IC

Viruses, Viroids, and Prions – Vocabulary Review

Distinctive Features of Viruses

  • Obligatory intracellular parasites

    • Cannot multiply outside living host cells; depend entirely on host metabolic and genetic machinery

  • Genetic material

    • Contain either DNA or RNA (never both)

    • Can be \text{ssDNA, dsDNA, ssRNA (+)\, ssRNA (−), dsRNA}; linear or circular, single- or double-stranded

  • Structural hallmarks

    • Protein coat (capsid); sometimes surrounded by lipid envelope with glycoprotein spikes

    • No ribosomes → cannot translate proteins independently

    • No ATP-generating systems → must hijack host energy supplies

  • Replication strategy

    • Synthesis of viral components occurs inside host; virions assembled de novo; released to infect new cells

Viruses vs. Cellular Microbes

  • Intracellular parasitism

    • Bacteria: usually free-living (exception: Rickettsia/Chlamydia are obligate intracellular)

    • Viruses: obligate intracellular

  • Plasma membrane present in bacteria, absent in virions (envelope ≠ true membrane)

  • Replication

    • Bacteria divide by binary fission; viruses assemble from pre-formed parts

  • Filterability

    • Viruses and some small bacteria pass through bacteriological filters (< 450\,\text{nm})

  • Genetic complement

    • Bacteria possess both DNA and RNA simultaneously; viruses possess one or the other

  • Ribosomes / ATP metabolism: present in bacteria; absent in viruses

  • Sensitivity

    • Antibiotics: usually affect bacteria, NOT viruses

    • Interferon: host cytokine effective against many viruses, not bacteria

Virus Sizes (Approximate)

  • Prion proteins ≈ 20\,\text{nm} (infectious protein aggregates)

  • Bacteriophage f2, MS2: 24\,\text{nm}

  • Poliovirus / Rhinovirus: 30\,\text{nm}

  • Coronavirus: 90\,\text{nm}

  • Rabies virus: 170 \times 70\,\text{nm} (bullet-shaped)

  • Bacteriophage T4: 225\,\text{nm} long

  • Ebola filovirus: 970\,\text{nm} length (filamentous)

  • Comparison objects

    • Chlamydia elementary body: 300\,\text{nm}

    • E. coli: 3000 \times 1000\,\text{nm}

    • Human RBC diameter: 10\,000\,\text{nm}

Host Range & Cell Tropism

  • Definition: spectrum of host species and cell types a virus can infect

  • Determinants

    • Specific attachment receptors on host surface (e.g., CD4 for HIV, ACE2 for SARS-CoV-2)

    • Intracellular factors permitting replication (polymerases, transcription factors, temperature, pH)

  • Examples

    • Bacteriophages: limited to particular bacterial strains (e.g., T4 → E. coli)

    • Animal viruses: may show organ or tissue tropism (e.g., hepatitis viruses → hepatocytes)

Virion Architecture

  • Nucleic Acid core: carries genetic information

  • Capsid

    • Composed of protein subunits (capsomeres)

    • Protects genome; provides attachment in non-enveloped viruses

  • Envelope (optional)

    • Lipid layer derived from host membrane during budding; contains viral spikes (peplomers)

    • Increases susceptibility to detergents, alcohols, drying

  • Spikes

    • Glycoproteins used for host receptor binding; antigenic (targets of neutralizing antibodies)

Morphological Types

  • Helical: rod-like; capsomeres arranged in spiral around nucleic acid → Ex: Tobacco mosaic virus, Ebola

  • Polyhedral (icosahedral): 20 triangular faces, 12 vertices → Ex: Adenovirus, Poliovirus

  • Enveloped versions of helical or icosahedral nucleocapsids (e.g., Influenza = enveloped helical; Herpesvirus = enveloped icosahedral)

  • Complex: additional structures (tails, tail fibers, plates) → T-even bacteriophages; Poxviruses (brick-shaped)

Complex Bacteriophages (T-Even)

  • Components

    • Head (icosahedral capsid) contains dsDNA

    • Tail sheath contracts to inject DNA through bacterial wall

    • Tail core, baseplate, pins, tail fibers for attachment and penetration

  • Dimensions: head ≈ 65\,\text{nm}; tail ≈ 80\,\text{nm}

One-Step Growth Curve Concept

  • Latent (eclipse) period: after entry, no infectious virions detectable externally

  • Rise period: assembly & release cause sharp increase in PFU

  • Burst size: average number of virions produced per infected cell (varies \approx 50–1000)

Bacteriophage Replication Strategies

Lytic Cycle (T-Even phages)

  1. Attachment – tail fibers bind specific cell wall proteins (e.g., LPS of E. coli)

  2. Penetration – phage lysozyme degrades peptidoglycan; sheath injects DNA like syringe

  3. Biosynthesis – host DNA & protein synthesis halted; viral genome replicated, proteins made

  4. Maturation – assembly of capsids, tails; DNA packaged (previous slide blank filled)

  5. Release – phage lysozyme lyses cell wall; hundreds of progeny exit → host death

Lysogenic Cycle (Lambda phage)

  1. Attachment & injection as above

  2. Circularization of phage DNA

  3. Integration into host chromosome via site-specific recombination → forms a prophage

  4. Host replicates normally; prophage passed to daughter cells (lysogeny = latency)

  5. Induction (UV, chemicals) excises prophage → enters lytic cycle

Consequences of Lysogeny

  1. Immunity to superinfection by same phage (repressor proteins)

  2. Phage conversion → host acquires new traits (e.g., diphtheria toxin, cholera toxin genes are prophage-encoded)

  3. Specialized transduction

    • Prophage excision errors package adjacent bacterial genes (e.g., gal, bio) with phage DNA

    • Gene transfer limited to regions flanking prophage insertion site → alters recipient genotype

Animal vs. Bacteriophage Life Cycles (Key Contrasts)

  • Attachment

    • Phage: tail fibers → cell wall

    • Animal virus: capsid or envelope spikes bind plasma-membrane glycoproteins

  • Entry/penetration

    • Phage inject nucleic acid only; capsid remains outside

    • Animal viruses enter whole particle via receptor-mediated endocytosis, membrane fusion, or direct penetration (rare)

  • Uncoating required only for animal viruses (enzymatic removal of capsid)

  • Biosynthesis site

    • DNA animal viruses → nucleus; RNA viruses → cytoplasm (except influenza uses nucleus for mRNA capping)

  • Release

    • Phage: host lysis

    • Animal: enveloped bud; non-enveloped rupture or exocytosis

  • Options for persistence

    • Animal viruses: latency (herpes), chronic slow infections, oncogenesis

Entry Pathways for Animal Viruses

  1. Direct penetration (non-enveloped) – capsid forms pore; genome passes (e.g., some picornaviruses)

  2. Membrane fusion (enveloped) – viral envelope merges with host membrane; nucleocapsid released (e.g., HIV, herpesvirus)

  3. Receptor-mediated endocytosis – virus engulfed in vesicle; low pH triggers fusion/uncoating (e.g., influenza, SARS-CoV-2)

Uncoating

  • Physical or enzymatic separation of nucleic acid from capsid

  • Mediated by lysosomal enzymes, viral proteases, or host cytosolic factors

Biosynthesis Pathways

DNA Viruses

  • Replicate DNA in nucleus using host DNA-dependent DNA polymerase (except poxviruses replicate in cytoplasm)

  • Early genes: enzymes/regulatory proteins; Late genes: structural proteins

  • Capsid proteins translated in cytoplasm, imported into nucleus for assembly

RNA Viruses (non-retro)

  • Carry or encode RNA-dependent RNA polymerase (RdRp)

  • +-strand RNA (sense): genome serves directly as mRNA (e.g., poliovirus)

  • −-strand RNA: must package RdRp to transcribe + mRNA (e.g., rabies, influenza)

  • dsRNA viruses (Reoviridae) also package RdRp to produce mRNA

Retroviruses (RNA → DNA)

  • Genome: two identical +-ssRNA molecules, tRNA primer, enzymes (reverse transcriptase, integrase, protease)

  • Steps

    1. Fusion entry

    2. Reverse transcriptase synthesizes complementary DNA → dsDNA

    3. Integrase inserts viral DNA into host genome → provirus (permanent, inherited by daughter cells)

    4. Host RNA polymerase II transcribes provirus → genomic RNA + mRNAs

    5. Assembly at plasma membrane; budding acquires envelope & spikes

  • Clinical link: HIV (Lentivirus); certain Oncoviruses can cause cancers (HTLV-1)

Maturation & Release

  • Assembly: self-assembly of capsomeres with genome; sometimes viral chaperones/protease processing required (e.g., HIV Gag-Pol cleavage)

  • Release

    • Budding (enveloped): capsid pushes through membrane containing viral glycoproteins; cell may survive → persistent infection

    • Rupture (lysis) for non-enveloped animal viruses; host cell death

Plant Viruses, Viroids & Virusoids

  • Entry through damaged cell walls, insect vectors, grafting

  • Cause crop losses (e.g., Tobacco mosaic virus, Barley yellow dwarf virus)

  • Viroids: 246–401 nt circular ssRNA with extensive internal base pairing; no capsid; replicate by host RNA polymerase II

    • Example: Potato spindle tuber viroid → spindle-shaped tubers, economic damage

  • Virusoids (satellite RNAs): viroid-like RNAs enclosed in helper virus capsid (e.g., Hepatitis D virus requires HBV)

Prions (Proteinaceous Infectious Particles)

  • No nucleic acid; composed solely of misfolded host protein PrP ^{Sc} (scrapie form)

  • Normal form: PrP ^{C} (cell surface glycoprotein, α-helical)

  • Pathogenesis

    1. PrP^{Sc} contacts PrP^{C} → induces conformational change to β-sheet-rich PrP^{Sc}

    2. Aggregates accumulate in neurons (plaques), resist proteases, cause vacuolation → spongiform encephalopathy

  • Transmission: ingestion (contaminated meat), iatrogenic (surgical instruments), inherited mutations (PRNP gene)

  • Human diseases: Creutzfeldt-Jakob (sporadic, familial, variant), Gerstmann-Sträussler-Scheinker, Fatal familial insomnia

  • Animal: BSE (mad cow), scrapie (sheep), chronic wasting disease (deer)

  • Resistant to autoclave 121^{\circ}\text{C}; require \geq 132^{\circ}\text{C} plus NaOH or bleach for decontamination—important hospital implication

Viral Detection & Identification

  • Cytopathic effect (CPE) in cell culture: rounding, syncytia, inclusion bodies

  • Serology: ELISA, neutralization, hemagglutination-inhibition → detect viral antigens or host antibodies

  • Molecular: PCR/RT-PCR, qPCR, sequencing → highly sensitive & specific

Cultivation Techniques

Bacteriophages

  • Plaque assay on bacterial lawns; each plaque = plaque-forming unit (PFU)

  • Allows enumeration & purification of individual phage clones

Animal Viruses

  1. Living animals (mice, rabbits, ferrets, primates)

    • Some human viruses do not replicate or cause disease in animals → ethical & cost issues

  2. Embryonated eggs (5–12 day chicken embryos)

    • Routes: chorioallantoic membrane, allantoic cavity, amniotic cavity, yolk sac

    • Utilized for influenza, YF vaccine production; look for embryo death, pocks, or hemagglutinin in fluids

  3. Cell culture

    • Primary cell lines: normal tissue; limited lifespan

    • Continuous (immortal) cell lines: HeLa, Vero; indefinite passage but genetic abnormalities

    • Detection by CPE, hemadsorption, plaque formation, immunofluorescence

Cytopathic Effects (Examples)

  • Cell rounding & detachment (adenovirus)

  • Syncytium formation (HSV, RSV, HIV) – fusion of infected cells

  • Inclusion bodies

    • Negri bodies in rabies (cytoplasmic)

    • Owl’s eye nuclear inclusions in CMV

  • Vacuolation or giant cell formation

Exam/Review Questions (Self-Check)

  • Define host range; explain determinants

  • Compare virion structures of animal viruses vs. bacteriophages

  • Distinguish entry mechanisms: direct penetration, fusion, endocytosis

  • Contrast budding vs. rupture for viral egress

  • Describe steps of T-even lytic vs. lambda lysogenic cycles; list their consequences

  • Enumerate viral genome types

  • Differentiate viruses, viroids, virusoids, prions (composition & replication)

Key Numerical & Formulaic Reminders

  • Burst size (T-even phage): \text{PFU}_\text{final} / \text{infected cells initial}

  • Filter pore sizes: bacteria retained at 0.45\,\mu\text{m}; most viruses pass <0.22\,\mu\text{m}

  • Reverse transcription: RNA \xrightarrow{RT} DNA \xrightarrow{Integrase} \text{Provirus}

  • Prion inactivation requires \geq 132^{\circ}\text{C},\, 1\,\text{h},\, 3\,\text{bar} with \text{NaOH} or \text{NaClO}

Ethical & Practical Implications

  • Prions highlight risks of iatrogenic transmission; surgical instrument sterilization protocols revised

  • Lysogenic conversion illustrates horizontal gene transfer → emergence of new bacterial pathogens/toxins

  • Plant viroid/virus outbreaks can devastate agriculture; strict quarantine and certification programs

  • Reliance on embryonated eggs for vaccine production poses supply and allergy concerns; cell-culture & recombinant platforms emerging