Virology: Viral Structure and Classification

• Viruses are nonliving pathogens, obligate intracellular parasites that cannot reproduce independently.
• Viral classification includes eight orders and 38 families.
• They are classified by structure, nucleic acid type, host organisms, and the diseases they cause.
• Viruses are ultramicroscopic infectious agents, some as small as 20 nanometers in diameter

Viewing Viruses

• Special equipment is needed to view viruses
• Electron microscopes are typically used

Viral Components

• Virion: A complete and fully developed viral particle capable of infecting a host
• Viruses contain a nucleic acid core of DNA or RNA, single or double-stranded
• Nucleic acids are encapsulated within a protective capsid composed of capsomers.
• Nuclear capsid: nucleic acid packaged within a capsid.
• Naked virus: nuclear capsid only
• Envelope virus: nuclear capsid within a lipid bilayer

Viral Spikes

• Glycoprotein spikes present on naked and enveloped viruses
• Help bind to the host surface
• Facilitate virus uptake into the host

Structural Capsid types include:

• Helical
• Icosahedral
• Complex

Helical Capsid Structure:

• Simpler, shaped like hollow cylinders.
• Capsomeres assemble into hollow disks, resembling a bracelet, with a hollow center that binds to viral nucleic acids
• Can be naked/enveloped, with naked nucleocapsids more rigid and enveloped ones more flexible.

Icosahedral Capsid Structure:

• Three-dimensional polyhedral shapes
• Have 20 sides and 12 evenly spaced corners
• Nucleic acid is packed into the center of the capsid
• Can be naked or enveloped

Complex Capsid Structure:

• Found in bacteriophages (viruses that infect bacteria)
• Nucleocapsids are generally naked

Viral Nucleic Acids

• Virus genomes can be DNA or RNA, single or double-stranded, linear, circular, or segmented.
• Viral genomes are efficient, carrying only genes for infection and replication within the host.
• The number of genes a virus carries varies from a few to hundreds.

DNA vs RNA Viruses

• DNA viruses: mostly double-stranded, can be single-stranded, genomes may be linear or circular.
• RNA viruses: mostly single-stranded, can be double-stranded, genomes can be segmented
• Single-stranded RNA viruses can be positive (+) or negative (-) sense.
• Positive-sense RNA viruses can be translated immediately by host ribosomes.
• Negative-sense RNA viruses must be transcribed into a positive-sense strand using RNA-dependent RNA polymerase before translation.
• Some RNA viruses encode reverse transcriptase to convert RNA to DNA.

Other Substances in Virus Particles:

• Polymerases: Enzymes that synthesize DNA or RNA.
• Replicases: Enzymes that replicate or synthesize RNA.
• Reverse transcriptase: Enzymes that synthesize DNA from an RNA template.
• Host ribosomes and tRNA molecules: Components of the host cell packaged along with the virus.

Viral Multiplication

• Five Steps:
  • Absorption
  • Penetration & Uncoating
  • Synthesis
  • Assembly
  • Release

Absorption

• Specific attachment of the virus onto the surface of the host cell.

Penetration and Uncoating

• Virus penetrates the cell, uncoats, and releases its nucleic acids into the cytoplasm
• Envelope viruses enter through membrane fusion
• Naked viruses enter using receptor-mediated endocytosis

Synthesis Stage

• Inside the cell, the virus replicates its genome and synthesizes proteins.
• DNA viruses (except pox viruses) replicate in the host nucleus.
• RNA viruses replicate and synthesize proteins in the cytoplasm.
• • RNA viruses act directly as mRNA and are translated into proteins.
• RNA viruses require RNA-dependent RNA polymerase to be transcribed into + RNA after uncoating.

Double Stranded RNA

• Rare, but have both + and - sense strands to produce viral proteins.

Retroviruses

• RNA viruses that encode reverse transcriptase.
• Converts RNA to DNA, which integrates into the host chromosome as a provirus.

Assembly and Release

• Viral components are assembled into protein capsids spontaneously.
• Release occurs through lysis (non-enveloped viruses) or budding (enveloped viruses).

Effects on the Host cell

• Viruses cause observable changes to the host cell, known as cytopathic effects (CPEs).
• Structural changes in cells result from viral damage, including cell shape and size
• Some viruses establish persistent infections, either chronic or latent.
• Chronic infections: viruses are continually produced over long periods
• Latent viral infections: the virus remains in the host without replication.

Transformation

• Acquisition of cancerous traits by cells

Oncoviruses

• Viruses that can cause cancer and encode oncogenes, activate protooncogenes, or have strong promoters/enhancers.

Viruses that Infect Bacteria

• Bacteriophages: viruses that infect bacteria
• Most have double-stranded DNA genomes; some have RNA genomes
• T-even phages (T2, T4, T6) are large, complex, and inject nucleic acids into bacterial hosts.

Lytic Cycle of T-even Bacteriophages

• Absorption: virus tail fibers attach to complementary receptors.
• Penetration: bacteriophages inject nucleic acids, degrade peptidoglycan via lysozymes.
• Duplication: Viral genetic material is duplicated.
• Synthesis: Host cell machinery is used to make copies of the genome and viral proteins.
• Assembly and Maturation: Capsid heads and tail portions of the virions are assembled separately
• Virus Lysis: Rupture of cell envelope and release of the viruses into the environment

Lysogeny

• Silent or inactive stage of infection.
• Temperate phages: DNA viruses that incorporate into host DNA.
• Phages insert into the chromosome and are called a prophage.
• Proteins suppress its transcription/expression, while viral genome replicates with host genome.
• Induction: Prophage reactivates, triggered by certain chemicals/UV light.
• Lysogenic conversion: Bacterium changes as a result of lysogeny.

Techniques for Cultivating Viruses

• In vivo: Conducted within a living organism.
• In vitro: Conducted outside of a living organism.
• Cell cultures consist of animal cells in a solution of nutrients and growth factors.
• Plaque assay is used to determine the number of bacteriophages in a sample

Other Noncellular Infectious Agents

• Prions: Proteinaceous infectious particles without nucleic acids that cause transmissible spongiform encephalopathies.
• Satellite viruses: Depend on other viruses for replication.
• Delta agent: A naked circle of RNA dependent on HPV for their replication.
• Viroids: Small, single-stranded RNA that infect plants.

Viruses and Human Health

• Viruses: The most common cause of acute infections.
• Examples of viruses are colds, hepatitis, chickenpox, influenza, herpes, and warts.
• Infections with high mortality rates includes rabies, AIDS, and Ebola.
• Infections that cause long term disability include polio and neonatal rubella.
• Antiviral drugs prevent viral replication; antibiotics do not work on viruses.
• Vaccines introduce a weakened/inactivated virus to elicit an immune response.