I loved Virology I, the first class in this two-part series by Vincent Racaniello of Columbia University. Virology II, How Viruses Cause Disease, is a 12-week course. This post contains my notes from the course. (The Week 1 notes are omitted.)
How Viruses Cause Disease: Week 2 – Immunity
Video 1: Innate Immune Responses
Humans and many other animals have 3 types of immune responses: intrinsic, innate, and adaptive. This first video covers the intrinsic and innate immune responses. The body has many intrinsic mechanisms for preventing viral infection, such as the skin, mucous, tears, a low pH, and surface cleansing.
The innate immune system functions continuously without prior exposure and is activated within minutes of an infection. Cytokines, sentinel cells (dendritic cells, macrophages, and natural killer cells), and complement make up the innate immune system, which can inform the adaptive response (the next link in the immunity chain) when infection reaches a dangerous threshold. Unlike the adaptive immune system, the innate immune system is not tailored to specific pathogens.
The discovery of toll-like receptors in fruit flies in 1996 and these receptors in mammals in 1997 provided a clue about how the innate immune system differentiates microbes from self. Toll-like receptors are transmembrane, pattern-recognizing receptors that recognize pathogen-associated molecular patterns. TLRs are conserved from plants and insects to humans. There are 13 varieties in humans and mice that dimerize on recognizing foreign molecules such as dsRNA, LPS, and flagellin (low-hanging fruit). Dimerization causes the intracellular domains of TLRs to link and start a phosphorylation cascade that eventually results in the production of cytokines including tumor necrosis factor (TNF) α, IL-6, IL-12, and interferons. TLRs are present on the cell membrane and in endosomes, where many viruses are found.
RIG-I-like helicases in the cytoplasm trigger cytokine production when detecting viral RNA. Cyclic GTP-ATP synthetase (cGAS) is a DNA sensor that, when binding DNA, catalyzes cAMP formation which results in a phosphorylation cascade that in turn triggers interferon and cytokine production.
Video 2: Interferon
Investigators in 1957 noted that the supernatant from infected chicken cells "interfered" with infection and other cells and called the substance at work interferon. Interferon alpha and beta are produced by most nucleated cells soon after viral infection, while interferon gamma is produced by T cells and natural killer cells later in the infection process and induces dendritic cells and other sentinel cells. Interferon alpha and beta bind to receptors to turn on a signaling pathway that causes the synthesis of more than 1000 cell proteins from genes known as interferon-stimulated genes (IFGs).
Several important interferon-induced proteins were introduced:
(1) Pkr: this protein kinase is activated by double-stranded RNA and can inhibit many viruses. It phosphorylates elF2α, which can trigger autophagy (programmed cell death). (2) RNAse L, (3) 2’,5’-oligo (A) synthetase is activated by dsRNA and in turn activates RNAse L, which degrades DNA in the cytoplasm, (4) nitric oxide synthetase (induced by interferon gamma) produces NO, which has antiviral effects, (5) promyelocytic (Pml) proteins, which in the nucleoplasm bind foreign DNA, repress transcription, and remodel nucleosomes, and (6) tetherin, a coil-like protein that stretches along the cell membrane surface to tether viruses and prevent escape, although many viruses have neutralizing proteins to overcome this challenge.
The interferon system is dangerous because it induces many deleterious gene products and has physiological consequences (the classic flu-like symptoms of fever, chills, nausea, malaise). These symptoms are not directly caused by viral and other infections but rather the immune response.
Video 3: Sentinels and Complement
Dendritic cells, macrophages, and natural killer cells patrol all tissues looking for disease. Dendritic cells, named for their dendrite-like shape, are found in the periphery when immature and carry TLRs, RLHs, and cytokine receptors. On maturing, they move to the lymph nodes, where they serve to link the innate and adaptive immune responses. Dendritic cells directly inhibit viral infections by producing interferon. When this doesn't counter an infection, dendritic cells present the antigens they accumulate to T cells in the lymph nodes and they also provide cytokines to activate these T cells. Dendritic cells can be like Trojan horses, carrying viruses into the lymph nodes (e.g., HIV-1, dengue virus). Basic research is underway to use this to increase the immune response to vaccination. The video did not discuss natural killer cells or macrophages.
Complement was identified in 1890 as a heat-liable factor in serum that lyses bacteria in the presence of antibodies (i.e., complemented antibodies). Complement bridges the innate and adaptive defense systems and is a collection of soluble serum and membrane proteins. Complement serves 4 functions: (1) cytolysis, or making holes in infected cells as indicated by the presence of bound antibody or unusual proteins on the surface, (2) inflammation by cytokines, (3) opsonization, or the coating of virus particles to facilitate macrophage uptake, and (4) solubilization of immune complexes, breaking up these organ-damaging complexes. C1q detects pathogens. Complement also binds to antibodies, producing a cascade that leads to pore formation in infected cells and ultimately cytolysis.
Video 4: Inflammation
Tumor necrosis factor alpha, an early warning cytokine, induces inflammation, which is characterized by the 4 signs of heat, pain, swelling, and redness. Inflammation serves to make blood vessels permeable to phagocytic cells. There are 3 cytokine groups: (1) proinflammatory: TNF, IL-1, 6, 12, (2) antiinflammatory: IL-10, 4, TGF-β, and (3) chemokines: IL-6 (which recruit immune cells during early immune response). Cytokines enter the bloodstream and therefore cause systemic effects far from the site of infection.
Cytopathic viruses cause inflammation because they promote cell and tissue damage, thereby activating the immune response. Adenovirus, pox viruses, and herpesviruses have genes that encode proteins to modulate the inflammatory response to increase their chance of success.
Non-cytopathic viruses do not kill cells and therefore do not stimulate the inflammatory response. Arenaviruses, paramyxoviruses, and other such viruses often lead to persistent infection.
The classic inflammatory response indicates the innate and adaptive immune defenses are communicating. Without effective inflammatory response, the adaptive response is poor. This is why adjuvants are used in noninfectious vaccines.
Video 5: Adaptive Immunity
The adaptive immune system (consisting of antibodies and T cells) is required to clear infections. Dendritic cells bring antigens to the lymph nodes, presenting them to B and T cells. B cells turn into plasma cells and produce antibodies. Dendritic cells also communicate with T cells, which began as naïve precursors (CD4 and CD8). CD8 cells identify viral infected cells and lyse them, while CD4 cells make cytokines.
Neutralizing antibodies bind to viruses to neutralize them. IgA at mucosal surfaces prevents infection. Other neutralizing antibodies help the body recover from infection. Passive antibodies protect against infection and may be injected into the site of an animal bite to prevent rabies. Antibodies interfere with viral infection by blocking attachment, clumping up virions, blocking endocytosis, and entering endocytotic capsids with viruses to prevent release.
Viral surfaces have many epitopes, or short amino acid sequences that antibodies recognize. Viruses, especially influenza, rapidly mutate to change their epitope and evade antibodies. This is why new flu vaccines need to be constantly developed.
In cell-mediated immunity, cytotoxic T cells recognize viral peptides presented by major histocompatibility complex (MHC) molecules on the cell surface. Cytotoxic T lymphocytes cause lysis by 2 mechanisms: (1) they transfer cytoplasmic granules containing perforin and granzymes and (2) induce apoptosis. Cell lysis stops infection spread but damages tissue (sometimes the outcome is better when CTLs are absent). How is the adaptive immune response modulated? Sentinel dendritic cells and macrophages exchange information with naïve Th cells in the lymph nodes. Th cells become Th1 cells (which stimulate CTLs) or Th2 (which stimulate B cells with cytokines for antibody production). The balance between the activation of these two cell types determines the outcome.
The adaptive immune response has memory. An initial adaptive response requires several weeks, but subsequent response requires only days. This memory is the basis of vaccination.
Bacteria also have an immune system with memory (Crispr/Cas) that cuts up the DNA of phages entering them.
Video 1: Innate Immune Responses
Humans and many other animals have 3 types of immune responses: intrinsic, innate, and adaptive. This first video covers the intrinsic and innate immune responses. The body has many intrinsic mechanisms for preventing viral infection, such as the skin, mucous, tears, a low pH, and surface cleansing.
The innate immune system functions continuously without prior exposure and is activated within minutes of an infection. Cytokines, sentinel cells (dendritic cells, macrophages, and natural killer cells), and complement make up the innate immune system, which can inform the adaptive response (the next link in the immunity chain) when infection reaches a dangerous threshold. Unlike the adaptive immune system, the innate immune system is not tailored to specific pathogens.
The discovery of toll-like receptors in fruit flies in 1996 and these receptors in mammals in 1997 provided a clue about how the innate immune system differentiates microbes from self. Toll-like receptors are transmembrane, pattern-recognizing receptors that recognize pathogen-associated molecular patterns. TLRs are conserved from plants and insects to humans. There are 13 varieties in humans and mice that dimerize on recognizing foreign molecules such as dsRNA, LPS, and flagellin (low-hanging fruit). Dimerization causes the intracellular domains of TLRs to link and start a phosphorylation cascade that eventually results in the production of cytokines including tumor necrosis factor (TNF) α, IL-6, IL-12, and interferons. TLRs are present on the cell membrane and in endosomes, where many viruses are found.
RIG-I-like helicases in the cytoplasm trigger cytokine production when detecting viral RNA. Cyclic GTP-ATP synthetase (cGAS) is a DNA sensor that, when binding DNA, catalyzes cAMP formation which results in a phosphorylation cascade that in turn triggers interferon and cytokine production.
Video 2: Interferon
Investigators in 1957 noted that the supernatant from infected chicken cells "interfered" with infection and other cells and called the substance at work interferon. Interferon alpha and beta are produced by most nucleated cells soon after viral infection, while interferon gamma is produced by T cells and natural killer cells later in the infection process and induces dendritic cells and other sentinel cells. Interferon alpha and beta bind to receptors to turn on a signaling pathway that causes the synthesis of more than 1000 cell proteins from genes known as interferon-stimulated genes (IFGs).
Several important interferon-induced proteins were introduced:
(1) Pkr: this protein kinase is activated by double-stranded RNA and can inhibit many viruses. It phosphorylates elF2α, which can trigger autophagy (programmed cell death). (2) RNAse L, (3) 2’,5’-oligo (A) synthetase is activated by dsRNA and in turn activates RNAse L, which degrades DNA in the cytoplasm, (4) nitric oxide synthetase (induced by interferon gamma) produces NO, which has antiviral effects, (5) promyelocytic (Pml) proteins, which in the nucleoplasm bind foreign DNA, repress transcription, and remodel nucleosomes, and (6) tetherin, a coil-like protein that stretches along the cell membrane surface to tether viruses and prevent escape, although many viruses have neutralizing proteins to overcome this challenge.
The interferon system is dangerous because it induces many deleterious gene products and has physiological consequences (the classic flu-like symptoms of fever, chills, nausea, malaise). These symptoms are not directly caused by viral and other infections but rather the immune response.
Video 3: Sentinels and Complement
Dendritic cells, macrophages, and natural killer cells patrol all tissues looking for disease. Dendritic cells, named for their dendrite-like shape, are found in the periphery when immature and carry TLRs, RLHs, and cytokine receptors. On maturing, they move to the lymph nodes, where they serve to link the innate and adaptive immune responses. Dendritic cells directly inhibit viral infections by producing interferon. When this doesn't counter an infection, dendritic cells present the antigens they accumulate to T cells in the lymph nodes and they also provide cytokines to activate these T cells. Dendritic cells can be like Trojan horses, carrying viruses into the lymph nodes (e.g., HIV-1, dengue virus). Basic research is underway to use this to increase the immune response to vaccination. The video did not discuss natural killer cells or macrophages.
Complement was identified in 1890 as a heat-liable factor in serum that lyses bacteria in the presence of antibodies (i.e., complemented antibodies). Complement bridges the innate and adaptive defense systems and is a collection of soluble serum and membrane proteins. Complement serves 4 functions: (1) cytolysis, or making holes in infected cells as indicated by the presence of bound antibody or unusual proteins on the surface, (2) inflammation by cytokines, (3) opsonization, or the coating of virus particles to facilitate macrophage uptake, and (4) solubilization of immune complexes, breaking up these organ-damaging complexes. C1q detects pathogens. Complement also binds to antibodies, producing a cascade that leads to pore formation in infected cells and ultimately cytolysis.
Video 4: Inflammation
Tumor necrosis factor alpha, an early warning cytokine, induces inflammation, which is characterized by the 4 signs of heat, pain, swelling, and redness. Inflammation serves to make blood vessels permeable to phagocytic cells. There are 3 cytokine groups: (1) proinflammatory: TNF, IL-1, 6, 12, (2) antiinflammatory: IL-10, 4, TGF-β, and (3) chemokines: IL-6 (which recruit immune cells during early immune response). Cytokines enter the bloodstream and therefore cause systemic effects far from the site of infection.
Cytopathic viruses cause inflammation because they promote cell and tissue damage, thereby activating the immune response. Adenovirus, pox viruses, and herpesviruses have genes that encode proteins to modulate the inflammatory response to increase their chance of success.
Non-cytopathic viruses do not kill cells and therefore do not stimulate the inflammatory response. Arenaviruses, paramyxoviruses, and other such viruses often lead to persistent infection.
The classic inflammatory response indicates the innate and adaptive immune defenses are communicating. Without effective inflammatory response, the adaptive response is poor. This is why adjuvants are used in noninfectious vaccines.
Video 5: Adaptive Immunity
The adaptive immune system (consisting of antibodies and T cells) is required to clear infections. Dendritic cells bring antigens to the lymph nodes, presenting them to B and T cells. B cells turn into plasma cells and produce antibodies. Dendritic cells also communicate with T cells, which began as naïve precursors (CD4 and CD8). CD8 cells identify viral infected cells and lyse them, while CD4 cells make cytokines.
Neutralizing antibodies bind to viruses to neutralize them. IgA at mucosal surfaces prevents infection. Other neutralizing antibodies help the body recover from infection. Passive antibodies protect against infection and may be injected into the site of an animal bite to prevent rabies. Antibodies interfere with viral infection by blocking attachment, clumping up virions, blocking endocytosis, and entering endocytotic capsids with viruses to prevent release.
Viral surfaces have many epitopes, or short amino acid sequences that antibodies recognize. Viruses, especially influenza, rapidly mutate to change their epitope and evade antibodies. This is why new flu vaccines need to be constantly developed.
In cell-mediated immunity, cytotoxic T cells recognize viral peptides presented by major histocompatibility complex (MHC) molecules on the cell surface. Cytotoxic T lymphocytes cause lysis by 2 mechanisms: (1) they transfer cytoplasmic granules containing perforin and granzymes and (2) induce apoptosis. Cell lysis stops infection spread but damages tissue (sometimes the outcome is better when CTLs are absent). How is the adaptive immune response modulated? Sentinel dendritic cells and macrophages exchange information with naïve Th cells in the lymph nodes. Th cells become Th1 cells (which stimulate CTLs) or Th2 (which stimulate B cells with cytokines for antibody production). The balance between the activation of these two cell types determines the outcome.
The adaptive immune response has memory. An initial adaptive response requires several weeks, but subsequent response requires only days. This memory is the basis of vaccination.
Bacteria also have an immune system with memory (Crispr/Cas) that cuts up the DNA of phages entering them.