2024-
2025
Virology
PETER DELPUTTE
FEMKE VAN NIMMEN
,1 What are viruses? Where do they originate?
1.1 Introduction
What are viruses?
• Most abundant biological entities on the planet
• Major roles in global ecology & evolution of the biosphere
• Obligate intracellular parasites that package their genomes into tiny protein/lipid particles
• All organisms on the planet harbour distinctive repertoires of viruses
• We breathe & eat billions of virus particles
• Human DNA consists partly of ancestral viral genetic material (transposable elements: ancestral viral material)
• A lot of viruses have a zoological background & comes over to humans
Astonishing number of viruses on earth:
• > 1016 HIV particles on Earth
• Viruses on plants, in oceans, on animals, in hot water, …
• More viruses in 1l sea water than people on earth → most abundant organisms
• In biomass: a very small part → viruses are minimal structures.
• > 1030 bacteriophages (living on bacteria) in our seas
The human microbiome:
• Bacteria are living on our skins & in major organ systems
• Bacteria: also covered by viruses (= virome) → viruses that feed on bacteria = bacteriophages
• The human virome and the global virome: each anatomical system mapped out which viruses are where and
which ones cause diseases → minimal fractur of viruses infect humans, only a fraction leads to disease.
The human genome contains remnants of viral genetic material:
• Bacteria regulate processes in our body, another layer keeps control of these bacteria: bacteriophages.
• A lot of our own human genome is ancestral viral genetic material
• Only 1,5% of human genome are protein coding genes → a lot of transposable items had relics of ancestral
viruses (functions at this moment is unknown)
Viruses are small:
• Bacteria: with light microscope
• Virus: at the edge of what we can see with the light microscope →
better visible with electron microscope
• Effect of virus on cell is visible
• Different microscopical approaches can be used (angstrom level)
• Mimivirus (400nm) & pandoravirus (1000nm): unusually large viruses:
o Recently discovered
o Approach the size of bacteria
o They live on amoeba → first thought they were bacteria, but not the typical build/organistaion of bacteria
o Pandora has a ‘mouth’ that it uses to attack the cell & release genome in the cell
o They have dsDNA
1
r
,Viruses are diverse in structure:
• Many particles are spherical = round shapes → can package a
lot of material in a round structure
• Other structures are more complex:
o Bullet shape
o Philomentous viruses
o Variola & pox viruses: more complex structures
Viruses are obligatory parasites:
• Found to infect each life form: plants, animals, eukaryotes, bacteria
• DNA or RNA, ss or ds, protein coat, with or without lipid envelope
• Rely on host cell for energy production, protein synthesis & reproduction
• All viral genomes are obligate molecular parasites → can only function after
replicating in a cell
• All viruses must make mRNA that can be translated by host ribosomes → they are
parasites of the host protein synthesis machinery
• Virion = infectious viral particle → must fuse the membrane of the virus with cellular membrane → release
genetic material in the cell → must be compatible with the protein synthesis machinery → new viral particle
that has to be released from the cell.
• Viruses are important disease-causing agents, but not all viruses make us sick
o Many viruses are just passengers through our body (food intake, breathing)
o Our immune system has learned to deal with (some) viruses
Virus replication:
• Not comparable to bacterial replication = binairy fision.
• Look at the timeline of replication cycle: virus attaches to the cell
→ virus goes silent: no trace of any virus → replicate, make
protein material in the cell → burst phase: one cell produces a
lot of virus particals → often the cells will die because they
release a huge amount of virus particals.
Steps
1. inoculation:
2. ecplise:
3. burst:
4. burst size
Viruses have high genome evolution rates:
• Viruses evolve rapidly → for example corona virus: there are a lot
of variants (alpha, beta, delta, gamma, omicron)
• Eukaryotes: large genomes becauwe the polymerase is extremly
good, so a lot of energy needed for copying this without mistakes
→ exact copy of genetic material is required
• RNA viruses: smaller genome, if the genome is to big they can not
replicate anymore
• All viruses typically have higher mutation rates than bacteria →
they have no proofreading → lot of mistakes
• Coronavirus is an RNA virus with largest genome we know (30kb)
(RNA molecules can tolerate a max. of 30 kb genome)
2
r
, • HIV: virus that is divers → accumulates a lot of mutations over its lifetime → every time a mutation is
incorporated → a variant arises → large diversity of variants that exist in 1 patiënt
Escape IS: changing a lot, like RNA viruses. Influenza is a good example. ddDNA will not envolve that rapidly. DNA
virusus often uses the enzylme of the infected cel, RNA dependent RNA polymerase, so they make their own
polymerase , but has no proofreading activity and this creates a lot of variation
3
r
2025
Virology
PETER DELPUTTE
FEMKE VAN NIMMEN
,1 What are viruses? Where do they originate?
1.1 Introduction
What are viruses?
• Most abundant biological entities on the planet
• Major roles in global ecology & evolution of the biosphere
• Obligate intracellular parasites that package their genomes into tiny protein/lipid particles
• All organisms on the planet harbour distinctive repertoires of viruses
• We breathe & eat billions of virus particles
• Human DNA consists partly of ancestral viral genetic material (transposable elements: ancestral viral material)
• A lot of viruses have a zoological background & comes over to humans
Astonishing number of viruses on earth:
• > 1016 HIV particles on Earth
• Viruses on plants, in oceans, on animals, in hot water, …
• More viruses in 1l sea water than people on earth → most abundant organisms
• In biomass: a very small part → viruses are minimal structures.
• > 1030 bacteriophages (living on bacteria) in our seas
The human microbiome:
• Bacteria are living on our skins & in major organ systems
• Bacteria: also covered by viruses (= virome) → viruses that feed on bacteria = bacteriophages
• The human virome and the global virome: each anatomical system mapped out which viruses are where and
which ones cause diseases → minimal fractur of viruses infect humans, only a fraction leads to disease.
The human genome contains remnants of viral genetic material:
• Bacteria regulate processes in our body, another layer keeps control of these bacteria: bacteriophages.
• A lot of our own human genome is ancestral viral genetic material
• Only 1,5% of human genome are protein coding genes → a lot of transposable items had relics of ancestral
viruses (functions at this moment is unknown)
Viruses are small:
• Bacteria: with light microscope
• Virus: at the edge of what we can see with the light microscope →
better visible with electron microscope
• Effect of virus on cell is visible
• Different microscopical approaches can be used (angstrom level)
• Mimivirus (400nm) & pandoravirus (1000nm): unusually large viruses:
o Recently discovered
o Approach the size of bacteria
o They live on amoeba → first thought they were bacteria, but not the typical build/organistaion of bacteria
o Pandora has a ‘mouth’ that it uses to attack the cell & release genome in the cell
o They have dsDNA
1
r
,Viruses are diverse in structure:
• Many particles are spherical = round shapes → can package a
lot of material in a round structure
• Other structures are more complex:
o Bullet shape
o Philomentous viruses
o Variola & pox viruses: more complex structures
Viruses are obligatory parasites:
• Found to infect each life form: plants, animals, eukaryotes, bacteria
• DNA or RNA, ss or ds, protein coat, with or without lipid envelope
• Rely on host cell for energy production, protein synthesis & reproduction
• All viral genomes are obligate molecular parasites → can only function after
replicating in a cell
• All viruses must make mRNA that can be translated by host ribosomes → they are
parasites of the host protein synthesis machinery
• Virion = infectious viral particle → must fuse the membrane of the virus with cellular membrane → release
genetic material in the cell → must be compatible with the protein synthesis machinery → new viral particle
that has to be released from the cell.
• Viruses are important disease-causing agents, but not all viruses make us sick
o Many viruses are just passengers through our body (food intake, breathing)
o Our immune system has learned to deal with (some) viruses
Virus replication:
• Not comparable to bacterial replication = binairy fision.
• Look at the timeline of replication cycle: virus attaches to the cell
→ virus goes silent: no trace of any virus → replicate, make
protein material in the cell → burst phase: one cell produces a
lot of virus particals → often the cells will die because they
release a huge amount of virus particals.
Steps
1. inoculation:
2. ecplise:
3. burst:
4. burst size
Viruses have high genome evolution rates:
• Viruses evolve rapidly → for example corona virus: there are a lot
of variants (alpha, beta, delta, gamma, omicron)
• Eukaryotes: large genomes becauwe the polymerase is extremly
good, so a lot of energy needed for copying this without mistakes
→ exact copy of genetic material is required
• RNA viruses: smaller genome, if the genome is to big they can not
replicate anymore
• All viruses typically have higher mutation rates than bacteria →
they have no proofreading → lot of mistakes
• Coronavirus is an RNA virus with largest genome we know (30kb)
(RNA molecules can tolerate a max. of 30 kb genome)
2
r
, • HIV: virus that is divers → accumulates a lot of mutations over its lifetime → every time a mutation is
incorporated → a variant arises → large diversity of variants that exist in 1 patiënt
Escape IS: changing a lot, like RNA viruses. Influenza is a good example. ddDNA will not envolve that rapidly. DNA
virusus often uses the enzylme of the infected cel, RNA dependent RNA polymerase, so they make their own
polymerase , but has no proofreading activity and this creates a lot of variation
3
r
