○ Denominator: total population size at MIDYEAR (July 1) ○ Numerator: number of deaths from a specific cause in a given year ● Case-Fatality Rate ○ Denominator (I): number of cases ○ Numerator (R-Removed): number of cases who died ○ Related to the virulence of the agent ● Prevalence ○ Denominator: number of individuals in a population at a given time ○ Numerator: number of cases at a given time ● Seroprevalence ○ Denominator: number of individuals in a population at a given time ○ Numerator: number of individuals with antibodies (IgG - past infection) against a particular virus Epidemiological Parameters ● Incubation Period ○ Time from infection to development of symptoms ● Latent Period ○ Time from infection to infectious mess ● Infectious Period ○ Time host is infectious ● Generation Time ○ Time from infection in one individual to transmission to another individual ● Basic reproduction number (Ro) ○ Number of new infections (secondary infections) in a susceptible population from a single infected individual ○ Indicator of contagiousness ○ Estimated through the SIR model ○ Ro < 1 - insufficient for outbreak to be maintained ○ Ro > 1 - epidemic is possible SIR Model ● system of derivatives ● dS/dt, dI/dt, dR/dt Surveillance ● Methods for Collection ○ Active surveillance - actively surveying the population ■ Field surveillance using wild and sentinel animals ■ Survey ■ Contact tracing ○ ● Passive surveillance - depending on notifications from hospitals since viral disease ar notifiable diseases kasi contagious (once may infected, irereport agad) ■ Notification ■ Registries ■ Google Fly Trends, Google Dengue Trends ■ Social media Methods for Analysis ○ Descriptive statistics ■ Frequencies, mean, median, mode ○ Analysis by time ■ Bar graphs ○ Analysis by place ■ Maps ○ Analysis by time and place ○ Analysis by person ■ Stratified analysis considering age (some ages are more susceptible), sex (HPV in males), occupation (occupational exposures such as healthcare workers during COVID-19) Infectious Disease Control ● Prevention Strategies ○ Herd immunity ■ Not necessarily needed for everyone to be vaccinated ○ Screening and surveillance ○ Isolation ■ For Those that are infected ○ Quarantine ■ For those that are exposed or come in contact