Summary Virology PH
3Ba BMW
2025-2026
Summary Virology
Chapter 1: Introduction
1. What are viruses? Where do they originate?
• Most abundant biological entities on the planet
o More viruses in 1 liter of seawater than people on earth
• Major roles in global ecology and evolution of the biosphere
• Obligate intracellular parasites with genome packaged in tiny protein/lipid particles
o Need a living host cell to replicate
• All organisms on the planet harbour distinctive repertoires of viruses
o We eat and breath billions of virus particles
• Human DNA consist partly of ancestral viral genetic material
o Remnants of retroviruses in LTR retrotransposons, SINEs and LINEs
o When the viral genome can reach the germline cells via infection → genome can
be passed down generations
• Viruses are small
o Almost size of a ribosome (30-300nm)
▪ In some plants in µm range
▪ Exceptions like Pandora virus = 1000nm (rivals bacteria)
o EM needed to visualize viruses (not LM)
• Viruses are diverse in structure
o Going from icosahedral to helical to snake-like
• All viruses are obligatory parasites
o Infect all life forms (archaea, bacteria, eukaryotes, plants, animals)
o Genome consists of EITHER DNA or RNA
▪ Can be ss or ds
o Has protein coat = capsid
▪ Protection of genetic material AND transmission of genetic material by
facilitating entry into host cell via receptor binding
o Some viruses CAN HAVE lipid envelope around capsid which they acquire from
the host cell
o Rely on host for Energy production, protein syntheses and reproduction
• Rules regarding viruses
o All viral genomes are obligate molecular parasites that can only function after
they replicate in a cell
o All viruses must make mRNA that can be translated by host ribosomes: they are
all parasites of the host protein synthesis machinery
o Viruses are important disease-causing agents, BUT not all viruses make us sick
▪ Many viruses are just passengers through our body (food intake, water,
environment, breathing)
▪ Our IS has learned to deal with (some) viruses
Page 1 of 28
,Summary Virology PH
3Ba BMW
2025-2026
Virus replication – quick overview
• Different replication than bacteria
and eukaryotic cells
o Eukaryotic cells → mitosis to
divide
o Bacteria → binary fission to
divide
o Viruses:
▪ Attachment to cell
▪ Entry in cell (where
capsid comes apart)
▪ Replication + gene
expression giving copies of
genome and viral proteins
▪ (re)assembly of virus
▪ Release → off to infect new cell
o Viral genome is small → encoding for
very few proteins including BUT NOT
LIMITED TO the capsid as well as
polymerases (which cannot do
proofreading)
o Small genome size = high mutation rate
(of enzymes responsible for copying the genome)
▪ Larger genomes → encode polymerases with proofreading capacities
smaller genomes encode bare minimum
▪ Epidemic causing viruses are usually RNA viruses (high mutation rate →
high variation → some variants will be able to evade the IS)
▪ Quasispecies: difference between virus that enters host cell and virus
that exits host cell due to high mutation rate → virus undergoes
mutations within the host cell and leaves as a virus with different genome
→ viruses are determined using sequencing rather than structure
Are viruses dead or alive?
• They don’t have energy production (C-metabolism)
• They cannot replicate or evolve by themselves only within host cells → without a cell
they are considered inanimate complex organic matter
• There are no ancestral viral lineages: there is no single gene that has been identified that
is shared by ALL viruses
o There are common protein motifs in viral capsids BUT these likely came about
from convergent evolution or horizontal gene transfer
• They don’t have structure derived from a common ancestor: cells for example get their
cell membrane from other cells during cell division (membrane is hereditary) BUT this
doesn’t occur in viruses
Page 2 of 28
, Summary Virology PH
3Ba BMW
2025-2026
Origin of viruses
• (1) “Primordial virus world” or “virus
early” hypothesis
o There were complex RNA and
DNA entities who replicated,
and viruses came from them
o Direct descendants of the first
replicons during pre-cellular
stage of evolution of life
• (2) “Reductive virus origine” or
“regression” hypothesis
o Ancestral cells (early proto cells) have degenerated and lost their anatomy and
transitioned into intracellular parasites
o This explains giant viruses that encode for almost everything but don’t have
cellular structures
o Viruses are the ultimate products of degeneration
• (3) “escaped genes” hypothesis
o Extracellular vesicles derived from cells have evolved into viruses after acquiring
a genome
A typical viral genome
• Genome consists of either DNA or RNA
which is ss and/or ds
• At least 2 core modules that consists
of genes encoding for proteins
required for genome replication (non-
structural proteins) and proteins involving virion formation (structural proteins)
• Chimeric origin of viruses (hypothesis)
o Replication machinery may have risen from primordial pool of genetic elements
(early)
o Structural proteins may have been acquired from hosts at different stages of
evolution (“after origin of cellular life”)
5 hallmarks of viral replication genes
• All RNA viruses (except satellite viruses)
have a RNA dependent RNA polymerase
(RdRp)→ this is universally conserved
across all RNA viruses
• All reverse-transcribing (RT-) viruses wit
RNA and DNA genomes have reverse
transcriptase
• All small-to-medium sized DNA viruses
have protein-primed family B DNAP
• Most ssDNA and some dsDNA viruses have rolling-circle replication endonuclease
• Most eukaryotic ssDNA and some dsDNA viruses, and many groups of ssRNA viruses
have superfamily 3 helicase
Page 3 of 28
3Ba BMW
2025-2026
Summary Virology
Chapter 1: Introduction
1. What are viruses? Where do they originate?
• Most abundant biological entities on the planet
o More viruses in 1 liter of seawater than people on earth
• Major roles in global ecology and evolution of the biosphere
• Obligate intracellular parasites with genome packaged in tiny protein/lipid particles
o Need a living host cell to replicate
• All organisms on the planet harbour distinctive repertoires of viruses
o We eat and breath billions of virus particles
• Human DNA consist partly of ancestral viral genetic material
o Remnants of retroviruses in LTR retrotransposons, SINEs and LINEs
o When the viral genome can reach the germline cells via infection → genome can
be passed down generations
• Viruses are small
o Almost size of a ribosome (30-300nm)
▪ In some plants in µm range
▪ Exceptions like Pandora virus = 1000nm (rivals bacteria)
o EM needed to visualize viruses (not LM)
• Viruses are diverse in structure
o Going from icosahedral to helical to snake-like
• All viruses are obligatory parasites
o Infect all life forms (archaea, bacteria, eukaryotes, plants, animals)
o Genome consists of EITHER DNA or RNA
▪ Can be ss or ds
o Has protein coat = capsid
▪ Protection of genetic material AND transmission of genetic material by
facilitating entry into host cell via receptor binding
o Some viruses CAN HAVE lipid envelope around capsid which they acquire from
the host cell
o Rely on host for Energy production, protein syntheses and reproduction
• Rules regarding viruses
o All viral genomes are obligate molecular parasites that can only function after
they replicate in a cell
o All viruses must make mRNA that can be translated by host ribosomes: they are
all parasites of the host protein synthesis machinery
o Viruses are important disease-causing agents, BUT not all viruses make us sick
▪ Many viruses are just passengers through our body (food intake, water,
environment, breathing)
▪ Our IS has learned to deal with (some) viruses
Page 1 of 28
,Summary Virology PH
3Ba BMW
2025-2026
Virus replication – quick overview
• Different replication than bacteria
and eukaryotic cells
o Eukaryotic cells → mitosis to
divide
o Bacteria → binary fission to
divide
o Viruses:
▪ Attachment to cell
▪ Entry in cell (where
capsid comes apart)
▪ Replication + gene
expression giving copies of
genome and viral proteins
▪ (re)assembly of virus
▪ Release → off to infect new cell
o Viral genome is small → encoding for
very few proteins including BUT NOT
LIMITED TO the capsid as well as
polymerases (which cannot do
proofreading)
o Small genome size = high mutation rate
(of enzymes responsible for copying the genome)
▪ Larger genomes → encode polymerases with proofreading capacities
smaller genomes encode bare minimum
▪ Epidemic causing viruses are usually RNA viruses (high mutation rate →
high variation → some variants will be able to evade the IS)
▪ Quasispecies: difference between virus that enters host cell and virus
that exits host cell due to high mutation rate → virus undergoes
mutations within the host cell and leaves as a virus with different genome
→ viruses are determined using sequencing rather than structure
Are viruses dead or alive?
• They don’t have energy production (C-metabolism)
• They cannot replicate or evolve by themselves only within host cells → without a cell
they are considered inanimate complex organic matter
• There are no ancestral viral lineages: there is no single gene that has been identified that
is shared by ALL viruses
o There are common protein motifs in viral capsids BUT these likely came about
from convergent evolution or horizontal gene transfer
• They don’t have structure derived from a common ancestor: cells for example get their
cell membrane from other cells during cell division (membrane is hereditary) BUT this
doesn’t occur in viruses
Page 2 of 28
, Summary Virology PH
3Ba BMW
2025-2026
Origin of viruses
• (1) “Primordial virus world” or “virus
early” hypothesis
o There were complex RNA and
DNA entities who replicated,
and viruses came from them
o Direct descendants of the first
replicons during pre-cellular
stage of evolution of life
• (2) “Reductive virus origine” or
“regression” hypothesis
o Ancestral cells (early proto cells) have degenerated and lost their anatomy and
transitioned into intracellular parasites
o This explains giant viruses that encode for almost everything but don’t have
cellular structures
o Viruses are the ultimate products of degeneration
• (3) “escaped genes” hypothesis
o Extracellular vesicles derived from cells have evolved into viruses after acquiring
a genome
A typical viral genome
• Genome consists of either DNA or RNA
which is ss and/or ds
• At least 2 core modules that consists
of genes encoding for proteins
required for genome replication (non-
structural proteins) and proteins involving virion formation (structural proteins)
• Chimeric origin of viruses (hypothesis)
o Replication machinery may have risen from primordial pool of genetic elements
(early)
o Structural proteins may have been acquired from hosts at different stages of
evolution (“after origin of cellular life”)
5 hallmarks of viral replication genes
• All RNA viruses (except satellite viruses)
have a RNA dependent RNA polymerase
(RdRp)→ this is universally conserved
across all RNA viruses
• All reverse-transcribing (RT-) viruses wit
RNA and DNA genomes have reverse
transcriptase
• All small-to-medium sized DNA viruses
have protein-primed family B DNAP
• Most ssDNA and some dsDNA viruses have rolling-circle replication endonuclease
• Most eukaryotic ssDNA and some dsDNA viruses, and many groups of ssRNA viruses
have superfamily 3 helicase
Page 3 of 28
