Chapter 6 — Viruses, Viroids, and Prions

Overview of Viruses, Viroids & Prions

  • Viruses are obligate intracellular parasites

    • Not alive in the classical sense; lack metabolic pathways

    • Contain no cellular structures (no membrane, nucleus, organelles)

    • Depend completely on host cells for energy, raw materials, and ribosomes

    • Infect every major domain of life: animals, plants, fungi, protozoa, bacteria

  • Viroids & prions discussed later are even simpler than viruses

Size & Complexity of Viruses

  • Viruses are extremely small—far below the resolution of a light microscope

    • Typical diameters well under 0.2 µm0.2\,\text{µm} (not explicitly in slides, but implicit in “really, really small”)

  • Viral particles (virions) are far less complex than cells

    • No independent metabolism

    • No binary fission or mitosis; reproduction only inside host

Basic Viral Structure

  • Fundamental parts of every virion

    • Capsid: protein coat built from sub-units called capsomers

    • Nucleic acid core: contains either RNA or DNA (never both)

  • Optional parts

    • Envelope: lipid bilayer stolen from previous host membrane, contains protein spikes (peplomers) for binding

  • Because of these minimalist features, viruses look nothing like cells (Ebola, Coronavirus, Influenza shown for contrast)

Capsid Architectures

  • Helical capsids

    • Capsomers wind around the nucleic acid forming a flexible or rigid helix

    • Examples: Coronavirus, Rabies virus, Influenza virus

  • Icosahedral capsids

    • Geometry of 2020 triangular faces; resembles a soccer ball

    • Examples: Poliovirus, Rhinovirus

  • Complex/atypical viruses

    • Possess elaborate structures (tails, fibers, multiple membranes)

    • Examples:

    • Bacteriophages (tail fibers, base plates, contractile sheaths)

    • Vaccinia virus (multiple envelopes, lateral bodies, soluble protein antigens)

Viral Genome & Taxonomic Classification

  • Genomic possibilities

    • Single-stranded RNA, double-stranded RNA

    • Single-stranded DNA, double-stranded DNA

    • Gene counts range from 44 to a “few hundred”

  • Classification criteria

    • Type of nucleic acid

    • Capsid symmetry (helical vs icosahedral)

    • Presence/absence of envelope

    • Natural host organism

Viral Host Range & Specificity

  • Binding to specific receptors on host membranes limits host range

    • Rabies virus → mammalian nerve cells

    • HIV → human CD4(^+) white blood cells

    • Hepatitis B → human liver cells

    • SARS-CoV-2 (Coronavirus) binds ACE-2 receptors (lungs, blood vessels)

  • “Key-to-lock” analogy underscores the biochemical precision

Bacteriophage (Prokaryotic) Multiplication Cycle

  1. Adsorption

  2. Penetration/Injection

  3. Synthesis of viral components

  4. Assembly (maturation)

  5. Lysis → release of progeny

    • Termed the lytic cycle; ends with rupture of bacterial cell wall

  • Lysogenic phase

    • Viral DNA integrates into host chromosome as a prophage

    • Host survives and replicates viral genes passively

    • Environmental triggers can switch prophage back to lytic phase

    • Each phage species is limited to one bacterial species (strict specificity)

Eukaryotic Virus Multiplication Cycle

  1. Adsorption

    • Viral spikes/capsid proteins bind host receptors

  2. Penetration & Uncoating

    • Fusion (enveloped viruses only): envelope merges with host membrane

    • Endocytosis/Engulfment: host membrane invaginates; vesicle acidification causes uncoating

  3. Synthesis

    • Host machinery directed to replicate viral nucleic acids & translate proteins

  4. Assembly of new virions

    • Burst sizes range from 3,0003{,}000 to 100,000100{,}000 particles per infected cell

  5. Release

    • Naked viruses → released via host lysis (cell death)

      • Examples: Poliovirus, Hepatitis A, Reovirus, Norovirus

    • Enveloped viruses → released by budding (exocytosis) through membranes

      • Examples: Influenza, Coronavirus, Zika virus

Cultivation of Viruses

  • Requires growth of a living host system

    1. Cell culture (in vitro)

    • Cells form a monolayer; viral infection creates plaques (clear zones from lysis)

    1. Embryonated eggs (in vitro)

    • Convenient because nearly every embryonic tissue can sustain viral growth

    1. Live animals (in vivo)

    • Still used for some viruses but is expensive, slow, and ethically fraught

Viral Detection & Diagnostic Methods

  • Clinical signs & symptoms (first clue)

  • Cytopathic effects (CPEs) in cell culture (rounding, syncytia, inclusion bodies)

  • Electron microscopy for direct visualization

  • Antigen detection assays (ELISA, rapid tests)

  • Nucleic-acid detection (PCR, RT-PCR, sequencing)

Antiviral Treatment Strategies

  • Most viral infections are not specifically treated; supportive care instead

  • Difficulty: antivirals must target viral processes without harming the host cell

  • Existing antiviral classes/examples

    • Influenza → neuraminidase inhibitors (Oseltamivir)

    • HIV → reverse transcriptase, integrase, protease inhibitors; HAART strategy

    • Hepatitis C → direct-acting antivirals (sofosbuvir, ledipasvir)

    • Herpes simplex → nucleoside analogs (Acyclovir)

Spongiform Encephalopathies & Prions

  • Neurodegenerative diseases with sponge-like brain tissue

    • Loss of coordination, weakness, weight loss, fatal outcomes

    • Examples: Scrapie (sheep), Mad Cow Disease (BSE), Creutzfeldt-Jakob Disease, Kuru

  • Prions (Proteinaceous Infectious Particles)

    • Composed solely of misfolded protein; contain no DNA or RNA

    • “Bad” conformers induce conformational change in normal prion proteins → exponential accumulation

    • Form long, insoluble chains & tangles within neural tissue

    • Represent the simplest known infectious agent; even simpler than viruses

Practical, Ethical & Philosophical Implications

  • Minimalist parasites challenge definitions of life

  • Viral cultivation in animals raises animal-welfare & biosafety concerns

  • High mutation rates in RNA viruses complicate vaccine design & drug resistance

  • Prion diseases underscore risks of iatrogenic transmission (surgical instruments, grafts)

  • Thin line between viral eradication & ecological balance: some bacteriophages may be explored as antibiotic alternatives