virus

• Virus


  • Small acellular infectious agents
  • Can not replicate outside a host
  • Outside host: non-living, not metabolically operating
• Disease


  Viruses cause disease
• Diseases caused by viruses


  • Covid-19
  • Influenza disease - RNA virus
  • Small pox - vaccination irradiated this disease
• Viruses can also infect crops: cotton, maize, tomato > economic crisis
• Vaccines can be grown in eggs
• CRISPR


  Bacterial anti-viral systems that allow bacteria to remember viruses and defend if they attack again
• siRNA


  Ability to control gene expressions in cells
• Relative size of viruses


  • Smaller than eukaryotic and prokaryotic cells but larger than ribosomes
  • 20-200 nm
• Largest/smallest viruses


  • Pithovirus sibericum > 610,000 DNA base pairs
  • Porcine circovirus 1&2 > 1800-3,800 DNA base pairs
• Structure of viruses


  • Genetic material is either DNA or RNA
  • Packaged in capsid which is a protein coat protecting the virion form environmental conditions
  • Nucleocapsid - nucleic acid and capsid
  • Membrane envelope - surrounds the nucleocapsid
  • Protein spikes - help viruses attach to hosts
• General properties of viruses


  • DNA or RNA
  • Some have circular DNA, most have linear
  • Nucleic acid classifies the virus - if it has DNA or RNA
• CAPSID


  • Protein shell that surrounds and protects the viral genome
  • Facilitates delivery of viral genome into the host cell
  • Composed of protein molecules which are arranged in a precise repetitive pattern around the nucleic acid
• Capsomere


  • Subunit of capsid
  • Smallest morphological unit visible with an electron microscope
• Viral capsid symmetry


  • Helical symmetry
  • Spherical viruses
  • Icosahedron - 20 equilateral triangle faces
  • Complex viruses
• Helical symmetry


  The protein subunits and nucleic acid are arranged in a helix
• Spherical viruses


  • Efficient arrangement of subunits in a closed shell
  • Require less energy
• Icosahedron

  • Permits greatest number of units for capsomeres to be packed in
  • Protein subunits assemble into a symmetrical shell that covers the nucleic acid containing core
• Complex viruses

  • Bacteriophages
  • Viruses which can only infect bacteria, not humans
  • Icosahedron head and helical tail
• Nature of the virion

  • Some virions contain enzymes which are critical to infection
  • Lysozyme - makes hole in cell wall and lyses bacterial wall
  • Nucleic acid polymerases - replicate the nucleic acids once inside host cells
  • Proteins that counter host defence
  • Neuraminidases - enzymes that cleave glycosidic bonds, allowing the liberation of viruses from cell
• Rules for infectivity

  • A susceptible cell - has a functional receptor for a particular cell
  • Resistant cell - has no receptors for particular virus
  • Permissive cell - has capacity to replicate virus
  • A susceptible and permissive cell is the only cell that can take up a virus and replicate it
• How are viruses detected?

  • Electron microscopy
  • Viral cultures
  • Immunoassays to detect antibodies - rapid, low sensitivity
  • Polymerase chain reaction (PCR) - molecular lab based method
  • Next generation sequency - sequence virus giving idea of sequences/variations between strains
• Plaque assay

  • Analogous to the bacterial colony
  • A method to study virus infectivity
• Generic virome workflow

  • Total collection of viruses in a particular viruses
  • Study of virome composition benefit from new non-culture based metagenomic methods
• Viral infection cycle

  • Virus replication is typically characterized by a one-step growth curve
  • Latent period: eclipse+ maturation - can not detect virus as it is maturing
  • Burst size: number of virions released - virus matured and can be detected
• General Features of Virus Replication

  • Attachment (adsorption) of the virus to a susceptible host cell
  • Entry (penetration) of the virion or its nucleic acid
  • Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
  • Assembly of capsids and packaging of viral genomes into new virions (maturation)
  • Release of mature virions from host cell
• Viral Attachment & Penetration

  • Attachment of virion to host cell is highly specific
  • Requires complementary receptors on the surface of a susceptible host and its infecting virus
  • Receptors on the host cells carry out normal functions for the cell (uptake proteins, cell to cell interaction)
  • Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes
  • The attachment of a virus to its host cell results in changes to both virus and cell surface that facilitate penetration
  • Permissive cell: host cell that allows the complete replication cycle of a virus to occur
• Bacteriophage T4 example

  • Virus of E. coli; one of the most complex penetration mechanisms
  • Virions attach to cells via tail fibres that interact with polysaccharides on E. coli cell envelope
  • Tail fibres retract and tail core makes contact with E. coli cell wall
  • Lysozyme-like enzyme forms small pore in peptidoglycan
  • Tail sheath contracts and viral DNA passes into cytoplasm
• Production of Viral Nucleic Acid and Protein

  • Once a host has been infected, new copies of the viral genome must be made and virus-specific proteins synthesized in order for the virus to replicate
  • Generation of messenger RNA (mRNA) occurs first
  • Viral genome serves as template for viral mRNA
  • In some RNA viruses, viral RNA itself is the mRNA
  • In some cases essential transcriptional enzymes are contained in the virion
• Viral infection

  • Attachment and entry
  • Translation
  • Genome replication
  • Assembly
  • Release of virus
• Lysogeny

  • The ability of some viruses to integrate into the host genome
  • Temperate viruses can infect cells using either lytic or lysogenic cycles
  • Lytic cycle ⇢ Infection ⇢ extra-chromosomal replication and production of viral proteins ⇢ lysis and reinfection
  • Lysogenic cycle ⇢ Infection ⇢ integration into host DNA ⇢ virus in this form is called a "prophage" ⇢ replication of viral DNA becomes part of natural growth and cell division of the host cell⇢ eventually cells enter the lytic cycle
• Main Criteria for classification of viruses

  • Nucleic acid - type, single/double-stranded, linear/circular, single molecule or segmented
  • Capsid symmetry - icosahedra, helical or complex
  • Presence or absence of lipid envelope
• Baltimore Classification of Viruses

  • dsDNA - double stranded DNA
  • ssDNA (+ve strand) - single stranded DNA
  • gapped dsDNA - gapped double stranded DNA - not in archaea
  • dsRNA - double stranded RNA
  • ssRNA (+ve) - single stranded RNA positive sense - not in archaea
  • ssRNA (-ve) - single stranded RNA negative sense - not in prokaryotes/archaea
  • ssRNA ⇢ ssDNA(-) - needs to be converted from RNA>DNA for it to be converted to mRNA
• Viroid

  • An infectious entity comprising solely nucleic acid with no outer coat protein
  • Primarily plant pathogens
  • Cell to cell transport or direct injection, by aphids feeding from the plant
  • Don't generally make proteins but simply replicate their nucleic acids
  • So far all of the viroid use circular RNA
• Prion

  • A replicating inheritable entity that does not rely on DNA or RNA
  • Responsible for a number of deadly diseases including Creutzfeldt-Jakob disease (CJD), scrapie and bovine spongiform encephalopathy (BSE)
  • Fungal prions are very interesting because they can confer a selective advantage to the host and protect against non-compatible strains
• Immunity to viruses

  • Host resistance mechanisms
  • Many eukaryotes possess mechanisms to diminish viral infections - e.g. immune defence mechanisms, RNA interference
  • Prokaryotes possess similar mechanisms - e.g. CRISPR - Similar to RNA interference
  • Restriction modification systems - DNA destruction system; only effective against double-stranded DNA viruses
• The viral genome is composed of nucleic acid, either DNA or RNA.