Viral Immunology — Questions

Each of these macrophage-produced cytokines has a characteristic systemic effect on the host.

Interleukin-1 (IL-1). Pyrogenic. Acts on the anterior hypothalamus to raise the thermoregulatory set-point, causing fever. It also drives the hepatic acute phase response (production of C- reactive protein, fibrinogen, and serum amyloid A). IL-1β is cleaved from its inactive precursor by caspase-1 within the inflammasome.

Tumour necrosis factor alpha (TNF-α). The classical cytokine of chronic catabolic illness. In sustained infection or malignancy, elevated TNF-α causes the cluster of muscle wasting, fat loss, and anorexia known as cachexia (originally called “cachectin”). In acute infection it also activates vascular endothelium and induces fever.

Interleukin-3 (IL-3). A haematopoietic growth factor. Together with granulocyte colony-stimulating factor (G-CSF), it drives neutrophil production in the bone marrow during acute infection, explaining the neutrophilia seen in many systemic infections.

The correct option pairs each cytokine with its principal systemic effect. The distractors swap real cytokines onto wrong endpoints.

Because VZV spreads largely from cell to cell, cell-mediated immunity rather than antibody is the decisive control. Children who cannot make antibody are not unusually susceptible to severe chickenpox, whereas any failure of T-cell immunity predisposes to severe primary disease and to reactivation.

The decline of this arm with age or immunosuppression is what permits zoster.

Dendritic cells (DCs) are the dominant antigen-presenting cells and the critical bridge between innate and adaptive immunity. They are found in two functional states.

Immature DCs are highly endocytic, with low surface MHC class II, low costimulatory molecule expression (CD80 / CD86), and limited T-cell priming capacity. They are positioned as sentinels at portals of viral entry (Langerhans cells in the skin, lung-resident DCs in the airway, intestinal DCs in the gut).

Maturation is triggered when the DC senses viral PAMPs through its pattern-recognition receptors (TLRs, RIG-I, MDA5, cGAS–STING), or when it receives cytokine signals (type I IFN, TNF-α) from the inflamed microenvironment. On maturation the DC:

• Downregulates endocytic activity (it has captured what it needs).
• Upregulates MHC class I and MHC class II loaded with processed viral peptides.
• Upregulates the costimulatory molecules CD80 (B7-1) and CD86 (B7-2) needed for naïve T-cell activation.
• Upregulates the chemokine receptor CCR7, which directs migration along CCL19 / CCL21 gradients toward T cell zones of draining lymph nodes.

Cross-presentation is the special capacity of certain dendritic cells (cDC1) to load externally acquired viral antigen onto MHC class I, allowing CD8+ cytotoxic T cell priming against viruses that do not infect dendritic cells directly.

The correct option captures this sequence. The distractors describe biology that does not occur: DCs mature in tissue (not the bone marrow), maturation requires PRR signalling, mature DCs are poorly phagocytic, and DCs can present antigen taken up from the environment without themselves being infected.

Measles vaccines (measles-rubella [MR], measles-mumps-rubella [MMR], and measles-mumps-rubella-varicella [MMRV]) contain live attenuated virus that must replicate in the recipient to provoke immunity. About 5 to 15% of vaccinees develop a mild, transient maculopapular rash 5 to 12 days after vaccination, often with low-grade fever. This is the expected immune response to vaccine-strain replication: the same immunopathology as wild-type measles, markedly attenuated.

The reaction is not a hypersensitivity to excipients, not contamination, and not reactivation of a latent virus, and it is not driven by maternal antibody. Where serology is positive and the clinical picture is ambiguous, a vaccine-associated reaction is distinguished from breakthrough wild-type infection by genotyping (the vaccine strain is genotype A) at a reference laboratory, and by a low immunoglobulin M (IgM) to immunoglobulin G (IgG) ratio compared with primary wild-type infection.

• What is recognised. A viral peptide displayed on major histocompatibility complex (MHC) class II by a professional antigen-presenting cell (dendritic cell, macrophage, or B cell).
• The molecular interaction. The T cell receptor (TCR), its α and β variable regions from V(D)J recombination, binds the peptide–MHC class II complex; the CD4 co-receptor binds the conserved β2 domain and recruits the kinase Lck; the CD28 co-stimulator binds CD80 or CD86 (B7) to give the second signal (TCR engagement without CD28 induces anergy).
• Restriction. Recognition is MHC class II-restricted, not class I.
• The epitope. A linear peptide of 13 to 18 amino acids that can overhang the open-ended class II groove, generated from extracellular antigen through the endocytic pathway (cathepsin cleavage, invariant-chain release, HLA-DM-mediated loading).
• HLA dependence. Only peptides fitting an individual’s HLA class II alleles (HLA-DR, HLA-DP, HLA-DQ) are presented. CD4+ cells then license both the cytotoxic and the B cell programmes, which is why HIV-1 depletion of CD4+ T cells disables antibody affinity maturation, CD8+ priming, and Th1 macrophage activation together.

• What is recognised. A viral peptide displayed on major histocompatibility complex (MHC) class I of an infected nucleated cell.
• The molecular interaction. The T cell receptor (TCR), its α and β variable regions generated by V(D)J recombination, binds the peptide–MHC class I complex; the CD8 co-receptor binds the conserved α3 domain and recruits the kinase Lck; naïve priming also needs CD28 to engage CD80 or CD86 (B7) on a mature dendritic cell, though effector killing needs no co-stimulation.
• Restriction. Recognition is MHC class I-restricted, and because every nucleated cell expresses class I, every cell is open to surveillance.
• The epitope. A linear peptide of 8 to 11 amino acids held in the closed-ended class I groove, derived from cytoplasmic viral proteins cleaved by the proteasome and imported to the endoplasmic reticulum by the TAP transporter.
• HLA dependence. Only peptides whose anchor residues fit an individual’s HLA class I alleles (HLA-A, HLA-B, HLA-C) are presented, so responses vary with HLA type; protective alleles such as HLA-B57 present conserved HIV-1 Gag epitopes that are hard for the virus to escape. Epitopes favour conserved internal proteins, making CD8+ responses more cross-reactive between strains than antibody.

• Definition. Affinity maturation is the progressive rise in antibody antigen-binding affinity during a response, so antibody made late or on re-exposure binds far more tightly than at first encounter.
• Where and when. In the germinal centres of secondary lymphoid organs (lymph nodes, spleen, Peyer’s patches), over the one to three weeks after a B cell is activated.
• Somatic hypermutation. Activation-induced cytidine deaminase (AID) introduces point mutations in the rearranged immunoglobulin variable (V) genes at about a million times the background rate, concentrated in the antigen-contacting complementarity-determining regions.
• Clonal selection. Mutated B cells compete for antigen held on follicular dendritic cells; higher-affinity receptors capture more antigen and present more peptide on MHC class II.
• Tfh help and cycling. T follicular helper cells deliver limiting survival signals (CD40 ligand, IL-21) to the best binders as B cells cycle between the dark zone (mutation) and light zone (selection). The outputs are long-lived bone-marrow plasma cells and affinity-matured memory B cells. Failure of the process (AID deficiency, X-linked CD40 ligand deficiency) causes hyper-IgM syndrome.

• Principle. Antibody made early in infection binds weakly; after affinity maturation in germinal centres it binds strongly, so IgG avidity separates recent from past primary infection.
• Affinity versus avidity. Affinity is the strength of a single antibody–antigen bond; avidity is the total binding of a complex, set by the individual affinities and the valency.
• Method. Two parallel ELISAs on the same sample, one with a brief chaotropic agent step (urea, diethylamine, ammonium thiocyanate) after binding that strips low-avidity bonds but not high-avidity ones.
• Avidity index. AI = (OD with chaotrope) ÷ (OD without chaotrope) × 100. Low (below ~30 to 40%) indicates recent primary infection in the past two to four months; high (above ~60%) indicates infection at least three to six months earlier.
• Clinical use. Greatest value is in pregnancy screening, where the timing of maternal infection sets fetal risk: high early-pregnancy avidity for toxoplasma, cytomegalovirus, or rubella excludes recent primary infection, while low avidity raises concern. It also clarifies persistent or non-specific IgM by checking whether IgG has matured.

The three nucleic-acid-sensing Toll-like receptors sit on the endosomal membrane, so that they detect viral nucleic acids only after the virus has been internalised by the cell.

• TLR3: double-stranded RNA.
• TLR7 and TLR8: single-stranded RNA.
• TLR9: unmethylated CpG DNA.

The wider family and its ligands:

Mechanism. The dominant mechanism is immune-complex disease driven by chronic B cell stimulation. Chronic exposure of B lymphocytes to hepatitis C virus (HCV) antigens (E2 binding CD81; antigen drive in intrahepatic lymphoid follicles) produces polyclonal, then oligoclonal, then monoclonal expansion. The expanded B cells secrete rheumatoid-factor-like immunoglobulin M (IgM) that binds polyclonal immunoglobulin G (IgG), forming type II mixed cryoglobulins. These and conventional immune complexes deposit in small- and medium-vessel walls, glomeruli and the dermoepidermal junction, activating complement and recruiting neutrophils.

Four examples (any four):

1. Mixed cryoglobulinaemic vasculitis: palpable purpura (leukocytoclastic vasculitis), arthralgia, peripheral neuropathy, glomerulonephritis.
2. Membranoproliferative glomerulonephritis: renal immune-complex deposition with proteinuria, haematuria, hypertension and progressive impairment.
3. B cell non-Hodgkin lymphoma (typically marginal zone): late clonal expansion; ~5 to 10% of those with mixed cryoglobulinaemia progress to overt lymphoma.
4. Porphyria cutanea tarda: photosensitive bullous skin disease on sun-exposed surfaces, via reduced hepatic uroporphyrinogen decarboxylase activity.

Other recognised manifestations include lichen planus, a Sjögren-like sicca syndrome, autoimmune thyroiditis and type 2 diabetes. Direct-acting antiviral (DAA) cure regresses most extrahepatic manifestations, an argument for treatment regardless of fibrosis stage.

• Capture step. The plate is coated with anti-human IgM antibody, which captures all IgM from the patient’s serum (specific and non-specific); other classes (IgG, IgA) are washed away.
• Detection step. Viral antigen is added and binds only the IgM of matching specificity; bound antigen is then detected with a labelled anti-viral reagent, giving a signal proportional to virus-specific IgM.
• Why the capture format is preferred. It solves two problems of a direct IgM ELISA: rheumatoid factor (itself an anti-IgG IgM) cannot cause false positives because no IgG remains in the captured fraction, and high-titre virus-specific IgG cannot outcompete IgM for antigen because it has been washed off.
• Clinical use. The test of choice for recent or current infection, since IgM appears in the first one to two weeks and decays over months. Applications include cytomegalovirus, rubella, toxoplasma, and parvovirus B19 in pregnancy, newborn screening for intrauterine infection (IgM does not cross the placenta), and anti-HBc IgM in acute hepatitis B. Combining it with IgG avidity improves discrimination of persistent IgM.

A cytokine storm is a massive, self-amplifying and dysregulated release of pro-inflammatory cytokines, principally interleukin-6 (IL-6), interleukin-1, tumour necrosis factor, and interferon-induced chemokines, that is neither scaled to the infection nor switched off as it resolves. The result is widespread tissue injury rather than controlled defence: diffuse alveolar damage and the acute respiratory distress syndrome (ARDS), capillary leak, hypotension and multi-organ failure.

In severe COVID-19 it marks the hyperinflammatory phase, with raised IL-6 and ferritin and a tendency to microvascular thrombosis, and the same mechanism drives the lethal pneumonias of highly pathogenic avian influenza and is thought to have contributed to the exceptional mortality of the 1918 influenza pandemic. Because the damage is immune-mediated, treatment targets the response, with corticosteroids and IL-6 blockade in the most inflamed patients.

Adaptive immunity removes virus-infected cells through several non-redundant mechanisms.

Cytotoxic T lymphocyte (CTL) killing. CD8+ CTLs recognise viral peptides on MHC class I of infected cells. After priming by a mature dendritic cell (with CD4+ help via CD40), effector CTLs kill by perforin and granzyme (synapse formation, pore-forming perforin, granzyme serine proteases driving caspase-mediated apoptosis) and by Fas ligand (FasL)–Fas (CD95), which assembles the death-inducing signalling complex and activates caspase-8. One CTL kills several targets serially.

Antibody-driven killing. Three routes. Neutralisation: IgG and secretory IgA bind viral glycoproteins and block receptor binding, uncoating, or fusion, the dominant means of preventing new infection. Antibody-dependent cellular cytotoxicity (ADCC): IgG on the infected-cell surface is recognised by natural killer (NK) cell CD16 (FcγRIII), triggering perforin and granzyme release. Complement: IgG and IgM activate the classical pathway via C1q, depositing C3b and assembling the membrane attack complex (MAC, C5b–C9).

Macrophage activation by CD4+ Th1 cells. Th1 cells secrete IFN-γ, which activates macrophages, upregulates MHC class I on bystander cells for CTL recognition, and recruits further effectors.

Intracellular antibody-mediated immunity (TRIM21). When antibody-coated virions reach the cytoplasm (a non-enveloped virus crossing the endosomal membrane), the intracellular Fc receptor TRIM21 ubiquitinates the antibody–virus complex for proteasomal degradation and activates innate sensors. It acts against adenoviruses and other antibody-coated non-enveloped viruses.

Clinical anchor. Patients with B cell defects (X-linked agammaglobulinaemia) clear most acute infections by CTL killing but cannot prevent re-infection and are uniquely vulnerable to enteroviruses; patients with T cell defects (SCID, DiGeorge) fail to mount CTL responses and die from disseminated herpesvirus disease and giant-cell measles pneumonitis. Each arm controls a distinct set of viral infections.

Virus-associated haemophagocytic lymphohistiocytosis (HLH) is a hyperinflammatory syndrome in which the immune response, rather than the virus itself, drives the disease.

It is the extreme of the hyperinflammatory axis: a relentless, self-sustaining activation of CD8 cytotoxic T cells and macrophages. Normally the cytotoxic response kills infected cells and then terminates itself through perforin-dependent killing; when that off-switch fails, through an inherited defect of the perforin pathway (familial HLH) or an acquired one, the response cannot be shut down.

The activated lymphocytes and macrophages pour out cytokines (interferon gamma, interleukin-6, tumour necrosis factor and others) in a self-amplifying loop. Activated macrophages then engulf the host’s own blood cells (haemophagocytosis) in the bone marrow, spleen and liver, producing the progressive cytopenias.

Epstein-Barr virus (EBV) is the commonest viral trigger, infecting T or natural killer (NK) cells and driving continuous cytokine production, often in a host with an underlying defect of perforin-dependent killing. Cytomegalovirus is another, particularly in the immunocompromised.

Because the immune response is the disease, immunosuppression is therapeutic (immunomodulation, and etoposide-based protocols when severe) while the triggering infection is treated, a reversal of the usual principle that immunosuppression worsens infection.

T cells see short peptides displayed by major histocompatibility complex (MHC) molecules. The pathway a peptide takes determines which MHC class presents it and which T cell subset inspects it.

MHC class I (endogenous) pathway. Every nucleated cell samples its own cytoplasmic proteins, including viral ones. Ubiquitin-tagged proteins are degraded by the proteasome into 8 to 11-residue peptides (interferon induces the immunoproteasome). Peptides enter the endoplasmic reticulum via the transporter associated with antigen processing (TAP), where calnexin, calreticulin, ERp57, and tapasin load them onto nascent MHC class I for CD8+ inspection. The groove is closed at both ends.

MHC class II (exogenous) pathway. Restricted to professional antigen-presenting cells (APCs): dendritic cells, macrophages, B cells. Extracellular antigen is taken up and digested by cathepsins into longer peptides (13 to 18 residues). The invariant chain blocks the groove until cathepsins trim it to CLIP, and HLA-DM swaps CLIP for antigenic peptide, presented to CD4+ helper T cells. The groove is open-ended.

Cross-presentation. The specialised cDC1 diverts extracellular viral antigen into the class I pathway, priming CD8+ T cells against viruses that do not infect dendritic cells directly, essential for hepatotropic and other tissue-restricted viruses primed in the draining lymph node.

CD1 and class Ib molecules. CD1 presents lipid and glycolipid antigens to unconventional T cells; class Ib molecules (HLA-E, HLA-F, HLA-G) present restricted peptides and regulate NK cells and feto-maternal tolerance.

Clinical anchor. TAP1 or TAP2 deficiency abolishes class I loading, giving chronic necrotising granulomatous skin lesions; severe viral disease is less profound than expected because cross-presentation and NK defence partly compensate.

(a) The B cell receptor (BCR). A membrane-anchored immunoglobulin (membrane IgM with IgD on a naïve cell), whose variable regions match the antibody the cell will secrete. Unlike the T cell receptor (TCR), which sees a processed peptide on MHC, the BCR binds native antigen directly; antigen cross-links it, triggering internalisation and presentation on MHC class II for T helper recognition.

(b) B cell epitopes. The surface an antibody binds. They are usually conformational (residues distant in sequence but folded together) and require native conformation, so denaturation often destroys antibody binding (relevant in Western blot) without affecting T cell recognition. Only some epitopes are exposed on the intact virion and so relevant to neutralising antibody.

(c) T-dependent and T-independent activation. Activation needs two signals: signal 1 is BCR cross-linking; signal 2 is either CD4+ help (T-dependent) or strong innate or repetitive-antigen co-stimulation (T-independent). T-dependent activation dominates for all protein (viral) antigens: the B cell presents peptide on class II to T follicular helper (Tfh) cells in a germinal centre, which deliver CD40 ligand and cytokines, driving hypermutation, affinity maturation, class switching, and memory. T-independent activation serves repetitive polymers (polysaccharides, capsids), producing mainly IgM with poor memory, which is why conjugate vaccines that add a protein carrier work where plain polysaccharide vaccines fail in infants.

(d) Class switching. The heavy-chain constant region sets isotype; switching substitutes IgM for IgG, IgA, or IgE while preserving specificity. It is a DNA recombination catalysed by activation-induced cytidine deaminase (AID), directed by cytokine context: IFN-γ to IgG1/IgG3, IL-4 to IgE, and TGF-β and the mucosal milieu to IgA. Defective switching causes hyper-IgM syndrome (X-linked CD40 ligand deficiency, or AID deficiency): only IgM, with severe Pneumocystis, cryptosporidium, and disseminated CMV.

A complete answer covers what defines a bNAb, the conserved epitope classes on Env, why the antibodies are so hard to elicit, and their therapeutic, preventive, and vaccine implications.

Definition. A broadly neutralising HIV antibody neutralises a wide cross-section of HIV-1 isolates across genetic clades, conventionally at least 50% of a pseudovirus panel. They arise spontaneously in around 10 to 20% of infected individuals, typically after two or more years of chronic viraemia.

Major epitope classes. The Env trimer of gp120 and gp41 carries six conserved targets: the CD4 binding site (VRC01, 3BNC117, N6); the V1V2 apex (PG9, PG16, CAP256-VRC26); the V3 glycan supersite at the N332 glycan (PGT121, 10-1074); the MPER of gp41 (2F5, 10E8, often autoreactive); the fusion peptide (VRC34); and the gp120–gp41 interface (PGT151, 8ANC195).

Why hard to elicit. Env defends through a glycan shield (about half its surface mass is host glycan), conformational masking of functional epitopes, hypervariable decoy loops, and a need for extreme somatic hypermutation (20 to 40% divergence from germline versus about 5% typically), requiring years of germinal-centre cycling.

Therapeutic and preventive use. Passive infusion (VRC01, 3BNC117, 10-1074) lowers viraemia and is explored for functional cure. The AMP trials showed VRC01 protected against neutralisation-sensitive viruses, proof of concept for prevention; triple-bNAb cocktails and Fc LS mutations for twice-yearly dosing are in development.

Vaccine implications. Inducing bNAbs is the central HIV vaccine challenge. Germline-targeting immunogens (eOD-GT8) activate VRC01-class precursors, and sequential immunisation then drives maturation. Earlier approaches reached at best 31% efficacy (RV144).

Hepatitis C virus (HCV) establishes chronic infection in 70 to 80% of exposed adults despite a vigorous innate and adaptive response. The paradox is resolved by integrated evasion at the innate, humoral, and cellular levels.

Innate immune evasion

NS3/4A cleavage of MAVS and TRIF. The NS3/4A serine protease cleaves both the viral polyprotein and two host interferon adaptors. Cutting MAVS (mitochondrial antiviral signalling protein) abolishes RIG-I/MDA5-driven IFN-β induction; cutting TRIF abolishes TLR3-driven induction. The infected hepatocyte cannot mount a type I interferon response. NS3/4A is also the target of the -previr drugs (glecaprevir, voxilaprevir). PKR inhibition. NS5A and E2 bind and inhibit protein kinase R (which phosphorylates eIF-2α to halt translation), preserving viral translation. Downstream sabotage. HCV induces SOCS1/SOCS3 and STAT1 hypomethylation, blunting JAK-STAT responses to interferon. ISG paradox. High pre-treatment intrahepatic ISG expression and plasma CXCL10 (IP-10) predict poor interferon-α response, reflecting a saturated, exhausted antiviral system; linked to the IFNL3 (IL28B) locus, where the rs12979860 CC genotype favours clearance and response. NK suppression. E2 cross-links CD81 on natural killer (NK) cells, inhibiting NK function and dendritic cell maturation.

Humoral evasion

HVR1 escape. Hypervariable region 1 of E2 is the immunodominant neutralising target and mutates within weeks under antibody pressure. Quasispecies. NS5B lacks proofreading (mutation rate ~10⁻⁴ to 10⁻⁵; about 10¹² virions per day), so escape variants pre-exist in the swarm. Glycan shielding of E1/E2 conserved epitopes and cell-to-cell spread further evade neutralising antibody.

Cellular evasion

CD4+ help failure is the hallmark of progression to chronicity: a broad, sustained CD4+ response predicts resolution, and its loss collapses CD8+ proliferative capacity. CD8+ exhaustion follows chronic antigen exposure, with PD-1, TIM-3, LAG-3 and CTLA-4 upregulation, lost cytokine production (IFN-γ, IL-2, TNF) and reduced cytotoxicity (as in chronic HBV, LCMV and cancer). CTL escape mutations in immunodominant epitopes expand in the quasispecies. Treg expansion in the liver dampens effector function. The core protein binds C1qR to directly inhibit T cells, and dendritic cell dysfunction (plasmacytoid and conventional) impairs interferon and antigen presentation.

The tolerogenic liver compounds these as a viral sanctuary. Because innate sensing, antibody and T cell arms are all disabled, sterilising immunity does not follow natural clearance (reinfection occurs in PWID, MSM and chimpanzees) and direct-acting antiviral (DAA) cure does not protect against reinfection, with direct implications for vaccine design and elimination.

The latent reservoir is the population of cells carrying integrated, transcriptionally silent but replication-competent provirus, from which infection rebounds if therapy stops. It is the central obstacle to curing HIV.

What and where. The best-characterised reservoir is the long-lived resting memory CD4+ T cell (central, transitional and effector memory subsets), but provirus also persists in tissue macrophages and in sanctuary sites such as lymphoid tissue and the central nervous system. It is established within days of infection, before therapy can realistically begin, which is why even very early ART does not prevent it.

Why it persists. Once integrated, the silent provirus is invisible to the immune system and unaffected by antiretrovirals (which block new infection, not established proviral DNA). The reservoir is maintained by the normal homeostatic proliferation and antigen-driven clonal expansion of the memory T cells that harbour it, so it is remarkably stable over decades.

Intact versus defective. The great majority of persisting proviruses are defective (hypermutated or deleted) and cannot rebound; only a small intact fraction is rebound-competent. Measuring the clinically relevant reservoir is therefore difficult: the quantitative viral outgrowth assay and the intact proviral DNA assay attempt to quantify the replication-competent pool, while total proviral DNA overestimates it.

Clinical consequence. Stopping suppressive ART is followed by viral rebound within about two to three weeks, confirming lifelong infection. Cure research targets the reservoir directly: latency reversal (“shock and kill”), latency-promoting “block and lock”, broadly neutralising antibodies, and gene therapy.

The defences fall into four layers: barriers, recognition machinery, soluble and cellular effectors, and cell-death programmes.

Barriers. Intact skin and the mucosal epithelium of the respiratory, gastrointestinal, and urogenital tracts block viral entry. Mucociliary clearance, gastric acid, bile, lysozyme, and pulmonary surfactant reduce the inoculum reaching the underlying immune system, all before any immune cell is involved.

Recognition. Infected and sentinel cells detect pathogen-associated molecular patterns (PAMPs) through germline-encoded pattern-recognition receptors (PRRs), in four families: Toll-like receptors (TLRs) on the surface (TLR2, TLR4) and in endosomes (TLR3 for double-stranded RNA, TLR7 / TLR8 for single-stranded RNA, TLR9 for unmethylated CpG DNA); cytoplasmic RIG-I-like receptors (RIG-I for short 5’-triphosphate dsRNA, MDA5 for long dsRNA); the cytoplasmic cGAS–STING pathway, detecting viral DNA; and NOD-like receptors (NLRs) assembling inflammasomes (NLRP3, AIM2). Engagement converges on IRF3, IRF7, and NF-κB, driving interferon and inflammatory cytokine production.

Soluble effectors. Type I interferons (IFN-α, IFN-β) act through IFNAR to switch on hundreds of interferon-stimulated genes (ISGs) via JAK–STAT, blocking replication at multiple steps: protein kinase R (PKR) shuts down translation, 2’–5’ OAS / RNase L degrades viral RNA, Mx GTPases block nuclear import, IFITM proteins block fusion. Type III (IFN-λ) acts on epithelium; type II (IFN-γ), from T and natural killer (NK) cells, activates macrophages and amplifies the type I response. Restriction factors, constitutively expressed and interferon-boosted, add to this: TRIM5α blocks early HIV-1 uncoating, APOBEC3G hypermutates retroviral cDNA, tetherin (BST-2) holds budding virions on the surface, and SAMHD1 depletes the dNTP pool needed for reverse transcription.

Cellular effectors. Phagocytes (macrophages, dendritic cells, neutrophils) engulf virions and debris; dendritic cells carry viral antigen to draining lymph nodes and prime the adaptive response, the critical innate-adaptive link. NK cells lyse infected cells by perforin and granzyme, recognising them through missing-self (loss of MHC class I) and stress-induced ligands (MICA, MICB).

Cell death. Apoptosis (caspase-mediated, silent), necroptosis (RIPK1 / RIPK3 / MLKL), and pyroptosis (inflammasome, caspase-1, gasdermin D pores, IL-1β release) all remove infected cells, pyroptosis additionally recruiting further immune cells. Every layer is triggered by viral PAMPs through PRRs or by cellular stress signals (DAMPs); the integration of these signals over the first hours determines whether infection is contained and programmes the adaptive response.

A complete answer covers the principle of passive immunisation, how monoclonal antibodies are made and engineered, the licensed preventive and therapeutic indications, the mechanisms of protection, and the limitations that constrain use.

Principle. A monoclonal antibody (mAb) is a population of antibodies of a single defined specificity. Given therapeutically, it provides immediate, defined-specificity humoral protection without depending on the recipient’s own B cell response: passive immunisation, the modern descendant of serum therapy.

Production and engineering. The original method (Köhler and Milstein, 1975) fuses an immunised mouse B cell with a myeloma cell to make an immortal hybridoma. Modern methods add phage display, single-B-cell sequencing from convalescent donors, and transgenic mice with human immunoglobulin loci. Engineering reduces immunogenicity along a ladder from murine (-omab) to chimeric (-ximab), humanised (-zumab), and fully human (-umab). The Fc region can be engineered to extend half-life (YTE and LS mutations enhance neonatal Fc receptor binding), to enhance ADCC (afucosylation), or to abolish effector function.

Prevention. Palivizumab (anti-RSV F glycoprotein) gives monthly prophylaxis in high-risk infants; nirsevimab adds an extended half-life so a single dose covers a season, with trial efficacy around 80% against medically attended RSV lower respiratory tract infection. Tixagevimab–cilgavimab was licensed for pre-exposure prophylaxis in profoundly immunocompromised adults until the Omicron variants escaped both antibodies.

Treatment. SARS-CoV-2 cocktails (casirivimab–imdevimab, sotrovimab, bebtelovimab) were each withdrawn as variants escaped their epitopes, the textbook demonstration of variant escape. Ebolavirus: Inmazeb (a three-mAb cocktail) and ansuvimab (single mAb) are licensed for Zaire ebolavirus, validated in the PALM trial. HIV-1: ibalizumab, an anti-CD4 entry inhibitor, treats multidrug-resistant infection, and broadly neutralising antibodies (VRC01, 3BNC117) are in trials.

Mechanisms. Neutralisation (blocking receptor binding, fusion, or uncoating) is dominant; ADCC via NK cell CD16 and complement activation also contribute; ibalizumab acts by receptor blockade.

Limitations. Variant escape (mitigated by non-overlapping-epitope cocktails), high cost of mammalian-cell production, parenteral administration, and finite half-life (extended by Fc engineering). mAbs are most valuable when a vaccine would be too slow (post-exposure rabies, ebolavirus), the recipient cannot respond (immunocompromised, infants), or the target is highly conserved (RSV F glycoprotein), so they complement rather than replace small-molecule antivirals and vaccines.

A complete answer centres on clonal, cell-associated persistence.

Persistence and spread. After reverse transcription and integration, HTLV-1 makes little infectious free virus. It spreads between cells by direct contact at the virological synapse, and it persists chiefly by driving the infected T cell to divide, so the provirus is copied by the host’s own machinery and passed to both daughter cells (clonal, mitotic spread). Host replication, not the viral enzyme, therefore maintains the infection and keeps the genome stable.

Why reverse-transcriptase inhibitors do not help. Established infection is sustained by proliferation of already-infected clones, not by ongoing reverse transcription, so inhibitors of reverse transcriptase and integrase do not lower the proviral load or treat the associated diseases; their only role is post-exposure prophylaxis, before integration is established.

NK cells recognise infected cells through three mechanisms.

Missing-self. Healthy cells display MHC class I, which engages NK inhibitory receptors (killer-cell immunoglobulin-like receptors, KIRs; and CD94 / NKG2A) and switches off cytotoxicity, so normal cells are spared. Many viruses, notably herpesviruses, downregulate MHC class I to escape CD8+ cytotoxic T cells; this loss removes the inhibitory signal and the cell is killed. The hypothesis was proposed by Klas Kärre in 1986.

Stress-induced ligands. Infected cells upregulate MICA, MICB, and the ULBP proteins, recognised by the activating receptor NKG2D; the natural cytotoxicity receptors NKp30, NKp44, and NKp46 are further activating receptors. Their engagement tips the balance towards killing even if some MHC class I remains.

Antibody-dependent cellular cytotoxicity (ADCC). CD16 (FcγRIII) binds IgG bound to viral antigens on the infected surface, triggering perforin and granzyme release independently of MHC class I and linking NK killing to the humoral response once virus-specific IgG is available.

The killing decision is the balance of activating and inhibitory signals: in a normal cell inhibition dominates; in an infected cell MHC class I loss reduces inhibition while stress ligands raise activation, and the NK cell kills through perforin and granzyme.

Chronic hepatitis C virus (HCV) drives a spectrum of B cell disorders from benign polyclonal expansion through mixed cryoglobulinaemia to overt B cell non-Hodgkin lymphoma (NHL).

Pathogenesis. The dominant mechanism is chronic B cell stimulation by HCV antigens: E2 binds CD81 on B lymphocytes, driving polyclonal then oligoclonal then monoclonal expansion. A subset acquires further genetic lesions (most often t(14;18) BCL2 rearrangement) and progresses to lymphoma.

Spectrum. Polyclonal expansion, then type II mixed cryoglobulinaemia, then marginal zone lymphoma (splenic, nodal, or extranodal; the commonest HCV-associated NHL), and less often lymphoplasmacytic lymphoma or diffuse large B cell lymphoma (usually transformation of indolent disease). Around ~5 to 10% of those with mixed cryoglobulinaemia progress to overt lymphoma.

Clinical features. B symptoms, lymphadenopathy, splenomegaly, cytopaenias, extranodal disease (parotid, stomach, skin).

Diagnosis. Tissue biopsy with histology, flow cytometry and cytogenetics. Screen all newly diagnosed B cell NHL for HCV, and HCV-associated cases for human immunodeficiency virus (HIV) and hepatitis B virus (HBV) before any rituximab (the highest-risk drug for HBV reactivation).

Treatment. Direct-acting antiviral (DAA) therapy regresses indolent HCV-associated lymphomas (notably splenic marginal zone lymphoma), with a haematological response in around half. Combined DAA plus rituximab is standard for aggressive disease, with mandatory tenofovir or entecavir prophylaxis in any HBsAg- or anti-HBc-positive patient.

The cGAS–STING pathway is the principal cytosolic DNA-sensing pathway in mammalian cells.

The mechanism in three steps:

1. Detection. Cyclic GMP-AMP synthase (cGAS) is a cytosolic enzyme that binds double-stranded DNA in a sequence-independent manner. Any DNA in the cytoplasm activates it: viral DNA from herpesviruses or DNA viruses, retroviral cDNA intermediates from HIV, mitochondrial DNA that has leaked out, or fragments of damaged self-DNA.
2. Second messenger. Activated cGAS catalyses the synthesis of the cyclic dinucleotide 2’3’-cGAMP (cyclic guanosine monophosphate–adenosine monophosphate) from ATP and GTP.
3. STING activation. cGAMP binds the stimulator of interferon genes (STING), a transmembrane protein anchored in the endoplasmic reticulum. STING traffics from the ER to the Golgi, recruits and activates the kinase TBK1, which phosphorylates IRF3. Activated IRF3 translocates to the nucleus and drives transcription of type I and type III interferons.

The cGAS–STING axis is also responsible for the type I interferon response to retroviral reverse-transcription intermediates (an important innate barrier to HIV) and is a major contributor to the interferonopathies seen in conditions such as Aicardi–Goutières syndrome, where impaired clearance of self-derived cytosolic nucleic acids leads to chronic activation of the pathway.

The other options describe correct molecules in the wrong roles: RIG-I and MDA5 sense cytosolic RNA (not DNA); TLR9 senses unmethylated CpG DNA in endosomes (not the cytoplasm); and the NLRP3 inflammasome triggers pyroptosis rather than the IRF3-driven interferon response.

The behaviour of an NK cell is governed by the balance between activating receptors (such as NKG2D, which recognises stress-induced ligands MICA and MICB) and inhibitory receptors (such as the killer-cell immunoglobulin-like receptors, KIRs, and CD94 / NKG2A, which all recognise MHC class I).

In a healthy cell, MHC class I is constitutively displayed and engages the inhibitory receptors, switching off NK cytotoxicity. Many viruses, especially the herpesviruses, downregulate MHC class I to escape recognition by CD8+ cytotoxic T cells. This is, however, a double-edged strategy: the loss of MHC class I removes the inhibitory signal to NK cells, and the cell becomes a target for missing-self killing. The hypothesis was formalised by Klas Kärre in 1986.

This is why some herpesviruses (most notably human cytomegalovirus) have evolved a second layer of evasion: HCMV’s UL18 protein is a class I MHC homologue that engages the NK inhibitory receptor LIR-1 with high affinity, restoring the inhibitory signal without making the cell visible to cytotoxic T cells.

The other options describe mechanisms that do not occur in this scenario: NK cells do not require MHC class II, do not require antibody for direct missing-self killing, and are not inhibited by interferon (interferon enhances NK activity).

A dendritic cell not infected by the virus has no viral protein in its cytoplasm to load onto MHC class I, so cross-presentation is what allows a CD8+ response against viruses that spare dendritic cells (hepatitis B, which replicates only in hepatocytes, is the classic example). The subset that performs it is the conventional dendritic cell type 1 (cDC1), marked in humans by CD141 (BDCA3), XCR1, and CLEC9A, and dependent on the transcription factors IRF8 and BATF3. It takes up antigen from infected cells and diverts it onto MHC class I by a cytosolic route (endosome to proteasome to TAP) or a vacuolar route (endosomal cathepsin loading onto recycling class I).

Plasmacytoid dendritic cells are the principal type I interferon producers, not cross-presenters; cDC2 and Langerhans cells specialise in MHC class II presentation to CD4+ cells; monocyte-derived dendritic cells do not specialise in cross-presentation.

IRF8 deficiency abolishes the cDC1 lineage and produces severe susceptibility to mycobacteria and viruses. cDC1-targeting vaccine strategies (anti-CLEC9A antigen fusions) aim to boost CD8+ responses.

Original antigenic sin is the host phenomenon in which memory of the first viral encounter dominates the response to later, related variants. Memory B cells recognising shared (cross-reactive) epitopes outcompete naïve B cells for antigen and Tfh help, so the boosted antibody is biased toward the priming strain even when the dominant neutralising epitopes have changed. If the new variant’s protective epitopes are not shared, the response is serologically impressive but clinically ineffective.

The distractors name different concepts. Antigenic drift is the gradual point-mutation of surface glycoproteins (a property of the virus), and antigenic shift the abrupt reassortment of a whole gene segment; both describe the virus, not the host response. Antibody-dependent enhancement is the downstream harm when cross-reactive, poorly neutralising antibody enhances rather than blocks infection, the textbook mechanism of severe secondary dengue. Heterologous immunity is cross-protection between unrelated viruses through cross-reactive memory T cells.

Universal influenza vaccine strategies try to circumvent the effect by directing the response toward conserved epitopes (the haemagglutinin stalk, the matrix protein) shared across strains.

The clinical pattern here, a previously healthy child who develops herpes simplex encephalitis (HSE) after primary HSV-1 infection while controlling other infections normally, points to a specific inborn error of immunity.

The biology. TLR3 sits on the endosomal membrane of cortical neurons, oligodendrocytes, and astrocytes in the central nervous system. It binds double-stranded RNA, which is generated during HSV-1 replication, and signals through the adaptor TRIF to activate IRF3 and produce type I and type III interferons. This localised interferon response is essential for restricting HSV-1 spread in the central nervous system.

The genetic syndrome. Autosomal-recessive or autosomal-dominant loss-of-function mutations in TLR3, or in its downstream signalling proteins UNC93B1 and TRIF, predispose specifically to herpes simplex encephalitis in children with primary HSV-1 infection. Patients control HSV at peripheral sites (skin, mucosa) normally, because peripheral defence relies on other pattern-recognition pathways, particularly the cytosolic cGAS–STING pathway and IFN-α / β from plasmacytoid dendritic cells.

Implication for the wider immunology of antiviral defence. This syndrome demonstrates two general principles. First, pattern- recognition receptor pathways are not redundant: a single sensor can be essential for control of a specific virus at a specific anatomical site. Second, the innate response is compartmentalised by tissue: the CNS relies more heavily on TLR3-mediated type III interferon than the periphery, which is why a partial defect in this pathway manifests as an organ-specific phenotype rather than a systemic immunodeficiency.

Similar tissue- and virus-specific susceptibilities have been identified for STAT1 mutations (mycobacterial and viral disease), IFNAR1 / IFNAR2 deficiency (severe disease from live-attenuated viral vaccines), and the more recently described autoantibodies against type I interferons in severe COVID-19.

Natural killer (NK) cells are governed by the balance between activating receptors (which detect stress-induced ligands such as MICA / MICB) and inhibitory receptors (which detect MHC class I on healthy cells). When a virus downregulates the host’s own MHC class I to escape CD8+ cytotoxic T cell recognition, the cell loses its inhibitory signal to NK cells and is killed by the missing-self mechanism. Several viruses circumvent this by encoding their own MHC class I homologues, which engage NK inhibitory receptors and restore the inhibitory signal without making the cell visible to cytotoxic T cells.

Viral mechanisms of NK evasion:

A well-characterised example is the HCMV protein UL18, a class I MHC homologue that binds the NK inhibitory receptor LIR-1 with very high affinity, suppressing NK cytotoxicity even when the virus has simultaneously downregulated genuine cellular MHC class I to escape CD8+ T cells. This dual strategy is why human cytomegalovirus is particularly dangerous in patients with profound T cell deficiency (transplant recipients, advanced HIV) and in congenital infection.

HAM/TSP (human T-lymphotropic virus type 1 [HTLV-1]-associated myelopathy / tropical spastic paraparesis) is a slowly progressive inflammatory myelopathy. It presents as a spastic paraparesis with brisk reflexes, bladder dysfunction and back pain, driven by immune-mediated infiltration of the thoracic spinal cord.

It is not a flaccid or acute process, not a peripheral neuropathy, not an optic neuritis, and not a cerebellar syndrome.

Natural killer cells kill cells that have lost class I, the “missing-self” signal. HCMV restores an inhibitory signal by expressing a class I homologue (UL18) and by supplying a peptide that stabilises HLA-E, both of which engage NK inhibitory receptors. The cell therefore escapes both cytotoxic T cell recognition, through loss of classical class I, and natural killer recognition, through the decoys.

Blocking degranulation, suppressing interferon and recruiting complement regulators are real viral tactics but do not answer missing-self, and upregulating activating ligands would invite NK killing, not prevent it.

Hepatitis A virus (HAV) is not directly cytopathic. Very high viral loads accumulate in the liver well before any biochemical or histological evidence of injury, and the ALT rise coincides with the appearance of anti-HAV immunoglobulin M (IgM) and the cellular immune response.

The injury is immune-mediated, predominantly by CD8 cytotoxic T cells and multifunctional CD4 T cells acting on infected hepatocytes. This also explains why hepatitis A is self-limiting: once the adaptive response clears infected hepatocytes, no reservoir remains.

Restriction factors are host proteins continuously expressed in many cell types and further upregulated by interferon. Each blocks a specific step of viral replication. The presence of a virus-encoded counter-evasion protein for each restriction factor is strong evidence of their functional importance.

The correct pairing is tetherin (BST-2), which holds budding virions on the cell surface. The distractors swap real mechanisms to wrong factors: APOBEC3G is the cytidine deaminase, TRIM5α targets capsid uncoating, SAMHD1 depletes the dNTP pool, and IFITM3 blocks membrane fusion.

T follicular helper (Tfh) cells provide the cognate help a B cell needs for a productive germinal centre response. Positioned in the B cell follicle by the chemokine receptor CXCR5 and the master transcription factor Bcl-6, their dominant cytokine output is IL-21, which supports somatic hypermutation, affinity maturation, and class switching.

Th1 (IFN-γ, T-bet) activates macrophages and supports CD8+ cytotoxic responses; Th2 (IL-4, GATA-3) drives helminth and allergic responses; Th17 (IL-17 and IL-22, RORγt) defends against extracellular bacteria and fungi; regulatory T cells (IL-10 and TGF-β, FoxP3) restrain responses and maintain self-tolerance. None supplies the germinal centre B cell help that defines Tfh.

Defects in the transcription factor STAT3 abolish Th17 development and produce hyper-IgE (Job) syndrome, with recurrent Staphylococcus aureus skin and lung infection. FoxP3 mutations cause IPEX (immunodysregulation polyendocrinopathy enteropathy X-linked), where loss of regulatory T cells drives severe autoimmunity in infancy.

The MHC class II (exogenous) pathway samples proteins taken up from outside the cell, and is restricted to professional antigen-presenting cells: dendritic cells, macrophages, and B cells. Antigen is endocytosed and cleaved by cathepsins in acidifying endosomes. Nascent class II carries the invariant chain (Ii), which blocks the groove; in the late endosomal compartment cathepsins trim it to a fragment called CLIP (class II-associated invariant chain peptide), and the chaperone HLA-DM swaps CLIP for an antigenic peptide before the complex reaches the surface.

Option A is the class I (endogenous) pathway; cross-presentation (D) is real but loads exogenous antigen onto class I, not class II; options B and E are fictitious.

Bare lymphocyte syndrome type II (mutations in CIITA, RFX5, RFXANK, or RFXAP) abolishes MHC class II expression: affected patients cannot prime CD4+ responses and develop a combined immunodeficiency that is fatal without haematopoietic stem cell transplantation.

The MHC class I (endogenous) pathway samples cytoplasmic proteins, including viral proteins made by an infected cell. Ubiquitin-tagged proteins are degraded by the proteasome into 8 to 11-residue peptides (interferon induces the immunoproteasome for class I-optimised peptides); the transporter associated with antigen processing (TAP) moves them into the endoplasmic reticulum, where calnexin, calreticulin, ERp57, and the adaptor tapasin load them onto nascent MHC class I for trafficking to the surface and CD8+ inspection.

Option A is the class II pathway; autophagy (B) delivers cytoplasmic material to lysosomes, not to class I; options C and D are fictitious.

TAP deficiency abolishes class I peptide loading, giving low surface MHC class I, chronic necrotising granulomatous skin lesions, and recurrent bacterial sinopulmonary infection. Viral disease is milder than expected because cross-presentation and NK cell missing-self recognition partly compensate.

Tissue-resident memory T cells (TRM), marked by CD103 and CD69, sit permanently in the tissue and can contain a local re-infection within minutes, before circulating cells could be recruited from the blood. Most viral infections enter through a mucosal or cutaneous surface, so this positioning matters: skin TRM suppress varicella-zoster reactivation, lung TRM give heterosubtypic influenza protection, and genital-tract TRM control herpes simplex virus type 2 recurrences.

Central and effector memory cells recirculate or patrol rather than residing at a fixed site; long-lived plasma cells are a B lineage; plasmacytoid dendritic cells are innate.

Tissue TGF-β drives CD103 expression and TRM commitment, and IL-15 maintains them long-term. Because parenteral vaccines induce mainly central memory and serum antibody, interest in intranasal and mucosal vaccines is driven largely by the need to seed TRM at the portal of entry.

The inflammasome is a cytosolic multiprotein complex that acts as a threshold sensor for intracellular danger. It consists of a sensor protein (such as NLRP3 or AIM2), the adaptor ASC, and pro-caspase-1.

Triggering:

• NLRP3 responds to a broad set of stress signals: viral replication intermediates, mitochondrial dysfunction, reactive oxygen species, potassium efflux, and lysosomal rupture.
• AIM2 binds cytosolic double-stranded DNA directly.

On activation the sensor oligomerises, recruits ASC through pyrin domain interactions, and ASC in turn recruits pro-caspase-1. Pro-caspase-1 self-cleaves into active caspase-1, which then cleaves two key substrates:

1. Pro-IL-1β and pro-IL-18 are cleaved into the mature pro-inflammatory cytokines IL-1β and IL-18, which are then released into the extracellular space.
2. Gasdermin D (GSDMD) is cleaved, and its N-terminal fragment oligomerises and inserts into the plasma membrane, forming pores. The cell lyses, releasing its contents and amplifying inflammation.

This lytic, inflammatory form of cell death is pyroptosis, the loud counterpart to apoptotic silent removal. Pyroptosis is a major driver of the severe inflammatory phenotype of influenza, hantavirus pulmonary syndrome, and severe COVID-19. Several viruses encode inflammasome inhibitors to dampen the response (e.g. Kaposi sarcoma herpesvirus ORF63).

Inflammasome activation is distinct from the apoptosis (caspases 3, 6, 7) and necroptosis (RIPK1 / RIPK3 / MLKL) pathways, and it is independent of cytotoxic T cell engagement.

Type III interferons comprise IFN-λ1 (also called IL-29), IFN-λ2 (IL-28A), IFN-λ3 (IL-28B), and IFN-λ4, all encoded on human chromosome 19. They bind the receptor complex IFNLR1 + IL-10R2, which is expressed predominantly on epithelial cells of the respiratory and gastrointestinal tracts, on hepatocytes, and on melanocytes. This receptor distribution restricts IFN-λ action to the mucosal and hepatic compartments where it acts as a tissue- specific antiviral defence, with less of the systemic inflammation that accompanies type I interferon signalling on most cell types.

Downstream signalling uses the same JAK and STAT components as type I interferons, leading to the same antiviral interferon-stimulated genes, but the restricted receptor distribution and the somewhat prolonged induction profile of IFN-λ produce a different functional niche.

Clinical relevance. A single-nucleotide polymorphism in the IFN-λ3 / IFN-λ4 region is the strongest known host genetic predictor of:

• Spontaneous clearance of acute hepatitis C virus infection.
• Treatment response to the older interferon-based hepatitis C regimens (the CC genotype at rs12979860 predicts a much higher sustained virological response rate than the CT or TT genotypes).

IFN-λ has also attracted attention as a potential therapeutic for respiratory viral infections (including SARS-CoV-2), since it can restrict viral replication at the mucosal portal of entry without the systemic cytokine effects of type I interferon.

Inactivated whole-virus vaccines present killed antigen that never reaches the cytoplasm, so it is loaded onto MHC class II but poorly onto MHC class I. The intact surface epitopes make excellent neutralising antibody, but CD8+ cytotoxic T cell priming is weak, which is why these vaccines are usually adjuvanted (alum, MF59, AS04) and given as several doses. Inactivated polio, hepatitis A, rabies, and inactivated influenza are examples.

The other platforms generate endogenous antigen inside host cells and so prime both antibody and CD8+ responses: live-attenuated (MMR, oral polio), viral-vector (adenovirus-vectored COVID-19, rVSV Ebola), and mRNA (BNT162b2, mRNA-1273). DNA vaccines work on the same endogenous-antigen principle but need efficient delivery and have no widely licensed human product.

Platform choice follows the protective mechanism the target virus needs: antibody-dominant threats (rabies, hepatitis B, HPV) suit subunit or inactivated vaccines, while viruses that need CD8+ control favour live-attenuated, viral-vector, or mRNA platforms. Live-attenuated vaccines are contraindicated in profound immunocompromise.

A complete answer explains what avidity measures, how it changes after primary infection, and how that dates the infection.

What avidity measures. Avidity is the strength with which IgG binds its antigen. Antibody from a recent primary infection binds weakly (low avidity) and matures to high avidity over about the following six months as germinal-centre affinity maturation proceeds.

How it dates the infection. Low-avidity CMV IgG in early pregnancy indicates a primary infection within roughly the preceding three to four months, the window of highest risk for fetal transmission. High-avidity IgG indicates a past infection and a much lower risk to the fetus.

Why it matters. Avidity resolves the ambiguity of a positive CMV IgM, which can persist for months or be falsely positive, and so helps avoid unnecessary intervention when the infection is in fact long-standing.

• Core principle. A vaccine exposes the immune system to a non-pathogenic facsimile of a virus, priming the same memory pools as natural infection without causing disease, so re-exposure draws a fast memory response rather than a slow naïve one.
• Memory generated. Memory B cells, long-lived bone-marrow plasma cells, and memory CD4+ and CD8+ T cells (central, effector, and tissue-resident).
• Levels of protection. Sterilising immunity prevents infection (rare; HPV vaccines come close); disease prevention allows infection but blocks illness; severity reduction blocks only severe outcomes (as with drifting influenza and SARS-CoV-2).
• Mucosal versus systemic. Parenteral vaccines give serum IgG but little mucosal cover; live mucosal vaccines (oral polio, intranasal influenza) induce secretory IgA at the portal of entry and block transmission better.
• Herd immunity. Above a coverage threshold the effective reproductive number falls below one and transmission collapses; the threshold tracks R₀ (around 95% for measles), and it underpins eradication strategy. Only smallpox has been eradicated by vaccine.

A genome of around 20,000 genes must generate a receptor repertoire of more than 10¹² specificities. The solution is somatic recombination of immunoglobulin and T cell receptor gene segments, discovered by Susumu Tonegawa (Nobel Prize 1987).

• V(D)J recombination. Each variable region is assembled from a few segments drawn from large V (variable), D (diversity), and J (joining) pools, joined during lymphocyte development by RAG1 and RAG2 (recombination activating genes).
• Combinatorial diversity. Random selection of one V, D, and J segment; for the immunoglobulin heavy chain alone this gives thousands of combinations before any further diversity.
• Junctional diversity. Imprecise joining, with terminal deoxynucleotidyl transferase (TdT) adding random nucleotides and nucleases trimming others, at the antigen-contacting junction.
• Chain pairing and exclusion. Any heavy chain may pair with any light chain (multiplying diversity), while allelic exclusion keeps each cell to one specificity.
• Somatic hypermutation. After antigen encounter, AID (activation-induced cytidine deaminase) mutates rearranged V regions in germinal centres, the basis of affinity maturation.

Children with RAG1 or RAG2 mutations cannot complete V(D)J recombination and develop severe combined immunodeficiency (SCID), lacking both T and B cells; hypomorphic mutations cause Omenn syndrome.

• Definition. Cross priming (cross-presentation) is the loading of extracellularly acquired viral antigen onto MHC class I by dendritic cells, priming CD8+ cytotoxic T cells.
• The problem it solves. The class I pathway normally samples only the presenting cell’s own cytoplasmic proteins, so a virus that does not infect dendritic cells would otherwise leave them nothing to load and no way to prime a CD8+ response. Many important viruses fit this pattern: hepatitis B replicates only in hepatocytes, and rabies in muscle and neurons.
• The cell responsible. Almost exclusively cDC1 (conventional dendritic cell type 1), marked by CD141 (BDCA3), XCR1, and CLEC9A and dependent on IRF8; a minority of dendritic cells but essential for most antiviral CD8+ responses.
• Mechanism. Two routes: the cytosolic route, where antigen escapes the endosome to the cytoplasm and enters the proteasome–TAP–class I pathway, and the vacuolar route, where cathepsins process it in the endosome for loading onto recycling class I.
• Importance. It primes hepatitis B-specific CD8+ cells in the draining lymph node despite strict hepatotropism, and underlies the ability of protein-subunit vaccines to elicit cytotoxic responses.

A naïve response is the first encounter with an antigen; a memory response is every subsequent one. They differ in kinetics, magnitude, antibody quality, and effector readiness.

• Cellular substrate of memory. Long-lived bone-marrow plasma cells (years of antibody), memory B cells (rapid plasma-cell differentiation on re-exposure), and the three memory T cell subsets: central (TCM), effector (TEM), and tissue-resident (TRM).
• Why it matters. A naïve host lets a new virus replicate unopposed for days; a memory host shuts the same virus down at the inoculum, often without symptoms. Vaccines exploit this by laying down memory in advance.
• Clinical use. The IgM-to-IgG transition underlies serological staging: IgM with low-avidity IgG indicates recent primary infection, while high-avidity IgG without IgM indicates past infection.

Active immunity is generated by the host’s own immune system in response to antigen; passive immunity is conferred by transferring pre-formed antibody from another source.

• Natural active. Wild-type infection leaves lasting memory, protecting for decades against viruses without antigenic variation.
• Natural passive. Chiefly transplacental maternal IgG, protecting the newborn for around six to twelve months (and the reason live measles vaccine is deferred to 9 to 12 months), plus secretory IgA in colostrum.
• Combined active-plus-passive prophylaxis covers the gap when the inoculum has already arrived: rabies (immunoglobulin around the wound plus vaccine series), and the newborn of an HBsAg-positive mother (HBIG within 12 hours plus hepatitis B vaccine). Passive immunity buys time; active immunity provides durable protection.

Measles produces a spectrum of central nervous system (CNS) complications defined by when they appear after the acute illness, the host’s immune status, and whether active or defective measles virus (MeV) is present in the brain.

Key discriminators. Time after rash separates them first: ADEM in days to weeks, MIBE in months, SSPE in years. Host status separates them next: MIBE is the encephalitis of the immunocompromised, whereas SSPE strikes the previously immunocompetent young child. Presence of virus in the brain distinguishes the three pathologies: absent in ADEM (autoimmune), actively replicating in MIBE, and defective in SSPE. All three are largely preventable by measles vaccination.

A complete answer traces the route into the memory B-cell reservoir, then maps the programmes onto the tumours.

Establishing latency. After entry into a B cell (gp350/220 binding CD21), the virus runs its full growth programme (latency III) to drive the cell to proliferate. The infected cell passes through the germinal centre and settles as a resting memory B cell, which expresses essentially no viral genes (latency 0) and so is invisible to the immune system, expressing EBNA1 only when it divides (latency I). This memory B-cell pool is the lifelong reservoir; reactivation to the lytic cycle occurs when such a cell differentiates into a plasma cell.

Mapping programmes to tumours. The programme a tumour runs reflects its origin and its visibility to T cells:

• Latency I (EBNA1 only): Burkitt lymphoma and gastric carcinoma.
• Latency II (adds LMP1 and LMP2): nasopharyngeal carcinoma and Hodgkin lymphoma.
• Latency III (the full growth programme): the lymphomas of immunosuppression, including post-transplant and HIV-associated disease, which can only persist where T-cell control has failed.

Natural killer (NK) cells are large granular lymphocytes that lyse infected cells without prior sensitisation or antigen specificity. Innate but sharing a lineage with T cells, they act within the first one to two days, and are identified by CD56 (neural cell adhesion molecule, NCAM) and CD16 (the low-affinity IgG receptor, FcγRIII).

Their activity is set by two opposing sets of receptors. Activating receptors (the natural cytotoxicity receptors NKp30, NKp44, NKp46, and NKG2D) recognise stress-induced ligands such as MICA and MICB on infected or transformed cells. Inhibitory receptors (killer-cell immunoglobulin-like receptors, KIRs; and CD94 / NKG2A) recognise major histocompatibility complex (MHC) class I on healthy cells and switch off cytotoxicity.

With normal MHC class I, inhibition dominates and no killing occurs. Viruses commonly downregulate MHC class I to escape CD8+ cytotoxic T cells; this removes the inhibitory signal, activation dominates, and the NK cell kills, the missing-self hypothesis of Klas Kärre.

Killing uses preformed granules of perforin (forming pores in the target membrane) and granzymes (serine proteases that enter and trigger caspase-mediated apoptosis), unlike CD8+ T cells, which need activation and clonal expansion first. Activated NK cells also secrete IFN-γ, TNF-α, IL-4, and IL-13, which activate macrophages, recruit leukocytes, and shape the adaptive response, so NK cells clear virus both directly by cytolysis and indirectly through cytokine-mediated priming.

The first line of defence is the host’s outer surfaces, blocking virus before any immune cell is involved, grouped as physical and chemical.

Physical barriers. Intact keratinised, multilayered skin is impermeable to almost all viruses unless broken (injection, trauma, surgery, sexual contact, arthropod bite). The mucosal epithelium of the respiratory, gastrointestinal, and urogenital tracts is sealed by tight junctions. Mucociliary clearance traps inhaled particles in a mucus blanket and sweeps them out by ciliary beating. Eyelashes, eyebrows, and other hairs filter ocular and respiratory surfaces, and tears, saliva, urine, and intestinal peristalsis flush virions mechanically.

Chemical barriers. Low-pH gastric acid inactivates most ingested viruses except acid-resistant agents (enteroviruses, hepatitis A virus, rotavirus, norovirus). Bile salts act as detergents on enveloped viruses, one reason most enteric viruses are non-enveloped. Lysozyme in saliva, tears, and nasal secretions cleaves bacterial peptidoglycan and has direct activity against some enveloped viruses. Lactoferrin in milk, tears, and secretions sequesters iron and is directly antiviral. Surfactant proteins in the alveolar lining bind and neutralise viral glycoproteins.

These barriers are not absolute, but they reduce the inoculum reaching the immune system and shape which viruses establish infection through each route.

Interferons (IFNs) are cytokines released by virus-infected cells that signal to neighbouring cells and to the wider immune system. Alick Isaacs and Jean Lindenmann first described them in 1957, showing that influenza-infected cells released a non-viral protein that protected fresh cells from the same or an unrelated virus. They are classified into three types by the receptor they bind.

Type I (IFN-α, IFN-β). The principal direct antiviral interferons, produced by almost any cell detecting intracellular infection. Secreted IFN binds IFNAR on neighbouring cells, triggering JAK–STAT signalling and ISG expression that places the cell in an antiviral state (the bystander effect). IFN-α is used in chronic hepatitis B and C, IFN-β in relapsing multiple sclerosis.

Type II (IFN-γ). Not directly induced by viral infection; produced by activated T cells (especially Th1) and NK cells. It activates macrophages, recruits leukocytes, and amplifies type I effects, and is the major cytokine of cell-mediated immunity against intracellular pathogens.

Type III (IFN-λ). The most recently described family, encoded on chromosome 19, using a distinct receptor (IFNLR1) expressed mainly on epithelial cells of the respiratory and gastrointestinal tracts, on hepatocytes, and on melanocytes. It provides tissue-specific mucosal and hepatic defence with less systemic inflammation than type I. A single-nucleotide polymorphism near IFNL3, which influences hepatocyte receptor density, is the strongest predictor of spontaneous and treatment-induced hepatitis C clearance.

All three converge on ISG induction. Notable products: protein kinase R (PKR), shutting down host translation via eIF-2α; the 2’–5’ oligoadenylate synthetase (OAS) / RNase L system, degrading viral RNA; the Mx GTPases, blocking nuclear import; the IFITM proteins, blocking enveloped virus entry; and ISG15, a ubiquitin-like modifier with broad antiviral activity.

Three forms of programmed cell death that remove virus-infected cells but differ in machinery, inflammatory output, and which viruses inhibit each.

Apoptosis. Caspase-mediated and immunologically silent: the cell shrinks, chromatin condenses, the membrane stays intact, and the cell is phagocytosed before its contents leak. Two pathways converge on the effector caspases (3, 6, 7): the intrinsic (mitochondrial) pathway, where stress drives BAX / BAK pores, cytochrome c release, and assembly of the APAF-1 / pro-caspase-9 apoptosome; and the extrinsic (death receptor) pathway, where Fas, TNF receptor 1, and TRAIL receptors assemble the DISC to activate caspase-8. Many viruses block it (HSV ICP6 and CMV vICA inhibit caspase-8) to preserve their replication factory.

Necroptosis. A lytic, inflammatory backup triggered when caspase-8 is blocked, usually by a viral inhibitor: RIPK1 and RIPK3 form the necrosome, which phosphorylates MLKL; MLKL oligomerises into membrane pores, lysing the cell and releasing DAMPs that recruit immune cells. The sensor ZBP1 triggers it in influenza-infected cells.

Pyroptosis. Inflammasome-driven and highly inflammatory: NLRP3 (stress signals) and AIM2 (cytosolic DNA) recruit ASC and activate caspase-1, which cleaves pro-IL-1β and pro-IL-18 to their mature secreted forms and cleaves gasdermin D, whose N-terminal fragment forms membrane pores that lyse the cell and release the cytokines. It is implicated in severe influenza, hantavirus pulmonary syndrome, and severe COVID-19.

Apoptosis is silent removal, necroptosis the lytic backup when apoptosis is blocked, pyroptosis inflammatory inflammasome-linked death; the balance shapes both clearance and disease severity.

The innate system cannot recognise the unique antigens of any particular virus. Instead it detects conserved molecular signatures shared across whole classes of pathogens, using germline-encoded sensors.

Pathogen-associated molecular patterns (PAMPs) are conserved microbial structures absent from the host. The major viral PAMPs are nucleic-acid structures either absent from healthy human cells or present in unusual compartments: double-stranded RNA (a replication intermediate of many RNA viruses), single-stranded RNA in endosomes, unmethylated CpG-rich DNA, and 5’-triphosphate RNA. Some envelope glycoproteins and capsid proteins also act as PAMPs.

Damage-associated molecular patterns (DAMPs) are endogenous molecules released by stressed or dying host cells: HMGB1 (a chromatin protein), ATP, uric acid, and heat-shock proteins. They signal tissue damage regardless of any pathogen. Many DAMPs engage the same receptors as PAMPs, which is why infection and sterile injury both trigger an innate response.

Pattern-recognition receptors (PRRs) are the host’s germline-encoded sensors for PAMPs and DAMPs, constitutively expressed in many cell types, in four main families relevant to viral infection.

Recognition and signalling. PRR engagement triggers cascades converging on a small set of transcription factors: IRF3 and IRF7 (driving type I and type III interferons) and NF-κB (driving inflammatory cytokines such as IL-6, TNF-α, and IL-1β). TLR3 in a dendritic-cell endosome detects dsRNA, signals through the adaptor TRIF, activates the kinases TBK1 and IKKε, and phosphorylates IRF3 to induce type I interferon. Cytosolic RIG-I detects 5’-triphosphate dsRNA, signals through the mitochondrial adaptor MAVS, and produces the same IRF3 and NF-κB activation. The cGAS–STING pathway responds to cytosolic DNA from DNA viruses or leaked self-DNA and likewise converges on IRF3.

The combined output is rapid local interferon and cytokine production, recruitment of innate cells, and priming of the adaptive response. Genetic defects produce specific susceptibilities: people with TLR3 or downstream signalling mutations are unusually prone to herpes simplex encephalitis, showing how a single PRR pathway can be essential for controlling a specific virus at a specific anatomical site.

Interferon production is triggered when pattern-recognition receptors (PRRs) detect viral pathogen-associated molecular patterns (PAMPs), mostly viral nucleic acids in compartments where they would not normally appear.

The major stimuli and their sensors:

All these pathways converge on the interferon regulatory factors IRF3 and IRF7 (driving type I and type III interferons) and NF-κB (driving inflammatory cytokines such as TNF-α and IL-6).

Plasmacytoid dendritic cells (pDCs) are the dominant type I interferon producers, constitutively expressing high TLR7, TLR9, and IRF7, and can make up to 1,000 times more per cell than other cell types.

Positive feedback amplification. Secreted type I IFN binds IFNAR on neighbouring and producing cells and, through JAK–STAT, induces interferon-stimulated genes (ISGs) including IRF7 itself, massively amplifying local interferon production.

Damage-associated molecular patterns (DAMPs) from stressed or dying cells (HMGB1, ATP, uric acid) also contribute through the same PRRs.

When secreted type I interferon (IFN-α or IFN-β) binds IFNAR on a neighbouring cell, it places that cell in an antiviral state: resistant to productive infection, primed to self-destruct if infected, and signalling its presence to the wider immune system.

Signalling cascade. IFN-α / β binding to IFNAR1 / IFNAR2 activates the kinases JAK1 and TYK2, which phosphorylate STAT1 and STAT2; these heterodimerise with IRF9 to form the ISGF3 complex, which binds interferon-stimulated response elements (ISREs) and switches on hundreds of interferon-stimulated genes (ISGs).

Direct antiviral ISG products block replication at multiple steps: protein kinase R (PKR), activated by dsRNA, phosphorylates eIF-2α and shuts down all protein synthesis; 2’–5’ oligoadenylate synthetase (OAS), also dsRNA-activated, makes 2’–5’ oligomers that switch on RNase L to cleave cytoplasmic single-stranded RNA; Mx GTPases (MxA, MxB) trap viral nucleocapsids and block nuclear import (influenza, hantaviruses); IFITM proteins (IFITM1–3) block enveloped-virus fusion at late endosomes (influenza, dengue, Zika, SARS-CoV-2); ISG15 conjugates to proteins (ISGylation) with broad antiviral effect; and viperin / RSAD2 disrupts the lipid rafts some enveloped viruses bud from.

Restriction factors, constitutively expressed and interferon-boosted: TRIM5α binds incoming retroviral capsids and triggers premature uncoating; APOBEC3G hypermutates nascent retroviral DNA (G-to-A); tetherin (BST-2) holds budding virions on the membrane; SAMHD1 depletes the dNTP pool needed for reverse transcription.

Indirect effects. ISGs upregulate MHC class I, making infected cells more visible to CD8+ cytotoxic T cells; lower the threshold for apoptosis; activate NK cells in the microenvironment; and drive dendritic-cell maturation and T cell priming, making type I IFN a critical adjuvant for the adaptive response.

Type II IFN-γ signals through STAT1 homodimers binding gamma-activated sites (GAS), inducing an overlapping gene set centred on macrophage activation. Type III IFN-λ uses a similar JAK–STAT cascade but on epithelium and hepatocytes, giving localised mucosal defence without systemic inflammation.

Once a virus penetrates the anatomical barriers, the innate response is the host’s first active defence. It engages within minutes to hours, needs no prior exposure, and works through integrated mechanisms that restrict early infection and limit spread to neighbouring tissue.

Immediate recognition through germline-encoded pattern-recognition receptors (PRRs) detecting generic pathogen-associated molecular patterns (PAMPs) rather than antigen-specific structures.

Activation and recruitment of innate cells (macrophages, dendritic cells, natural killer cells, neutrophils) to the site, driven by cytokines and chemokines.

Direct antiviral action through the type I and type III interferon programme, switching on hundreds of interferon-stimulated genes (ISGs) in neighbouring cells and making them resistant before the virus arrives, the bystander effect.

Elimination of infected cells by NK cell lysis and by apoptosis, necroptosis, or pyroptosis, removing the factories the virus depends on.

Shaping the adaptive response. Dendritic cells carry viral antigen to draining lymph nodes to prime T and B cell responses, and the innate cytokine context biases helper T cells towards Th1 against most viruses.

The innate response is broadly specific rather than antigen-specific, short-lived, and lacks memory; the innate-adaptive line is blurred, because the same pathways that limit early replication also prime and direct the adaptive response that follows.

Several cell populations contribute, each with a distinct role and timescale.

Phagocytes. Macrophages are tissue-resident phagocytes named by location (Kupffer cells in liver, alveolar macrophages in lung, microglia in the central nervous system, Langerhans cells in skin, technically dendritic, and splenic macrophages); they engulf virions and debris, make inflammatory cytokines (TNF-α, IL-1β, IL-6, IL-12), present antigen, and dominate by 24 hours. Dendritic cells (DCs) are the most efficient antigen-presenting cells: plasmacytoid DCs are the major source of type I interferon, conventional DCs carry antigen to draining lymph nodes to prime adaptive immunity, making DCs the critical innate-adaptive bridge. Neutrophils are short-lived granulocytes recruited by CXCL8 / IL-8, important against bacteria but with a more limited antiviral role.

Cytotoxic cells. Natural killer (NK) cells are large granular lymphocytes that lyse infected cells via missing-self (loss of MHC class I) and stress-induced ligands; they appear within one to two days and produce IFN-γ.

Sentinel cells. Mucosal epithelial cells express PRRs and produce interferons, defensins, and chemokines on infection. Innate lymphoid cells (ILCs) are tissue-resident lymphocytes lacking antigen-specific receptors but making the same cytokines as T helper subsets; NK cells are group 1 ILCs.

Soluble defences also support the response: complement, natural antibodies from B1 lymphocytes, and hepatic acute phase reactants.

A network of soluble signalling molecules coordinates the innate response: pro-inflammatory cytokines, recruiting chemokines, antimicrobial peptides, the interferon system, and complement.

Pro-inflammatory cytokines. TNF-α (from macrophages and NK cells) activates vascular endothelium for leukocyte recruitment, induces fever, and drives cachexia, acting through NF-κB. IL-1β is pyrogenic, drives the hepatic acute phase response, and activates lymphocytes; caspase-1 cleaves it from pro-IL-1β in the inflammasome. IL-6 drives acute phase reactants (C-reactive protein, fibrinogen, serum amyloid A) and B cell differentiation. IL-12 (from macrophages and dendritic cells) activates NK cells and polarises naïve CD4+ T cells towards Th1. IL-15 maintains NK and memory CD8+ T cell populations. IL-18, an inflammasome product, amplifies IFN-γ from NK and T cells.

Chemokines. CXCL8 / IL-8 recruits neutrophils; CXCL10 / IP-10 (IFN-γ-inducible) recruits activated T cells; CCL2 / MCP-1 recruits monocytes; CXCL12 / SDF-1 is constitutive and serves as a co-receptor for HIV-1 entry through CXCR4.

Antimicrobial peptides. Small cationic peptides that disrupt enveloped virus membranes, some with antibacterial activity: α-defensins (neutrophils, Paneth cells), β-defensins (skin and mucosal epithelium), and cathelicidins (LL-37).

Interferons. The central antiviral cytokines: type I IFN-α / β, type II IFN-γ, and type III IFN-λ.

Complement. A serum cascade (classical, alternative, lectin pathways) that opsonises virions, lyses enveloped virions via the membrane attack complex, and recruits neutrophils through anaphylatoxins (C3a, C5a).