Viruses, Viroids, and Prions – Chapter 13 (A) Study Notes

Fundamental Properties of Viruses

• Non-cellular infectious agents.

  • Possess either DNA or RNA (never both).

  • Always enclosed in a protein coat (capsid).

  • Some virions additionally surrounded by a lipid-rich envelope derived from host membranes.

  • Surface projections (spikes) present on many enveloped viruses; composed of glycoprotein—key for host-cell attachment & antigenicity.

• Host specificity (host range)

  • Most viruses infect only one species and a limited set of cell types within that species.

  • Determined by complementary interaction between viral attachment proteins (spikes, capsomers, tail fibers, etc.) and specific host-cell receptors, plus compatibility of intracellular factors.

Relative Sizes (Fig 13.1 – comparative scale)

• Human red blood cell diameter ≈ 10{,}000\;\text{nm}; plasma membrane thickness ≈ 10\;\text{nm}.

• Selected pathogens (approximate dimensions):

  • Vaccinia: 300\times200\times100\;\text{nm}; Rabies: 170\times70\;\text{nm}.

  • Adenovirus: 90\;\text{nm}; Rhinovirus & Poliovirus: 30\;\text{nm}.

  • Bacteriophage M13: 800\times10\;\text{nm}; Ebola: 970\;\text{nm} filament.

  • Viroid particle: \sim300\times10\;\text{nm}; Prion rods: 200\times20\;\text{nm}.

  • E. coli cell: 3000\times1000\;\text{nm}; Chlamydia elementary body: 300\;\text{nm}.

Capsid Symmetry & Viral Morphologies

• Helical

  • Capsomeres form hollow cylinders; nucleic acid coiled inside.

  • Ex: Tobacco Mosaic Virus; Ebola virus (elongated filament with helical nucleocapsid inside envelope).

• Polyhedral (Icosahedral)

  • Roughly spherical with 20 triangular faces & 12 vertices.

  • Example particle pictured; Mastadenovirus (adenoviruses) as representative.

• Complex

  • Possess additional structures (tail sheath, fibers, baseplate, pins) beyond simple head.

  • T-even bacteriophages (e.g., T4) typify this class. Head ≈ 65\;\text{nm} in diagram.

Standard Nomenclature (Viral Taxonomy)

• Family names → suffix –viridae (e.g., Herpesviridae).

• Genus names → suffix –virus (e.g., Lentivirus).

• Viral species defined by shared genome characteristics & ecological niche; referred to by common name (e.g., Human herpesvirus 1).

• Subspecies (strains) indicated by numbers (HHV-1, HIV-2, etc.).

• Example hierarchy:

  • Herpesviridae → Herpesvirus → HHV-1, HHV-2, HHV-3.

  • Retroviridae → Lentivirus → HIV-1, HIV-2.

Cultivation Techniques

• Obligate intracellular parasites; require living host systems.

1. Bacteriophage culture

   • Inoculate phage onto "lawn" of susceptible bacteria (agar plate).

   • Clear zones (plaques) correspond to lysis foci; each arises from a single virion.

2. Animal virus culture

   • Whole animals (e.g., mice, rabbits) for pathogenesis studies.

   • Embryonated chicken eggs: inoculation into allantoic cavity, amniotic cavity, chorioallantoic membrane, or yolk sac (Fig 13.7). Classical for influenza vaccines.

3. Cell culture

   • Primary, diploid, or continuous lines.

   • Continuous lines (e.g., HeLa—cervical carcinoma) divide indefinitely; convenient for routine viral replication.

Laboratory Identification of Viruses

• Cytopathic effect (CPE): morphological changes (rounding, syncytia, inclusion bodies, lysis) visible under light microscopy.

• Serological assays:

  • Detect patient antibodies (ELISA, hemagglutination inhibition, neutralization).

  • Identify virus by using specific antibodies (immunofluorescence, Western blot).

• Nucleic-acid-based methods:

  • RFLP analysis of viral genomes.

  • PCR amplification—high sensitivity for low-titer specimens.

Bacteriophage Multiplication

Lytic Cycle (Fig 13.10 & Growth Curve)

1. Attachment – tail fibers bind specific cell wall receptors.

2. Penetration – phage lysozyme breaches peptidoglycan; sheath contracts injecting DNA through tail core.

3. Biosynthesis – host ribosomes & enzymes synthesize phage nucleic acid and proteins.

4. Maturation – self-assembly of capsid, tail, fibers into virions.

5. Release – phage lysozyme lyses cell; progeny liberated.

• One-step growth curve parameters:

  • Burst time ≈ 20$–$40\;\text{min} (lag + synthesis + maturation).

  • Burst size (virions released/cell) logarithmic scale shown ~50$–$1000 depending on phage/host.

Lysogenic Cycle (Fig 13.12)

• Viral DNA integrates into host chromosome ⇒ prophage.

• Bacterial cell replicates normally; each daughter inherits prophage.

• Environmental trigger (UV, chemicals) → excision → entry into lytic cycle.

Specialized Transduction (Fig 13.13)

1. Prophage excises, mistakenly carrying adjacent bacterial genes (e.g., gal operon).

2. Defective phage infects new host lacking that gene.

3. Integration yields recombinant bacterium expressing donor trait (galactose metabolism).

Animal Virus Replication Cycle

1. Attachment – binding to plasma-membrane receptors; spikes or capsid proteins mediate.

2. Penetration

   • Endocytosis (non-enveloped or enveloped).

   • Membrane fusion (enveloped viruses).

3. Uncoating – separation of capsid from genome via host lysosomal enzymes or viral uncoating proteins.

4. Biosynthesis – transcription/translation of early enzymes & viral nucleic-acid replication.

5. Maturation – assembly of nucleic acid with capsomeres.

6. Release

   • Budding → enveloped virions acquire host lipid bilayer + viral envelope proteins; often non-lytic.

   • Rupture/lysis → typical for many non-enveloped viruses.

DNA Virus Strategy (Fig 13.15)

• Early mRNA → early proteins (e.g., DNA polymerase).

• Viral DNA replication in nucleus (except poxviruses).

• Late transcription/translation → structural proteins.

• Assembly & release.

RNA Virus Pathways (Fig 13.17)

(a) +ssRNA (sense)

• Genome functions as mRNA directly.

• Viral RNA-dependent RNA polymerase (RdRp) synthesizes complementary - strand → template for more + genomes.
  (b) –ssRNA (antisense)

• RdRp packaged within virion converts genome to + mRNA, which then serves for protein synthesis and as template to make new - strands.
  (e) dsRNA (Reoviridae)

• RdRp produces mRNA from each strand inside capsid; cytoplasmic replication ensues.

Retrovirus Replication (Fig 13.19)

1. Entry & uncoating of two identical + ssRNA molecules + reverse transcriptase.

2. Reverse transcription: \text{RNA} \rightarrow \text{DNA} (RNA-DNA hybrid → double-stranded DNA).

3. Integration as provirus into host chromosome (permanent genetic change).

4. Provirus either:

   • Remains latent as host divides, or

   • Transcribed to genomic RNA + mRNA for capsid/envelope proteins.

5. Assembly in cytoplasm; budding through plasma membrane acquires envelope.

Viruses & Oncogenesis (Cancer Induction)

• Oncogenes (proto-oncogenes) activated by viral integration → uncontrolled cell division.

• Traits of transformed cells:

  • Rapid proliferation; loss of contact inhibition (pile-up of cells).

  • Tumor-specific transplantation antigen (TSTA) on surface.

  • T-antigen detectable in nucleus.

Oncogenic DNA Viruses

• Adenoviridae

• Herpesviridae (e.g., HHV-8 → Kaposi’s sarcoma; Epstein–Barr → Burkitt’s lymphoma, nasopharyngeal carcinoma).

• Papovaviridae (Papillomavirus; high-risk HPVs cause cervical carcinoma).

• Poxviridae (some animal poxviruses linked to tumors experimentally).

• Hepadnaviridae (HBV predisposes to hepatocellular carcinoma).

Oncogenic RNA Viruses

• Retroviridae

  • Viral RNA reverse-transcribed & integrated as provirus.

  • Human T-cell leukemia viruses HTLV-1 & HTLV-2 cause adult T-cell leukemias/lymphomas.

Latency & Persistent Infections

• Latent infections: virus harbored silently; periodic reactivation.

  • HSV-1 → cold sores; Varicellovirus (VZV) → chickenpox latency, reactivation as shingles.

• Persistent (slow) infections: continuous viral replication; disease develops gradually, often fatal.

  • Subacute sclerosing panencephalitis (SSPE) years after measles infection.

Fundamental Properties of Viruses

• Non-cellular infectious agents.

• Possess either DNA or RNA (never both).

• Always enclosed in a protein coat (capsid).

• Some virions additionally surrounded by a lipid-rich envelope derived from host membranes.

• Surface projections (spikes) present on many enveloped viruses; composed of glycoprotein—key for host-cell attachment & antigenicity.

• Host specificity (host range)

  • Most viruses infect only one species and a limited set of cell types within that species.

  • Determined by complementary interaction between viral attachment proteins (spikes, capsomers, tail fibers, etc.) and specific host-cell receptors, plus compatibility of intracellular factors.

Relative Sizes (Fig 13.1 – comparative scale)

• Human red blood cell diameter ≈ 10{,}000\;\text{nm}; plasma membrane thickness ≈ 10\;\text{nm}.

• Selected pathogens (approximate dimensions):

  • Vaccinia: 300\times200\times100\;\text{nm}; Rabies: 170\times70\;\text{nm}.

  • Adenovirus: 90\;\text{nm}; Rhinovirus & Poliovirus: 30\;\text{nm}.

  • Bacteriophage M13: 800\times10\;\text{nm}; Ebola: 970\;\text{nm} filament.

  • Viroid particle: \sim300\times10\;\text{nm}; Prion rods: 200\times20\;\text{nm}.

  • E. coli cell: 3000\times1000\;\text{nm}; Chlamydia elementary body: 300\;\text{nm}.

Capsid Symmetry & Viral Morphologies

• Helical

  • Capsomeres form hollow cylinders; nucleic acid coiled inside.

  • Ex: Tobacco Mosaic Virus; Ebola virus (elongated filament with helical nucleocapsid inside envelope).

• Polyhedral (Icosahedral)

  • Roughly spherical with 20 triangular faces & 12 vertices.

  • Example particle pictured; Mastadenovirus (adenoviruses) as representative.

• Complex

  • Possess additional structures (tail sheath, fibers, baseplate, pins) beyond simple head.

  • T-even bacteriophages (e.g., T4) typify this class. Head ≈ 65\;\text{nm} in diagram.

Standard Nomenclature (Viral Taxonomy)

• Family names → suffix –viridae (e.g., Herpesviridae).

• Genus names → suffix –virus (e.g., Lentivirus).

• Viral species defined by shared genome characteristics & ecological niche; referred to by common name (e.g., Human herpesvirus 1).

• Subspecies (strains) indicated by numbers (HHV-1, HIV-2, etc.).

• Example hierarchy:

  • Herpesviridae → Herpesvirus → HHV-1, HHV-2, HHV-3.

  • Retroviridae → Lentiviru s → HIV-1, HIV-2.

Cultivation Techniques

• Obligate intracellular parasites; require living host systems.

1. Bacteriophage culture

   • Inoculate phage onto "lawn" of susceptible bacteria (agar plate).

   • Clear zones (plaques) correspond to lysis foci; each arises from a single virion.

2. Animal virus culture

   • Whole animals (e.g., mice, rabbits) for pathogenesis studies.

   • Embryonated chicken eggs: inoculation into allantoic cavity, amniotic cavity, chorioallantoic membrane, or yolk sac (Fig 13.7). Classical for influenza vaccines.

3. Cell culture

   • Primary, diploid, or continuous lines.

   • Continuous lines (e.g., HeLa—cervical carcinoma) divide indefinitely; convenient for routine viral replication.

Laboratory Identification of Viruses

• Cytopathic effect (CPE): morphological changes (rounding, syncytia, inclusion bodies, lysis) visible under light microscopy.

• Serological assays:

  • Detect patient antibodies (ELISA, hemagglutination inhibition, neutralization).

  • Identify virus by using specific antibodies (immunofluorescence, Western blot).

• Nucleic-acid-based methods:

  • RFLP analysis of viral genomes.

  • PCR amplification—high sensitivity for low-titer specimens.

Bacteriophage Multiplication

Lytic Cycle (Fig 13.10 & Growth Curve)

1. Attachment – tail fibers bind specific cell wall receptors.

2. Penetration – phage lysozyme breaches peptidoglycan; sheath contracts injecting DNA through tail core.

3. Biosynthesis – host ribosomes & enzymes synthesize phage nucleic acid and proteins.

4. Maturation – self-assembly of capsid, tail, fibers into virions.

5. Release – phage lysozyme lyses cell; progeny liberated.

• One-step growth curve parameters:

  • Burst time ≈ 20$–$40\;\text{min} (lag + synthesis + maturation).

  • Burst size (virions released/cell) logarithmic scale shown ~50$–$1000 depending on phage/host.

Lysogenic Cycle (Fig 13.12)

• Viral DNA integrates into host chromosome ⇒ prophage.

• Bacterial cell replicates normally; each daughter inherits prophage.

• Environmental trigger (UV, chemicals) → excision → entry into lytic cycle.

Specialized Transduction (Fig 13.13)

1. Prophage excises, mistakenly carrying adjacent bacterial genes (e.g., gal operon).

2. Defective phage infects new host lacking that gene.

3. Integration yields recombinant bacterium expressing donor trait (galactose metabolism).

Animal Virus Replication Cycle

1. Attachment – binding to plasma-membrane receptors; spikes or capsid proteins mediate.

2. Penetration

   • Endocytosis (non-enveloped or enveloped).

   • Membrane fusion (enveloped viruses).

3. Uncoating – separation of capsid from genome via host lysosomal enzymes or viral uncoating proteins.

4. Biosynthesis – transcription/translation of early enzymes & viral nucleic-acid replication.

5. Maturation – assembly of nucleic acid with capsomeres.

6. Release

   • Budding → enveloped virions acquire host lipid bilayer + viral envelope proteins; often non-lytic.

   • Rupture/lysis → typical for many non-enveloped viruses.

DNA Virus Strategy (Fig 13.15)

• Early mRNA → early proteins (e.g., DNA polymerase).

• Viral DNA replication in nucleus (except poxviruses).

• Late transcription/translation → structural proteins.

• Assembly & release.

RNA Virus Pathways (Fig 13.17)

(a) +ssRNA (sense)

• Genome functions as mRNA directly.

• Viral RNA-dependent RNA polymerase (RdRp) synthesizes complementary - strand → template for more + genomes.
  (b) –ssRNA (antisense)

• RdRp packaged within virion converts genome to + mRNA, which then serves for protein synthesis and as template to make new - strands.
  (e) dsRNA (Reoviridae)

• RdRp produces mRNA from each strand inside capsid; cytoplasmic replication ensues.

Retrovirus Replication (Fig 13.19)

1. Entry & uncoating of two identical + ssRNA molecules + reverse transcriptase.

2. Reverse transcription: \text{RNA} \rightarrow \text{DNA} (RNA-DNA hybrid → double-stranded DNA).

3. Integration as provirus into host chromosome (permanent genetic change).

4. Provirus either:

   • Remains latent as host divides, or

   • Transcribed to genomic RNA + mRNA for capsid/envelope proteins.

5. Assembly in cytoplasm; budding through plasma membrane acquires envelope.

Viruses & Oncogenesis (Cancer Induction)

• Oncogenes (proto-oncogenes) activated by viral integration → uncontrolled cell division.

• Traits of transformed cells:

  • Rapid proliferation; loss of contact inhibition (pile-up of cells).

  • Tumor-specific transplantation antigen (TSTA) on surface.

  • T-antigen detectable in nucleus.

Oncogenic DNA Viruses

• Adenoviridae

• Herpesviridae (e.g., HHV-8 → Kaposi’s sarcoma; Epstein–Barr → Burkitt’s lymphoma, nasopharyngeal carcinoma).

• Papovaviridae (Papillomavirus; high-risk HPVs cause cervical carcinoma).

• Poxviridae (some animal poxviruses linked to tumors experimentally).

• Hepadnaviridae (HBV predisposes to hepatocellular carcinoma).

Oncogenic RNA Viruses

• Retroviridae

  • Viral RNA reverse-transcribed & integrated as provirus.

  • Human T-cell leukemia viruses HTLV-1 & HTLV-2 cause adult T-cell leukemias/lymphomas.

Latency & Persistent Infections

• Latent infections: virus harbored silently; periodic reactivation.

• HSV-1 → cold sores; Varicellovirus (VZV) → chickenpox latency, reactivation as shingles.

• Persistent (slow) infections: