W3: Virus Notes – Chapter 2: Viruses (Summary from transcript)

What is a virus?

• Viruses cannot reproduce unless they are within a host cell; they are obligate intracellular parasites.
  • Outside of a host cell, viruses:
  • Do not grow
  • Do not move or adapt to their environment
  • Display few biochemical structures or processes typical of living things
  • Do not produce any metabolic energy
• Key idea: viruses require a host to replicate and carry out their life cycle.

The virion, The provirus

• The virus can exist in different forms:
  • The virion: a complete, infective viral particle outside a host cell.
  • The provirus: viral genome integrated into the host genome (concept important for certain viruses).
• The virion consists of:
  • A genome – nucleic acid (either $ext{DNA}$ or $ext{RNA}$)
  • A protein coat (capsid)
  • Some viruses contain a lipid envelope
• Nucleocapsid: the combination of the viral genome and the capsid.
• The provirus refers to viral genetic material that is integrated into the host DNA and can be used to establish latency or ongoing expression in the host.

Virus size, symmetry, genome, and capsid

• Size range: from $20\mathrm{nm}$ to $1\mathrm{mm}$
• Symmetry:
  • Helical (tightly wound coil)
  • Icosahedral ($20\text{ triangular faces}$ and $12\text{ vertices}$)
  • Complex viruses
• Genome: $ext{DNA or RNA}$
• Capsid: composed of one or several proteins (capsomeres);
  • Gives the virus its symmetrical shape and provides protection for the genome
  • Helps package the genome for delivery to the cell
  • Note: the packaging efficiency or constraints can vary among viruses (example mention: relatively low for HIV)

Virus envelopes

• Envelopes are derived from cellular membranes and are composed of:
  • Lipid bilayers (with the same composition as the cellular membrane from which they were derived)
  • Viral glycoproteins (embedded in the envelope)
• Envelopes can adopt a variety of shapes

The viral life cycle (seven steps)

1. Binding to the cell receptor
2. Entry and uncoating
3. Early gene expression
4. Replication of the viral genome
5. Late gene expression
6. Assembly of virions
7. Exit

• These steps outline a general framework for how viruses infect cells and propagate.

Steps in virus entry

• How virions enter cells varies by host domain:
  • Viruses of bacteria, archaea, algae, and plants use entry mechanisms different from animal viruses
  • Bacteriophages may puncture through the bacterial/archaeal cell wall
  • Plant viruses may enter through mechanical means and then spread through plasmodesmata in plant tissues
• For animal viruses, cell entry often involves specific interactions with cell surface components

Virus receptors and entry

• A variety of cell surface proteins can serve as receptors or attachment factors for viruses
• Virus Receptor: the specific molecule on the host cell that a virus recognizes
• ENTRY: the process by which the virus gains access to the cell interior after receptor binding

Virus classification

• Classification bases:
  • Molecular architecture
  • Genetic relatedness
  • Host organism
• Viruses are grouped into species, genera, and families
• Distinct naming conventions and classification schemes exist across different domains of virology

Inactivating viruses

• Methods of inactivation:
  • Formaldehyde: combines with free amino groups on nucleic acid bases
  • Metals and phenol: react with viral capsid protein
  • Chlorine: combines chemically with nucleic acids in viruses
  • Heat: denatures proteins of the capsid
  • Ultraviolet radiation: causes thymine dimer formation by binding thymine and distorting the nucleic acid

Examples of viruses (as shown in the figures)

• Tobacco mosaic virus (a) Helical viruses
• Rabies virus
• Poliovirus
• Herpes simplex virus
• Bacteriophages
• Variola (smallpox) virus

Optional context and resources

• Virology resources and researchers mentioned in the transcript (e.g., Vincent Racaniello and TWIV) for further exploration