2025-2026 Molecular Virology Peter Delputte
MOLECULAR VIROLOGY AND INFECTIONS
GENERAL INTRODUCTION
WHY DO WE STUDY VIRUSES?
• Viruses are everywhere
o There are more viruses than stars in the universe
o They infiltrate every aspect of our natural world, seething in seawater, drifting through the
atmosphere, and lurking in miniscule motes of soil
o Whales and zooplanktons are commonly infected with marine caliciviruses à infected whales
excrete more than 1013 caliciviruses daily (106 per gram feces) and remain viable for more
than 14 days in 15°C seawater
§ Why has it evolved to become this stable (most human viruses don’t live longer than
a day in the environment)? Whales don’t come in close contact with each other
o Viruses are classified based on their genome (researchers used to have to culture the virus
and its host)
• Viruses come in all shapes and sizes
o Eukaryotic viruses are small (they don’t code for anything and use the host cells machinery)
o Some viruses code for everything = these are big
• Viruses cause human diseases
o Even with constant exposure to viruses everywhere, the vast majority of viruses that infect
us have little or no impact; these viruses just pass through us
§ We ingest many non-animal viruses regularly with foods (e.g. cabbage in US
supermarkets contain 108 virus particles)
§ This relative safety depends on our elaborate immune defense system, which has
evolved to fight microbial infections à if this immune defense system is
compromised, even the most common infections can be lethal
o Despite such defenses, some of the most devastating human diseases have been or are still
caused by viruses
§ E.g. smallpox, COVID 19, measles, HIV, influenza…
§ Can lead to life-threatening diseases that impact virtually all organs, including the
lungs, liver, CNS and intestines
§ Viruses are responsible for 20% of the human cancer burden
§ Viral infections of the respiratory and gastro-intestinal tract kill millions of children
in developing world each year
• Viruses can be beneficial
o In marine ecology, virus particles are the most abundant biological entities
§ 94% of all nucleic acid-containing particles in the oceans
§ 15x more abundant than the Bacteria and Archaea
§ Viral infections in the ocean kill 20-40% of marine microbes daily à release essential
nutrients that supply phytoplankton (food), as well as carbon dioxide and other
gases that affect the climate of the earth
1
,2025-2026 Molecular Virology cc
o Pathogens can also influence one another: infection by one virus can have an ameliorating
effect on the pathogenesis of a second virus or even bacteria
§ HIV virus-infected AIDS patients show a substantial decrease in their disease
progression if they’re persistently infected with hepatitis G
§ Mice latently infected with some murine herpesviruses are resistant to infection
with the bacterial pathogens Listeria monocytogenes and Yersinia pestis
• Viruses can cross species boundaries
o Viruses generally have a limited host range, yet they can and do spread across species
barriers
§ Viruses are usually confined to 1 host species because of co-evolution
o As the world’s human population continues to expand and imping on the wilderness, cross-
species (zoonotic) infections of humans are occurring with increasing frequency
§ E.g. HIV pandemic, Ebola hemorrhagic fever and SARS-CoV-2 pandemic
§ Currently: influenza virus H5N1 in avian (avian flu) = frightening possibility of
transmission to humans of a highly pathogenic strain
o Why are zoonotic infections such a burden? We do not have any pre-existing immunity
• Viruses drive human evolution
o Every cell in our body contains viral DNA
o Human endogenous retroviruses, and elements thereof,
make up about 5 to 8% of our DNA
§ Most are inactive, fossil remnants from
infections of germ cells that have occurred over
millions of years during our evolution
§ Some of them are suspected to be associated
with specific diseases
o Protein products of other endogenous retroviruses are essential
o Transposable elements (TE) = 40% of our genome
§ Discovered in 1940s = took half a century before we understood the importance
§ A crucial stage was reached with the completion of the first human genome
sequence à nearly half our genome is derived from different types of TE
§ Retrotransposons = copy and paste themselves into different genomic locations by
converting RNA back into DNA using reverse transcriptase
§ DNA transposons = discrete DNA pieces which can move from site to site within
genomes = jumping genes
§ SINES/LINES = short and long interspersed nuclear elements that invade new
genomic sites using RNA intermediates (copy and paste)
o Viruses have been part of all human history: they were present long before us, and the
majority of human infections were likely acquired from animals (zoonoses)
o Epidemics most likely have shaped which species and populations have been successful to
reproduce and expand
o As viruses continue to be discovered, our understanding of how human health and well-being
are affected by these agents remain incomplete
o E.g. protein products of endogenous retroviruses are essential for who we are as a species
§ A gene of viral origin encodes for a protein that plays a key role in long-term
memory formation by moving information between cells in the nervous system
§ Evolution of the mammalian placenta and the timing of gene expression in human
pregnancy depends on a bit of genetic code that was co-opted from ancient
retroviruses that infected our ancestors > 130 million years age
2
,2025-2026 Molecular Virology cc
o The disappearance of viruses would impact the evolutionary potential for all life on the
planet, including humans
§ Since viruses are constantly replicating and mutating, they hold a massive repository
of genetic innovation that other organisms can incorporate
§ Viruses replicate by inserting themselves into host cells and hijacking their
replication tools à if this happens in germ line cells, the viral code can be passed on
to the next generation and become permanently integrated
§ The insertion of new DNA into genomes is major mode of evolution!
o How do we know this is beneficial? Otherwise, this viral DNA would not be incorporated in
our genome anymore (negative selection!
• Viruses are unique tools for studying cell biology
o Studying viruses = inherently studying cells
o Because viruses are dependent on their host for propagation, studies that focus on viral
reprogramming of cellular mechanisms have provided unique insights into cellular biology
and functioning of host defenses
o Groundbreaking studies of viruses that infect bacteria (= bacteriophages), laid the
foundations of modern molecular biology
WHAT IS A VIRUS?
• = generally considered non-living entities, which can only replicate with the help of a host and are
capable of hijacking organisms from every branch of the tree of life, including multitude of human cells
• = an infectious, obligate intracellular parasite comprising genetic material (RNA or DNA), often
surrounded by a protein coat, and sometimes a membrane
• Virus size = diverse
o Generally between 30-300nm
o LM is not sufficient enough for studying viruses, we usually
use EM or X-ray/NMR for structure analysis
• All viruses have 2 things in common
o Each encases its genome in a protein-based shell (= capsid)
o Each relies on its host (=person, spider or plant) to reproduce itself
à beyond that general pattern lie endless variations
• All viruses have 2 phases
o Virion (= infectious particle): the complete, infective form of a virus outside the host cell, with
a core of RNA/DNA and a capsid
o Virus particle in the infected cell
• Properties of a virus
o A virus is an infectious, obligate intracellular parasite
o The viral genome comprises DNA or RNA
o The viral genome directs the synthesis of viral components by cellular systems within an
appropriate host cell
o Infectious progeny virus particles, called virions, are formed by de novo-self-assembly from
newly synthesized components
o A progeny virion assembled ruing the infectious cycle is the vehicle for transmission of the
viral genome to the next host cell or organism, where its disassembly initiates the next
infectious cycle
3
, 2025-2026 Molecular Virology cc
• While viruses lack the complex energy-generating and biosynthetic systems necessary for independent
existence, they are not the simplest biologically active agents
o Viroids = infectious agents of a variety of economically important plants, comprise a single
small molecule of noncoding RNA (just RNA’s which are folded to be quite stable and are
replicated inside the host cell)
o Prions = single protein molecules = misfolded proteins with the ability to transmit their
misfolded shape onto normal variants of the same protein (therefore infectious)
§ They characterize several fatal and transmissible neurodegenerative diseases in
humans and other animals
• Viruses do not think = be careful to avoid anthropomorphic analyses
o They do not achieve their goals in a human-centered manner
§ Evolution of viruses is driven by their environment, they don’t really ‘adapt’ like we
do, they’re simply co-evolving
o They are passive agents!
DISCOVERY OF VIRUSES
• Filterable viruses
o They knew liquids caused infections
o Then, they discovered bacteria which could be filtered
out, but if viruses caused the disease they could not filter
it from the liquid à thought the liquid was poison
o 1892 Ivanovsky
o 1898 Beijerinck: contagium vivum fluidum virus = poison (in liquid form)
à the agent of tobacco mosaic disease passed through filter that retain bacteria
o Only in 1939 they discovered viruses were not liquids!
• Virus propagation
o Infection in animals
§ Animal viruses could not be routinely propagated in cultured cells at first
§ Most viruses were grown in laboratory animals
o Embryonated chicken eggs
§ Before the advent of cell culture, many viruses were propagated in embryonated
chicken eggs
§ 5-14 days after fertilization, a hole is drilled in the shell and the virus is injected into
the site appropriate for its replications à still routinely used for influenza virus!
o Cell culture
§ Cytopathic effect (CPE) = refers to the structural changes in cells caused by virus,
which can lead to cell destruction or altered morphology (e.g. syncytium formation)
§ Can be done in HeLa cells (= human derived cervical cancer cells) à commonly used
Discovery of viruses
in research Virus propagation – infection: quantification
§ Can be done in Vero cells (= cells derived from monkey kidney cells) à commonly
Determination of infectious virus: PLAQUE ASSAY
used in virological research since they lack an interferon system, meaning viruses
can replicate in them more easily
o Quantification: how many viruses are present in the
sample
§ Plaque assay: an infected cell releases viruses
that infect new cells around it à formation of plaques/holes in the monolayer
• We need to treat with layer on top of the culture, so the virus only infects 52
neighboring cells and does not disseminate throughout the culture
Virology Lectures 2020 • Prof. Vincent Racaniello • Columbia University 4 ©Principles of Virology, AS
MOLECULAR VIROLOGY AND INFECTIONS
GENERAL INTRODUCTION
WHY DO WE STUDY VIRUSES?
• Viruses are everywhere
o There are more viruses than stars in the universe
o They infiltrate every aspect of our natural world, seething in seawater, drifting through the
atmosphere, and lurking in miniscule motes of soil
o Whales and zooplanktons are commonly infected with marine caliciviruses à infected whales
excrete more than 1013 caliciviruses daily (106 per gram feces) and remain viable for more
than 14 days in 15°C seawater
§ Why has it evolved to become this stable (most human viruses don’t live longer than
a day in the environment)? Whales don’t come in close contact with each other
o Viruses are classified based on their genome (researchers used to have to culture the virus
and its host)
• Viruses come in all shapes and sizes
o Eukaryotic viruses are small (they don’t code for anything and use the host cells machinery)
o Some viruses code for everything = these are big
• Viruses cause human diseases
o Even with constant exposure to viruses everywhere, the vast majority of viruses that infect
us have little or no impact; these viruses just pass through us
§ We ingest many non-animal viruses regularly with foods (e.g. cabbage in US
supermarkets contain 108 virus particles)
§ This relative safety depends on our elaborate immune defense system, which has
evolved to fight microbial infections à if this immune defense system is
compromised, even the most common infections can be lethal
o Despite such defenses, some of the most devastating human diseases have been or are still
caused by viruses
§ E.g. smallpox, COVID 19, measles, HIV, influenza…
§ Can lead to life-threatening diseases that impact virtually all organs, including the
lungs, liver, CNS and intestines
§ Viruses are responsible for 20% of the human cancer burden
§ Viral infections of the respiratory and gastro-intestinal tract kill millions of children
in developing world each year
• Viruses can be beneficial
o In marine ecology, virus particles are the most abundant biological entities
§ 94% of all nucleic acid-containing particles in the oceans
§ 15x more abundant than the Bacteria and Archaea
§ Viral infections in the ocean kill 20-40% of marine microbes daily à release essential
nutrients that supply phytoplankton (food), as well as carbon dioxide and other
gases that affect the climate of the earth
1
,2025-2026 Molecular Virology cc
o Pathogens can also influence one another: infection by one virus can have an ameliorating
effect on the pathogenesis of a second virus or even bacteria
§ HIV virus-infected AIDS patients show a substantial decrease in their disease
progression if they’re persistently infected with hepatitis G
§ Mice latently infected with some murine herpesviruses are resistant to infection
with the bacterial pathogens Listeria monocytogenes and Yersinia pestis
• Viruses can cross species boundaries
o Viruses generally have a limited host range, yet they can and do spread across species
barriers
§ Viruses are usually confined to 1 host species because of co-evolution
o As the world’s human population continues to expand and imping on the wilderness, cross-
species (zoonotic) infections of humans are occurring with increasing frequency
§ E.g. HIV pandemic, Ebola hemorrhagic fever and SARS-CoV-2 pandemic
§ Currently: influenza virus H5N1 in avian (avian flu) = frightening possibility of
transmission to humans of a highly pathogenic strain
o Why are zoonotic infections such a burden? We do not have any pre-existing immunity
• Viruses drive human evolution
o Every cell in our body contains viral DNA
o Human endogenous retroviruses, and elements thereof,
make up about 5 to 8% of our DNA
§ Most are inactive, fossil remnants from
infections of germ cells that have occurred over
millions of years during our evolution
§ Some of them are suspected to be associated
with specific diseases
o Protein products of other endogenous retroviruses are essential
o Transposable elements (TE) = 40% of our genome
§ Discovered in 1940s = took half a century before we understood the importance
§ A crucial stage was reached with the completion of the first human genome
sequence à nearly half our genome is derived from different types of TE
§ Retrotransposons = copy and paste themselves into different genomic locations by
converting RNA back into DNA using reverse transcriptase
§ DNA transposons = discrete DNA pieces which can move from site to site within
genomes = jumping genes
§ SINES/LINES = short and long interspersed nuclear elements that invade new
genomic sites using RNA intermediates (copy and paste)
o Viruses have been part of all human history: they were present long before us, and the
majority of human infections were likely acquired from animals (zoonoses)
o Epidemics most likely have shaped which species and populations have been successful to
reproduce and expand
o As viruses continue to be discovered, our understanding of how human health and well-being
are affected by these agents remain incomplete
o E.g. protein products of endogenous retroviruses are essential for who we are as a species
§ A gene of viral origin encodes for a protein that plays a key role in long-term
memory formation by moving information between cells in the nervous system
§ Evolution of the mammalian placenta and the timing of gene expression in human
pregnancy depends on a bit of genetic code that was co-opted from ancient
retroviruses that infected our ancestors > 130 million years age
2
,2025-2026 Molecular Virology cc
o The disappearance of viruses would impact the evolutionary potential for all life on the
planet, including humans
§ Since viruses are constantly replicating and mutating, they hold a massive repository
of genetic innovation that other organisms can incorporate
§ Viruses replicate by inserting themselves into host cells and hijacking their
replication tools à if this happens in germ line cells, the viral code can be passed on
to the next generation and become permanently integrated
§ The insertion of new DNA into genomes is major mode of evolution!
o How do we know this is beneficial? Otherwise, this viral DNA would not be incorporated in
our genome anymore (negative selection!
• Viruses are unique tools for studying cell biology
o Studying viruses = inherently studying cells
o Because viruses are dependent on their host for propagation, studies that focus on viral
reprogramming of cellular mechanisms have provided unique insights into cellular biology
and functioning of host defenses
o Groundbreaking studies of viruses that infect bacteria (= bacteriophages), laid the
foundations of modern molecular biology
WHAT IS A VIRUS?
• = generally considered non-living entities, which can only replicate with the help of a host and are
capable of hijacking organisms from every branch of the tree of life, including multitude of human cells
• = an infectious, obligate intracellular parasite comprising genetic material (RNA or DNA), often
surrounded by a protein coat, and sometimes a membrane
• Virus size = diverse
o Generally between 30-300nm
o LM is not sufficient enough for studying viruses, we usually
use EM or X-ray/NMR for structure analysis
• All viruses have 2 things in common
o Each encases its genome in a protein-based shell (= capsid)
o Each relies on its host (=person, spider or plant) to reproduce itself
à beyond that general pattern lie endless variations
• All viruses have 2 phases
o Virion (= infectious particle): the complete, infective form of a virus outside the host cell, with
a core of RNA/DNA and a capsid
o Virus particle in the infected cell
• Properties of a virus
o A virus is an infectious, obligate intracellular parasite
o The viral genome comprises DNA or RNA
o The viral genome directs the synthesis of viral components by cellular systems within an
appropriate host cell
o Infectious progeny virus particles, called virions, are formed by de novo-self-assembly from
newly synthesized components
o A progeny virion assembled ruing the infectious cycle is the vehicle for transmission of the
viral genome to the next host cell or organism, where its disassembly initiates the next
infectious cycle
3
, 2025-2026 Molecular Virology cc
• While viruses lack the complex energy-generating and biosynthetic systems necessary for independent
existence, they are not the simplest biologically active agents
o Viroids = infectious agents of a variety of economically important plants, comprise a single
small molecule of noncoding RNA (just RNA’s which are folded to be quite stable and are
replicated inside the host cell)
o Prions = single protein molecules = misfolded proteins with the ability to transmit their
misfolded shape onto normal variants of the same protein (therefore infectious)
§ They characterize several fatal and transmissible neurodegenerative diseases in
humans and other animals
• Viruses do not think = be careful to avoid anthropomorphic analyses
o They do not achieve their goals in a human-centered manner
§ Evolution of viruses is driven by their environment, they don’t really ‘adapt’ like we
do, they’re simply co-evolving
o They are passive agents!
DISCOVERY OF VIRUSES
• Filterable viruses
o They knew liquids caused infections
o Then, they discovered bacteria which could be filtered
out, but if viruses caused the disease they could not filter
it from the liquid à thought the liquid was poison
o 1892 Ivanovsky
o 1898 Beijerinck: contagium vivum fluidum virus = poison (in liquid form)
à the agent of tobacco mosaic disease passed through filter that retain bacteria
o Only in 1939 they discovered viruses were not liquids!
• Virus propagation
o Infection in animals
§ Animal viruses could not be routinely propagated in cultured cells at first
§ Most viruses were grown in laboratory animals
o Embryonated chicken eggs
§ Before the advent of cell culture, many viruses were propagated in embryonated
chicken eggs
§ 5-14 days after fertilization, a hole is drilled in the shell and the virus is injected into
the site appropriate for its replications à still routinely used for influenza virus!
o Cell culture
§ Cytopathic effect (CPE) = refers to the structural changes in cells caused by virus,
which can lead to cell destruction or altered morphology (e.g. syncytium formation)
§ Can be done in HeLa cells (= human derived cervical cancer cells) à commonly used
Discovery of viruses
in research Virus propagation – infection: quantification
§ Can be done in Vero cells (= cells derived from monkey kidney cells) à commonly
Determination of infectious virus: PLAQUE ASSAY
used in virological research since they lack an interferon system, meaning viruses
can replicate in them more easily
o Quantification: how many viruses are present in the
sample
§ Plaque assay: an infected cell releases viruses
that infect new cells around it à formation of plaques/holes in the monolayer
• We need to treat with layer on top of the culture, so the virus only infects 52
neighboring cells and does not disseminate throughout the culture
Virology Lectures 2020 • Prof. Vincent Racaniello • Columbia University 4 ©Principles of Virology, AS
