Virus

• Our contact with viruses is continuous
• Viruses infect all living things
• We eat and breathe billions of virions regularly
• Around 8% of the human genome is derived from sequences with similarity to infectious endogenous retroviruses (ERVs)
• The human virome is diverse
• Once infected, it is for life: HSV-1, HSV-2, VZV, HCMV, EBV, HHV-6, HHV-7, HHV-8
• Virus

  A simple, miniscule, infectious, obligate intracellular parasite comprising of genetic material (DNA or RNA) surrounded by a protein coat (capsid) and/or an envelope derived from a host cell membrane
• Genetic material in a cell

  • Double-stranded DNA (dsDNA)
  • Single-stranded RNA (ssRNA) (mRNA)
  • Peptides/proteins
• Influenza virus: 11 genes against >22000; SARS-COV-2: 23 genes
• Viruses contain either DNA or RNA genomes
• 2mm=2000 microns
• 500 million rhinoviruses
• Sneezing once can shed viruses enough to infect thousand
• 1mm = 1000 um; 1um = 1000nm
• Viruses

  • Very small: Usually 20 – 300 nm
  • Can be seen with an electron microscope
• Giant viruses

  • Much bigger than we initially thought!
  • Mimiviruses: 750 nm
  • Bigger than bacteria
  • Can be even seen under light microscope
• Pandoravirus


  • Biggest virus known so far
  • 2.9 megabytes (MB) genome size (>2.5 million base pairs)
  • Enclosed 2556 genes (compared to 11 genes in influenza)
  • Fortunately, only infect Amoeba
• Virion

  Extracellular virus particle (outside the host cell) - for transmission
• Virus

  Intracellular virus (after infecting the host cell) - for replication
• Bacterial multiplication

  Asexual reproduction, or cell division, of a bacterium into two daughter cells, in a process called binary fission
• Viral replication

  Formation of biological viruses during the infection process in the target host cells
• Tools of viral structural biology

  • Electron microscopy
  • X-ray crystallography
  • Cryo-electron microscopy
  • Nuclear magnetic resonance spectroscopy (NMR)
• Capsomers

  Structural protein units that made up the capsid
• Nucleocapsid

  The nucleic acid plus the capsid
• Capsid


  Protein coat/shell (made up of many protein subunits = capsomers)
• Virion


  Virus particle (outside the cell)
• Shapes of viruses: Capsid symmetry

  • Helical
  • Polyhedral (Icosahedron)
  • Binal (Complex)
• Functions of Capsid

  • Protects the nucleic acid from digestion by enzymes
  • Contains special sites on its surface that allow the virion to attach to a host cell
  • Provides proteins that enable the virion to penetrate the host cell membrane and, in some cases, to inject the infectious nucleic acid into the cell's cytoplasm
  • Under the right conditions, viral RNA in a liquid suspension of protein molecules will self-assemble a capsid to become a functional and infectious virus
• Naked viruses

  Lacking envelope
• Enveloped virion

  Nucleocapsid enclosed inside an envelope containing proteins encoded by the virus
• Hosts for viruses

  • Bacteria (T4 bacteriophages)
  • Protozoa (Trichomonas, Leishmania, Giardia, Plasmodium, Entamoeba)
  • Algae (members of Phycodnaviridae family)
  • Fungi (mycoviruses)
  • Plants (tobacco mosaic viruses)
  • Animals (avian influenza virus)
  • Virophage (viruses that infect viruses)
• Bacteriophages


  Viruses of bacteria
• More than 10^30 bacteriophage particles in the world's waters
• A bacteriophage particle weights about a femtogram (10^-15 grams)
• 10^30 x 10^-15 = the biomass on the planet of bacterial viruses alone exceeds the biomass of elephants by more than 1000-fold!
• The length of a head-to-tail joining of 10^30 phages = 1.25x10^21 km = 100 million lights years
• Bacteriophage genomes

  • Only few with envelopes
  • Most have dsDNA
  • Many are complex
• Replication cycle of the lytic Bacteriophage T4

  1. Adsorption: Attachment to specific receptors

  2. Penetration: (entry of DNA)

  3. Replication: Synthesis of viral nucleic acids and protein

  4. Maturation: Assembly and packaging of new virions

  5. Release: Release of new virions (lysis)

  6. Reinfection
• Lytic phage


  Virulent and kills the host
• Temperate/Lysogenic phage


  Doesn't kill the host, genome integrates into host chromosome as a prophage