Viruses: Structure, Infection & Replication (Chapter 5)

• Viruses are discussed in chapter 5.

Viruses

• Acellular.
• Genome material is nucleic acid.
• Can be either DNA or RNA, double-stranded or single.
• Lack a membrane and can’t have a cell membrane.
• Observed using an electron microscope or a probe microscope.
• Can infect bacteria; such a virus is called a phage.
• Extremely small, ranging from 10-100 nm.
• "Ultramicroscopic".
• "Microbes".
• Obligate intracellular parasites.
• Genomic material is not always in the form of DNA.

Viral Structures

• Capsid: a protein that protects nucleic acid.
• Helical or icosahedral.
• Genomes contain RNA or DNA that's single or double-stranded.
• Genomes can be linear, circular, or segmented.
• Have attachment (glyco)proteins and accessory proteins.
• Can be enveloped or naked.
• RNA genomes must use RNA polymerase for replication.

Viral Infection & Replication

• Any cell can be infected by a virus.
• Viruses don't have ribosomes and nucleic acids.
• Exhibit tropism and have a host range.
• Bacteriophages are viruses that infect bacteria.
• Virus infection steps include attachment, entry, synthesis to make more DNA/protein, assembly, and release.
• A permissive cell allows viral replication.
• Host range/tropism affects permissivity.
• Burst size/burst time are infection characteristics

Viral Entry - Animal

• A virus attaches to a cell receptor and initiates endocytosis.
• An endosome forms with the virus inside.
• Nucleocapsid escapes to the cytoplasm and uncoats to release the genome.
• A conformational change occurs in the virus protein after it attaches to the receptor initiating the viral envelope to fuse to the cell membrane and releasing the nucleocapsid.

Viral Entry - Other

• Bacteriophages attach to the receptors on the outside of the cell using tail fibers. Conformational changes then allow the base of the tail to contact the host cell surface.
• Proteins rearrange allowing the core to come into contact with the cell membrane
• Genetic material is delivered into the cell via a created pore.
• Plants and fungi need to be damaged for viral entry.

Lytic vs. Lysogeny (Phage)

• Specific to bacterial infections.
• In the lytic cycle, the phage attaches and injects its DNA, which circularizes and enters the lytic cycle.
• The cell then lyses, releasing phage virions.
• Meanwhile in the lysogenic cycle the injected DNA circularizes and the bacterial chromosome recombines becoming a prophage.
• The phage can then excise from the bacterial chromosome initiating a lytic cycle.

Measuring Viruses

• Can use plaque assay:

• Viruses can grow on agar.

• Small amounts of susceptible bacterial host cells added to molten nutrient-rich agar, and then quickly mixed.

• The agar mixture is poured onto a nutrient agar base where it solidifies.

• Plaques, or holes, appear after sufficient incubation.

• For animal virus an assay is used.

• Cytopathic Effects (CPE) and TCID50.

• Hemagglutination can be used to measure virus levels.

Classifying Viruses

• ICTV (International Committee on Taxonomy of Viruses) classifies viruses based on order, family, subfamily, genus, and species.
• The Baltimore system classifies viruses based on their genome.
• Seven categories:
  • dsDNA
  • ssDNA
  • dsRNA
  • (+) sense ssRNA
  • (-) sense ssRNA
  • Reverse transcriptase ssRNA
  • Reverse transcriptase dsDNA

Viroids & Prions

• Viroids are infectious RNA, replicated by RNA replicase, and typically infect plants.
• Prions are infectious proteins that cause spongiform encephalopathy.
• Prion diseases include:
  • Scrapie (sheep)
  • Mad cow disease (BSE)
  • Chronic wasting disease (elk & deer)
  • Kuru
  • Creutzfeldt-Jakob Disease (people)

Virus-like particles

• Satellite viruses need another virus for infection, like HepD.