Viruses, Viroids, & Prions (Acellular Microbiology)

Chapter 12: Viruses, Viroids, & Prions (Acellular Microbiology)

12.1 Basic Viral Structure and Diversity

  • Definitions:

    • Viruses: Noncellular particles containing a genome that can replicate only inside a host cell, infecting various organisms like bacteria, archaea, animals, plants, and fungi.

    • Bacteriophage (Phage): A specific type of virus that infects bacteria.

    • Virion: A complete virus particle.

  • Characteristics of Acellular Infectious Biological Agents:

    • No plasma (cell) membrane.

    • No binary fission.

    • No way to generate ATP.

    • No way to synthesize proteins (absence of ribosomes).

  • Obligate Intracellular Parasite:

    • Relies on host cells for energy and substrates.

    • Hijacks host cell's replication machinery.

    • Directs host cell to express viral genes and proteins.

    • Need a host culture to study viruses in the lab.

12.2 Viral Structure

Nucleocapsid Structure

  • Nucleocapsid:

    • Nucleic Acid (viral genome):

    • Can be DNA or RNA.

    • Forms can be linear, circular, or segmented.

    • Can be double-stranded or single-stranded.

    • Capsid:

    • Protein coat surrounding the genome.

    • Composed of identical protein subunits called capsomeres.

    • Determines the overall shape of the virus.

Types of Viruses

  1. Naked Viruses (Non-Enveloped):

    • Composed only of nucleocapsid.

    • More resistant to disinfectants.

  2. Enveloped Viruses:

    • Nucleocapsid is enclosed in a lipid bilayer.

    • Contains a matrix/tegument layer, which is a protein layer attaching the envelope to the nucleocapsid.

    • Possesses viral attachment proteins on the surface, determining host range.

      • May be recognized by the immune system.

      • Used for viral identification.

    • Spike Proteins: Glycoproteins on envelopes.

    • Tail Fibers: Present on phages, assisting in attachment.

Common Viral Shapes

  • Icosahedral Nucleocapsids:

    • Have radial symmetry based on an icosahedron (20 sides).

    • Example: Herpesvirus exhibits icosahedral capsid symmetry.

  • Helical Nucleocapsids:

    • Formed by a helical capsid tube around the genome, generating a flexible filament.

  • Complex/Amorphous Nucleocapsids:

    • Lacking symmetrical form, with a core made of capsid proteins enveloping the genome.

    • Complex-tailed bacteriophages have an icosahedral head that contains the genome, with a tail that injects this genome into host cells.

12.3 Viral Replication: General Scheme

  • Viral Replication Steps:

    1. Host Cell Recognition & Attachment:

    • Viral surface proteins bind to host receptor proteins.

    1. Genome Entry:

    • Nucleic acid must enter the host cell to replicate.

    • Mechanisms of entry depend on the type of virus (e.g., genome alone or whole virus particle).

    1. Biosynthesis:

    • Involves replication of the viral genome and expression of viral proteins, mechanisms varying based on viral genome types (DNA, RNA, etc.).

    1. Assembly / Maturation:

    • New virions are assembled, often happening before release.

    • Enveloped viruses continue to mature even during or after release.

    1. Release and Transmission:

    • Virions exit the host to infect new cells, with variable outcomes including cell lysis or budding.

Bacteriophage Replication

  • Types of Bacteriophages:

    • Lytic (Virulent) Phage:

    • Infect host cells, lead to productive cycles (many virions produced).

    • Cause host cell lysis, results in cell death.

    • Temperate Phage:

    • May follow a lysogenic pathway, integrating into host genome as a prophage.

    • Can switch to a lytic cycle upon induction.

Lytic Infection Process

  1. Attachment: Tail fibers bind to bacterial receptor proteins (like LPS, pili).

  2. Genome Entry: Phage injects genome into the host cell, sometimes using lysozyme to breach the cell wall.

  3. Biosynthesis: Phage takes over host cell machinery to digest bacterial genome and express viral genes.

  4. Assembly: Complicated, step-by-step assembly of phage components.

  5. Release: Many phages lyse and kill host, resulting in a burst size of virions released.

Lysogenic Infection Process

  • Lysogeny: Temperature phages can integrate their genome into the bacterial genome, forming a prophage. They can replicate with the host genome without killing the host, exhibiting a latent state. Induction can trigger the switch to the lytic cycle.

  • Prophage genes can confer new properties to host bacteria (known as bacteriophage conversion), influencing virulence.

Bacterial Defenses Against Phages

  1. Restriction-Modification Systems: Bacteriophage introduction trigger restriction enzymes that cut foreign DNA, and methylation helps to distinguish self from non-self.

  2. CRISPR System: Bacteria can integrate sequences from phages into their genome, creating a memory system to protect future generations from similar infections. Cas proteins are used to cleave viral DNA based on complementary crRNA.

12.4 Viral Replication in Animal Viruses

  1. Host Cell Recognition & Attachment: Viral spikes or surface proteins engage with host cells.

  2. Genome Entry: Often involves the whole nucleocapsid. Can occur via endocytosis or fusion with the plasma membrane. Naked viruses have specific entry mechanisms.

  3. Biosynthesis: Involves making more viral genomes and proteins dependent on the viral genome type.

  4. Assembly / Maturation: Enveloped viruses utilize ER and Golgi systems for assembling proteins that will form the envelope.

  5. Release: Enveloped viruses can be released through budding or exocytosis, while naked viruses typically lead to host cell death.

Latency in Animal Viruses

  • Some viruses can enter non-productive states, where they do not actively replicate (latent). They can reactivate, leading to symptoms and potential transmission.

12.5 Viroids and Prions

Viroids

  • Definition: Viroids are virus-like infectious agents with a single strand of RNA, lacking a protective capsid or virions.

  • Characteristics: No ORFs for protein coding, primarily infect plants. Their replication and mechanisms of causing disease are relatively poorly understood.

Prions

  • Definition: Infectious agents composed solely of abnormal forms of proteins, without nucleic acids.

  • Characteristics: Very stable against heat, UV, and proteases. Lead to aggregates in brain tissues, causing transmissible prion diseases, including Kuru, Creutzfeldt-Jakob Disease, and Mad Cow Disease. Their aberrant structure leads to neurodegenerative conditions.

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