Prescott's Microbiology: Chapter 06 - Viruses and Other Acellular Infectious Agents

Chapter 06: Viruses and Other Acellular Infectious Agents

Introduction to Viruses

• Beyond Disease Causation: Viruses are commonly associated with disease, but they have other crucial roles:

  • Aquatic Ecosystems: Vital members, influencing nutrient cycling and microbial populations.

  • Cancer Therapy: Can be engineered to destroy cancer cells (oncolytic viruses).

  • Human Microbiome Regulation: Bacteriophages in the human gut may regulate the bacterial microbiome, impacting health.

  • Model Organisms: Serve as important model systems in molecular biology due to their simple structure and well-defined life cycles.

6.1 Viruses Are Acellular

• Virology: The scientific study of viruses.

• Viruses: Unique infectious agents characterized by their simple, acellular organization and specific pattern of multiplication. They are major causes of disease, as evidenced by the global SARS-CoV-2 pandemic in $2020$. Additionally, they are important model systems in molecular biology research.

• Extracellular vs. Intracellular Viruses:

  • Extracellular Viruses: Inactive outside of living cells, unable to reproduce on their own.

  • Intracellular Viruses: Actively commandeer host cells, utilizing host cellular machinery to synthesize viral components. These components are then assembled into mature progeny viruses, which are subsequently released from the host cell.

• Host Range: Viruses can infect all types of cells.

  • Bacteriophages (phages): Viruses that specifically infect bacteria.

  • Archaeal Viruses: A small number of viruses that infect archaea have been identified.

  • Eukaryotic Viruses: The majority of known viruses, infecting plants, animals, protists, and fungi.

6.2 Virion Structure: Capsid Symmetry and Envelope Presence

• Virion: A complete, mature virus particle found outside its host cell. It is infectious and capable of initiating an infection.

• Virion Size Range:

  • Extremely diverse, ranging from approximately $20 \ nm$ in diameter (e.g., Human papillomavirus) up to the size of a rod-shaped bacterial cell ($1.5 \ \mu m \times 0.5 \ \mu m$) (e.g., Mimivirus, Poxviruses).

  • Most viruses are too small to be seen with a light microscope and require an electron microscope for visualization.

• Virion Contents:

  • Nucleocapsid: The core structure of a virion, composed of the viral genetic material (nucleic acid) and a protective protein coat (capsid).

  • Nucleic Acid: Can be either DNA or RNA, but never both in a single virion.

  • Capsid: The protein coat surrounding the nucleic acid.

  • Enveloped Viruses: Possess an outer lipid membrane derived from the host cell, enclosing the nucleocapsid. Viral proteins are embedded within this envelope.

  • Nonenveloped Viruses (Naked Viruses): Lack a lipid envelope; their outermost layer is the capsid.

• Capsids:

  • Large macromolecular structures that serve as the protein coat of the virus.

  • Composed of protein subunits called protomers.

  • Primary Functions:

    • Protect viral genetic material from degradation.

    • Aid in the transfer of viral genetic material between host cells.

  • Nonenveloped Viruses: Construct a capsid primarily from many copies of a single type of protein.

  • Enveloped Viruses: Require nucleocapsid proteins and additional proteins to anchor the nucleocapsid to the viral envelope.

• Types of Capsid Symmetry:

  • Helical Capsids:

    • Shaped like hollow tubes with protein walls.

    • Protomers self-assemble into a rigid, cylindrical tube.

    • The size of the helical capsid is influenced by the protomer characteristics and the length of the viral genome it encloses.

  • Icosahedral Capsids:

    • An efficient way to enclose a maximum volume with a minimum amount of surface area.

    • An icosahedron is a regular polyhedron with $20$ equilateral triangular faces and $12$ vertices.

    • Capsomers: Ring or knob-shaped units composed of $5$ or $6$ protomers.

      • Pentamers (pentons): Capsomers made of $5$ protomers, typically found at the vertices.

      • Hexamers (hexons): Capsomers made of $6$ protomers, forming the faces of the icosahedron.

  • Complex Symmetry Capsids:

    • Viruses that do not fit neatly into helical or icosahedral categories.

    • Poxviruses: Among the largest animal viruses, having a complex internal structure and an ovoid- to brick-shaped exterior (e.g., Vaccinia Virus Virions, approximately $240-300 \ nm$ in length and $200 \ nm$ in breadth).

    • Large Bacteriophages: Often exhibit binal symmetry, combining an icosahedral head (containing the nucleic acid) with a helical tail (e.g., T4 bacteriophage virion, which has a capsid head, collar, spiral sheath, baseplate, long tail fibers, short tail fibers, and tail pins).

• Viral Envelopes and Enzymes:

  • Many viruses are encased by an outer, flexible, membranous layer called an envelope.

  • Origin of Envelopes: Animal virus envelopes, composed of lipids and carbohydrates, usually arise from the host cell's plasma membrane or internal organelle membranes (e.g., Golgi, ER) during budding.

  • Envelope Proteins: These are viral-encoded proteins that may protrude from the envelope surface as spikes or peplomers.

    • Attachment: Spikes are crucial for viral attachment to specific receptors on the host cell surface.

    • Enzymatic Activity: Some surface proteins can have enzymatic activity, necessary for entry into or exit from the host cell (e.g., neuraminidase, hemagglutinin).

    • Identification: These proteins are often used for the identification and classification of viruses.

    • Example: Varicella-zoster virus particle, approximately $200 \ nm$ in diameter, has an envelope coated with glycoproteins and an internal tegument layer surrounding an icosahedral capsid.

6.3 Viral Genomes Are Structurally Diverse

• Nucleic Acid Type: A virus may contain either single-stranded (ss) or double-stranded (ds) DNA or RNA, but not both.

• Genome Size: Varies greatly, from approximately $4,000$ nucleotides to $2$ million nucleotides.

• Genome Topology: Genomes can be linear or circular.

• Segmented Genomes: Some RNA viruses have genomes divided into multiple distinct segments.

6.4 Viral Life Cycles Have Five Steps

• One-Step Growth Curves:

  • Early experiments in $1939$ by Delbruck and Ellis with bacteriophage T4 and E. coli host cells provided foundational understanding of viral life cycles.

  • Eclipse Period: An initial phase during infection when no new infectious virus particles are present within the host cells, as viral components are being synthesized but not yet assembled.

  • Burst Size: The average number of new viruses produced and released per infected cell.

  • Latent Period: The time from infection until the first virions are released.

  • Rise Period: The time during which virions are actively being released.

• Five Steps of Viral Multiplication: The specific mechanism depends on the viral structure and genome, but generally includes:

  1. Attachment (Adsorption)

  2. Entry into the Host (Penetration)

  3. Synthesis (Replication)

  4. Assembly (Maturation)

  5. Virion Release

• 1. Attachment (Adsorption):

  • Viruses require a specific host cell to multiply.

  • Ligand-Receptor Interaction: A viral ligand (a protein on the virion surface, e.g., SARS-CoV-2 spike protein) attaches to a specific receptor (a molecule) on the host cell surface (e.g., human ACE2 receptor).

  • Host Preference (Tropism): The specificity of the receptor determines the host range and tissue tropism, meaning viruses will bind to specific tissue receptors.

  • Plant Viruses: Generally, plant cell receptors have not been identified; instead, damage to the host cell wall is often required for viral entry.

• 2. Entry into the Host:

  • After attachment, either the virus's genome alone or the entire nucleocapsid enters the host cell cytoplasm.

  • In some cases (e.g., many bacteriophages), only the nucleic acid enters, leaving the capsid attached to the outside of the cell.

  • In other cases, the genome remains enclosed within the capsid during entry.

  • Three Common Methods for Animal Viruses:

    1. Fusion of the viral envelope with the host cell's plasma membrane: The viral envelope fuses directly with the host membrane, releasing the nucleocapsid into the cytoplasm.

    2. Receptor-mediated endocytosis (for enveloped viruses): Viral envelope spikes bind to receptors, triggering endocytosis. The virus is enclosed in an endosome, and increased acidity within the endosome allows the nucleocapsid to escape into the cytosol.

    3. Receptor-mediated endocytosis (for nonenveloped viruses): Capsid proteins bind to receptors, triggering endocytosis. The nonenveloped virus enters an endosome, and the nucleic acid is then extruded from the endosome into the cytosol.

• 3. Synthesis (Replication):

  • This step varies most significantly between different types of viruses, as the viral genome dictates the events.

  • dsDNA Viruses: Typically follow the host cell's genome replication, transcription, and translation machinery.

  • RNA Viruses: Must either carry necessary enzymes (e.g., RNA-dependent RNA polymerase) within the virion or synthesize them upon entry to complete replication.

  • Viral Replication Complexes: Many viruses form specialized structures that enclose the machinery needed for genome replication and sometimes assembly, sequestering them from host defenses.

  • Regulation: Viral gene expression and protein synthesis are tightly regulated to ensure efficient production of progeny virions.

• 4. Assembly:

  • Involves the sophisticated organization of newly synthesized viral components into mature virions.

  • Late Proteins: Proteins produced later in the infection cycle are often involved in assembly.

  • Complex Process: The assembly process can be highly intricate; for example, in bacteriophage T4, components like the baseplate, tail fibers, and head are assembled independently before being combined into a complete virion.

• 5. Virion Release:

  • Two Primary Mechanisms:

    1. Host Cell Lysis: Nonenveloped viruses typically cause the host cell to burst (lyse), releasing progeny virions.

    2. Budding (for enveloped viruses): Enveloped viruses are released through a budding process.

       • Envelope Formation: Virus-encoded proteins are inserted into specific regions of the host cell membrane (plasma membrane, Golgi, ER).

       • Nucleocapsid Exit: The nucleocapsid migrates to these modified membrane regions and simultaneously pushes through the membrane, acquiring an envelope as it exits.

       • Host Actin Tails: Some viruses can utilize host actin tails to propel themselves through the host membrane, allowing for direct cell-to-cell spread.

       • Example: Sulfolobus turreted icosahedral virus (STIV) can produce pyramid-like structures on the cell surface during release.

6.5 Types of Viral Infections

• Bacterial and Archaeal Viral Infections:

  • Virulent Phage (Lytic Phage):

    • Has only one reproductive choice: to multiply immediately upon entering a bacterial host cell.

    • Releases progeny virions by lysing (destroying) the host cell.

  • Temperate Phage:

    • Has two reproductive options:

      1. Lytic Cycle: Can reproduce lytically, similar to virulent phages, leading to host cell lysis.

      2. Lysogenic Cycle: Can remain within the host cell without destroying it.

         • Lysogeny: The relationship between a temperate phage and its host, where the viral genome is integrated into the host's chromosome or exists as an extrachromosomal plasmid without causing immediate lysis.

         • Prophage: The form of the virus that resides within its host cell during lysogeny, replicated along with the host genome.

         • Lysogenic Bacteria: Bacteria that are infected with a temperate phage and carry a prophage.

         • Immunity: Lysogenic bacteria become immune to superinfection by the same type of phage.

         • Replication and Inheritance: The prophage is replicated and inherited as part of the host cell's genome by all progeny cells.

         • Induction: Under certain stress conditions (e.g., UV light), the prophage can be excised from the host chromosome and initiate the lytic cycle.

• Lysogenic Conversion:

  • A temperate phage changes the phenotype of its host bacterial cell.

  • Phenotypic Alterations: This can include alterations in surface characteristics (e.g., O-antigens in Salmonella, leading to changes in pathogenicity), or the acquisition of new virulence factors (e.g., toxin production in Corynebacterium diphtheriae leading to diphtheria).

  • Immunity to Superinfection: Lysogenic bacteria also become immune to further infection by the same type of phage.

  • Advantages for the Virus:

    1. Allows the viral nucleic acid to persist within a host population without destroying it, ensuring long-term survival.

    2. Can occur even with a high multiplicity of infection (many phages per bacterium), allowing host cell survival in an environment with high phage numbers and potentially few uninfected cells.

• Archaeal Viruses:

  • Can be either virulent or temperate.

  • Many establish chronic infections within their hosts.

  • Less is known about the mechanisms they use to regulate their replicative cycles compared to bacterial or eukaryotic viruses.

• Infection in Eukaryotic Cells:

  • Cytocidal Infection: Results in the death of the host cell, typically through lysis, similar to the lytic cycle in bacteria.

  • Persistent Infections: Can last for extended periods, even years, where the virus is continually or intermittently produced (e.g., HIV, Hepatitis B).

    • Latent Infection: Viral components are present (e.g., viral genome persists), but little or no actively replicating virus is produced, and the host cell is not harmed. Latent infections can be activated later, leading to cell death and virus release (e.g., Varicella-zoster virus causing chickenpox then shingles).

    • Chronic Infection: Slow and continuous release of virus particles without immediate host cell death (e.g., some Hepatitis C cases).

  • Cytopathic Effects (CPEs): Observable degenerative changes or abnormalities in host cells caused by viral infection (e.g., cell rounding, inclusion bodies, syncytia formation).

  • Transformation to Malignant Cell: Some viruses can transform normal host cells into malignant (cancerous) cells. This can occur through:

    • Activation of host proto-oncogenes.

    • Insertion of viral oncogenes.

    • Inactivation of tumor suppressor proteins by viral proteins.

    • Example: Human papillomavirus (HPV) causing cervical cancer.

6.6 Virus Cultivation and Enumeration

• Cultivation of Viruses: Viruses cannot be cultured like cellular microorganisms (e.g., bacteria on nutrient agar) because they require living host cells for replication.

  • Bacteriophages: Relatively simpler to culture. Lytic phages are grown by mixing virus and bacteria in liquid broth or on agar. Temperate phages require an additional step of inducing the lytic phase from lysogeny.

    • Plaques: Clear zones observed on bacterial lawns on agar cultures, indicating areas where host cells have been lysed by active viral replication.

  • Animal Viruses:

    • Suitable Host Animals: Inoculating live animals (e.g., mice) for in vivo studies or vaccine production.

    • Embryonated Eggs: Fertilized chicken eggs (incubated for $6$ to $8$ days after laying) serve as excellent living hosts due to their variety of tissues and immunological immaturity (e.g., influenza vaccine production).

    • Tissue (Cell) Cultures: Most common method. Animal cells are grown as monolayers on solid surfaces in culture dishes. Viral infection leads to observable Cytopathic Effects (CPEs).

  • Plant Viruses:

    • Plant Tissue Cultures: Cultures of separated plant cells or protoplasts.

    • Suitable Whole Plants: Direct inoculation of entire plants.

    • Mechanical Inoculation: Rubbing a mixture of virus and an abrasive material onto plant leaves to create microscopic wounds for entry.

    • Symptoms: May cause localized necrotic lesions (spots of dead tissue) or generalized symptoms of infection throughout the plant.

• Quantification of Viruses:

  • Plaque Assays: A standard method to quantify infectious virions.

    • Serially diluted virus samples are mixed with appropriate host cells (bacterial or animal) and plated on a suitable medium.

    • After incubation, plaques (zones of host cell clearing or death) are counted.

    • Plaque-Forming Units (PFU): The results are expressed as PFUs, where each plaque theoretically originates from a single infectious virion. The number of PFUs is directly proportional to the number of infectious viruses in the original sample.

6.7 Viroids and Satellites: Nucleic Acid-Based Subviral Agents

• Viroids:

  • Simple infectious agents that consist only of RNA.

  • Structure: Closed, circular, single-stranded RNAs ($ssRNAs$), typically very small (e.g., potato spindle tuber viroid, PSTVd).

  • Protein Encoding: Do not encode any proteins; their pathogenicity is due to the direct action of their RNA.

  • Replication: Replication requires specific host cell enzymes.

  • Diseases: Primarily cause diseases in plants (e.g., potato, coconut, citrus).

  • Mechanism of Pathogenicity: Often involve RNA silencing pathways in the host, where the viroid RNA interferes with normal gene expression.

• Satellites:

  • Infectious nucleic acids (DNA or RNA).

  • Dependence: Unable to replicate independently; they require a helper virus to replicate.

  • Capsid Proteins: Some satellites (satellite viruses) encode their own capsid proteins, which package the satellite nucleic acid.

  • Replication Enzymes: But they still rely on the helper virus for the enzymes and machinery needed for their replication.

  • Hosts: Most satellites use plant viruses as their helper viruses, but some animal virus satellites exist (e.g., Hepatitis D virus, a satellite-like virus requiring Hepatitis B virus).

6.8 Prions Are Composed Only of Protein

• Prions (Proteinaceous Infectious Particles):

  • Unique infectious agents composed only of protein; they lack nucleic acid.

  • Diseases: Cause a variety of fatal neurodegenerative diseases in humans and animals, collectively known as Transmissible Spongiform Encephalopathies (TSEs) due to the characteristic sponge-like lesions in the brain.

  • Animal Prion Diseases:

    • Scrapie: In sheep and goats.

    • Bovine Spongiform Encephalopathy (BSE): Commonly known as "mad cow disease," in cattle.

    • Chronic Wasting Disease (CWD): In deer, elk, and moose.

  • Human Prion Diseases:

    • Kuru: Historically associated with ritualistic cannibalism.

    • Fatal Familial Insomnia (FFI): A genetic form.

    • Creutzfeldt-Jakob Disease (CJD): Can be sporadic, familial, or acquired (e.g., variant CJD from consuming BSE-contaminated meat).

    • Gerstmann-Sträussler-Scheinker Syndrome (GSS): A genetic form.

• Current Model of Disease Production by Prions:

  • PrP^c (cellular prion protein): That is present in “normal” cells and can misfold into the infectious form, PrPsc (scrapie prion protein), which leads to neurodegeneration. The conversion is irreversible.

  • Still unknown if the loss of PrP^C or the accumulation of PrP^SC leads to the disease