The document discusses the immune response to viruses. It begins by describing viral properties and replication cycles. The innate immune response includes epithelial barriers, interferons, natural killer cells, and macrophages. Adaptive immunity involves antigen presentation, CD4+ T cell help, CD8+ T cell cytotoxicity, and antibody production. Viruses employ various evasion strategies like antigenic variation. SARS-CoV-2 pathogenesis is still under research but involves interfering with interferon induction and signaling pathways. The take-home message is that immune responses aim to control viral replication through innate effectors and generate adaptive memory, while viruses evolve ways to evade these defenses.

1. Immune response to
virus
Ritasman Baisya

2. Points of discussion
• Properties of a virus
• Viral replication
• Innate immune response
• Adaptive immune response
• Immune evasion by virus

3. Properties of virus
• Virus is obligate intracellular parasite
• It requires host cell for survival
• Have either RNA or DNA as their genetic material.
• The nucleic acid may be single- or double-stranded.
• Either naked nucleo-capsid or with an envelope
• The entire infectious virus particle, called a virion
• Viral components assemble ,they do not replicate by division
Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000. Section 6.3, Viruses: Structure, Function, and Uses.

4. Enveloped vs nonenveloped

5. Classification
Gaurab Karki Classification of virus . Microbiology, Virology September 17, 2017

6. SARS – COV 2

7. Replication

8. 1
2
4
3
5
5
4
6
Golgi
Apparatus
mRNAs
Nucleus
Ribosomes
Penetration by
Endocytosis
Viral attachment-
TROPISM
uncoating –
release of viral
genome
Genomic replication
Assembly
Transcription &
Translation Release

10. Virion release
There are two methods of viral release: lysis or budding –
• Lysis results in the death of an infected host cell, these types of viruses are
referred to as cytolytic. example -smallpox.
• Enveloped viruses, such as Corona virus, are typically released from the host
cell by budding.
It is this process that results in the acquisition of the viral phospholipid
envelope.
These types of virus do not usually kill the infected cell and are termed
cytopathic viruses.

11. Innate immune response to
virus

12. Components of innate immune response
• Epithelial barrier
• Early non-specific or innate immune –
o Interferon (IFN) –
Type I IFNs (IFN α and IFN β)
Type II IFN (IFN γ)
o Natural killer cells
o Macrophages

13. Physical barrier
Killing of viral particle by locally
produced microbicidal agent –
• Defensin
• Cathelicidin
• Intraepithelial lymphocyte

15. Interferon
• IFNs are a large family of multifunctional secreted proteins involved in antiviral defense,
cell growth regulation, and immune activation.
• Two dominant types - Type I IFNs ( IFN-α , IFN-β) are produced in direct response to
viral infection
• Type II IFN ( IFN-γ ) - rather than being induced directly by viral infection, is synthesized
in response to the recognition of infected cells by activated T lymphocytes & NK cells.
• IL-29, IL-28A, and IL-28B have been classified as the type III IFN group, designated IFN-λ
molecules 1, 2, and 3, respectively

16. Type 1 Interferon -
• Large family of structurally related cytokines that mediate the early innate immune response
to viral infections
• There are many type I interferons, which are structurally homologous and are encoded by
genes in a single cluster on chromosome 9
• The most important type I interferons in viral defense are IFN-α (which actually includes 13
different closely related proteins) and IFN-β, which is a single protein.
• Plasmacytoid DCs are the major sources of IFN-α, but it also may be produced by
mononuclear phagocytes.
• IFN-β is produced by many cell types in response to viral infection

17. Characteristic
• The most potent stimuli for type I interferon synthesis are viral nucleic acids
• The receptor for type I interferons, which binds both IFN-α and IFN-β, is a
heterodimer of two structurally related polypeptides, IFNAR1 and IFNAR2,
which are expressed on all nucleated cells
• This receptor signals to activate STAT1, STAT2, and IRF9 transcription factors,
which induce expression of several different genes whose protein products
contribute to antiviral defense in various ways

18. Pattern recognition receptor
• The most studied are the Toll-like receptors (TLRs), retinoic acid-inducible
gene I (RIG-I; also known as DDX58) and NOD-like receptors (NLRs).
• Virus infections usually activate the endosomal TLRs (TLR3, TLR7, TLR8 and
TLR9) that recognize viral nucleic acids and double-stranded RNA
intermediates

24. Anti viral effects of type 1 IFN
• Induced genes include double-stranded DNA & RNA –activated serine/threonine
protein kinase (PKR), which blocks viral transcriptional and translational events,
and 2′,5′-oligoadenylate synthetase and RNase L, which promote viral RNA
degradation.
• Primarily , a paracrine action in that a virally infected cell secretes interferon to
act on and protect neighboring cells that are not yet infected
• Interferon secreted by an infected cell may also act in an autocrine fashion to
inhibit viral replication in that cell

25. Other actions
1. Sequestration of lymphocytes in lymph nodes, thus maximizing the opportunity
for encounter with microbial antigens.
The mechanism for this effect of type I interferons is the induction of a
molecule on the lymphocytes called CD69, which forms a complex with and reduces
surface expression of the sphingosine 1-phosphate (S1P) receptor S1PR1
2 . Increase the cytotoxicity of NK cells and CD8+ CTLs & promote the differentiation
of naive T cells to the Th1 subset of helper T cells.
These effects of type I interferons enhance both innate and adaptive
immunity against intracellular infections, including viruses and some bacteria.

26. IFN gamma – a few notes
• IFN-γ is the principal macrophage-activating cytokine
• IFN-γ is also called immune or type II interferon.
• Although its name interferon is shared with the antiviral type 1 interferons, it is
not a potent antiviral cytokine, and it functions mainly as an activator of effector
cells of the immune system.
• IFN-γ is a homodimeric protein belonging to the type II cytokine family
• CD4+ Th1 cells ( main source ) , NK cells and CD8+ T cells produce IFN-γ.
• NK cells secrete IFN-γ in response to activating ligands on the surface of infected
or stressed host cells

27. Few notes about IFN gamma
1. IFN-γ activates macrophages to kill phagocytosed microbes
2. IFN-γ promotes the differentiation of CD4+ T cells to the Th1 subset and inhibits the
development of Th2 and Th17 cells.
3. IFN-γ stimulates expression of several different proteins that contribute to enhanced
antigen presentation and T cell activation
4. IFN-γ acts on B cells to promote switching to certain IgG subclasses, notably IgG2a or
IgG2c (in mice), and to inhibit switching to IL-4–dependent isotypes, such as IgE

29. NK cells
• NK cells kill virus-infected cells and are an important mechanism of immunity
against viruses early in the course of infection, before adaptive immune
responses have developed.
• Class I MHC expression is often shut off in virus-infected cells as an escape
mechanism from CTLs. This enables NK cells to kill the infected cells because the
absence of class I releases NK cells from a normal state of inhibition
• Viral infection may also stimulate expression of activating NK cell ligands on the
infected cells.

31. Macrophages
• Phagocytosis of virus and virus-infected cells;
• Killing of virus-infected cells;
• Production of antiviral molecules - TNFα, nitric oxide, and IFNα.
• Many viruses that persist trigger innate cells such as dendritic cells (DCs), natural
killer (NK) cells and macrophages to produce anti-inflammatory molecules such
as interleukin-10 (IL-10) and transforming growth factor-β (TGFβ)

32. Interference with innate immune responses
1. HCV - Blocks RIG-I pathway by degrading IPS1 117
2. Influenza A virus NS1 protein inhibits RIG-I by direct interaction
3. Paramyxovirus V protein inhibits RIG-I by interacting with MDA5
4. HIV and human herpesvirus Inhibit IRF3
5. Hanta virus, CCHFV and Borna disease virus - Viral RNA is
undetectable by PRRs owing to removal of 5ʹ triphosphate

33. Adaptive immune response

35. Antigen presentation and processing

38. Cross presentation
If the infected cell is a tissue cell and not an antigen-presenting cell
(APC), such as a dendritic cell, the infected cell may be phagocytosed
by the dendritic cell, which processes the viral antigens and presents
them to naive CD8+ T cells- cross-presentation, or cross-priming

39. • Most efficient cross-presenting APCs are the lymphoid tissue dendritic
cells that express CD8 or the peripheral tissue subset that expresses
the CD103 integrin
• The corresponding specialized cross-presenting dendritic cells in human
tissues express high levels of CD141, also known as BDCA-3.
Cross presentation

41. Response by CD8 T cell
• CD8+ T cells undergo massive proliferation during viral infection &
become CTL
• The antiviral effects of CTLs are mainly due to killing of infected cells
• Other mechanisms include activation of nucleases within infected
cells - degrade viral genomes
• IFN-γ secretion which activates phagocytes and may have some
antiviral activity.

43. Role of CD4 T cell
• CD4+ T cell-derived IL-2: CD8+ T cell growth factor
• CD4+ T cell-derived chemokines: recruit CD8+ T to site of infection
• CD4+ T cells secrete IFNγ and TNFα to recruit and activate macrophages

46. Antibody mediated immune response
• The most effective antibodies are high-affinity antibodies produced in T-dependent
germinal center reactions
• Antibodies are effective against viruses only during the extracellular stage of the lives
of these microbes
• Antiviral antibodies bind to viral envelope or capsid antigens
• Prevent both initial infection and cell-to-cell spread
• Secreted antibodies ( IgA isotype ) - important for neutralizing viruses within the
respiratory and intestinal tracts

48. http://www.virology.ws/2009/07/24/virus-neutralization-by-antibodies/

50. Latent infection
• In latent infections, viral DNA persists in host cells, but the virus does not
replicate or kill infected cells
• CTLs generated in response to the virus can control the infection but are unable
to eradicate it.
• As a result, the virus persists in infected cells, sometimes for the life of the
individual.
• Reactivation of the infection is associated with expression of viral genes that are
responsible for cytopathic effects and for spread of the virus

51. Tissue injury
• In some viral infections, tissue injury may be caused by CTLs.
• Some degree of immunopathology accompanies host responses.
• The livers of patients with acute and chronic active hepatitis contain large
numbers of CD8+ T cells, and hepatitis virus-specific, class I MHC-restricted
CTLs - These findings support that the CTL response is the main cause of
tissue injury in viral hepatitis.
• LCMV induced meningitis is basically due to tissue injury

55. Immune evasion

56. Immune Evasion by Viruses- antigenic change
• Viruses can alter their antigens and are thus no longer targets of immune
response
• The principal mechanisms of antigenic variation are point mutations and
reassortment of RNA genomes (in RNA viruses), leading to antigenic drift
and antigenic shift. These processes are of great importance in the spread
of influenza virus
• Genomic mutation in virus- antigenic shift
• Genetic reassortment – antigenic drift

57. Antigenic drift

58. MHC escape phenomenon
• Some viruses inhibit class I MHC–associated presentation of cytosolic protein
antigens.
• Such viruses cannot be recognized or killed by CD8+ CTLs.
• NK cells are activated by infected cells, especially in the absence of class I MHC
molecules.
• Some viruses may produce proteins that act as ligands for NK cell inhibitory
receptors and thus inhibit NK cell activation

60. Viruses produce molecules that inhibit the immune response
• Cytokine binding protein is secreted by pox virus and acts as competitive
antagonist of cytokines
• EBV produces a protein homologous to IL-10 inhibits activation of
macrophages and dendritic cells
• Viruses have acquired genes encoding endogenous inhibitors of immune
responses during their passage through human hosts

61. Exhaustion
• Some chronic viral infections are associated with failure of CTL
responses, called exhaustion which allows viral persistence
• Persistent antigen stimulation may lead to upregulation of T cell
inhibitory receptors, such as PD-1
• There is evidence for CD8+ T cell exhaustion including HIV and
hepatitis virus infection.

62. Inhibitory response
to limit tissue damage

63. Inhibitory response
to limit tissue damage

64. METHOD OF IMMUNE EVASION with examples
Antigenic variation Influenza, HIV
Inhibition of antigen processing- Blockade of TAP transporter,
Removal of class I molecules from the ER
HSV CMV
Production of “decoy” MHC molecules to inhibit NK cells Cytomegalovirus (murine
Production of cytokine receptor homologues Vaccinia, poxviruses
Production of immunosuppressive cytokine Epstein-Barr (IL-10)
Infection and death or functional impairment of immune cells HIV
Inhibition of complement activation Recruitment of factor H Incorporation of CD59 in viral
envelope
HIV, vaccinia, human CMV
Inhibition of innate immunity - Inhibition of access to RIG-I RNA sensor Inhibition of PKR
(signaling by IFN receptor)
Vaccinia, HIV
HIV, HCV, HSV, polio

65. Li et al., Molecular immune pathogenesis and diagnosis of COVID-19, Journal of Pharmaceutical Analysis,
https://doi.org/10.1016/j.jpha.2020.03.001

66. Coronavirus immune evasion
• Can induce the production of double-membrane vesicles that lack PRRs and then replicate in
these vesicles, thereby avoiding the host detection of their dsRNA
• IFN-I (IFN-α and IFN-β) has a protective role but the pathway is inhibited in infected mice
• Gene expression related to antigen presentation is down-regulated
• Destroying the immune evasion of SARS-CoV-2 is imperative in its treatment and specific
drug development.

67. At IFN level
• At the step of type I IFN induction, SARS-CoV interferes with the signaling
downstream of RNA sensors directly or indirectly such as ubiquitination
• It can cause degradation of RNA sensor adaptor molecules MAVS and
TRAF3/6 and inhibiting IRF3 nuclear translocation.
• Inhibits STAT1 phosphorylation – decrease IFN signaling
• The viral proteins involved - both structural proteins (such as M, N) and non-
structural proteins (ORF proteins).

68. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic
Eakachai Prompetchara, Chutitorn Ketloy, Tanapat Palaga.APJAI

70. Take home message
• Viral cycle involves – entry , replication , assembly , release ( budding / lysis )
• Innate response involves Type 1 IFN , NK , macrophages
• Adaptive response starts when dendritic cell presents MHC1 to naïve CD8 cell
• Cross-presentation is unique for virus
• CTL is predominant effector cell causing tissue injury – immunopathology-immunity crosstalk
• Th1 cell stimulates CTL and cytokine (IFN gamma ) release
• Humoral immunity acts by neutralization mainly
• Immune evasion – by multiple mechanism –exhaustion and MHC escape important
• SARS-COV2 pathogenesis –still at research level

71. References
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Philadelphia: Elsevier Saunders;2015.
2. Borrow P, Nash AA. Immunity to viruses. In: Male D, Brostoff J, Roth D, Roitt I, editors.
Immunology. 8th ed. Philadelph
3. Rouse BT, Sehrawat S. Immunity and immunopathology to viruses: what decides the
outcome?. Nat Rev Immunol. 2010;10(7):514–526.
4. Murray PR, Rosenthal KS, Pfaller MA, editors. Medical microbiology. 8th ed. Philadelphia:
Elsevier Saunder; 2014
5. Li et al., Molecular immune pathogenesis and diagnosis of COVID-19, Journal of
Pharmaceutical Analysis