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Summary Molecular Virology and Infections (19/20)
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This is a summary of the course that is given in the Master Infectious and Tropical Diseases.
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Summary Virology1. Introduction
A. Why do we study viruses?
− Viruses are everywhere. There are more viruses than stars in the universe. An estimated 10
nonillion (10 to the 31st power: 1031) individual viruses exist on our planet—enough to assign one
to every star in the universe 100 million times over. Viruses infiltrate every aspect of our natural
world, seething in seawater, drifting through the atmosphere, and lurking in miniscule motes of
soil.
− The number of phages (bacterial viruses) in the biosphere has been estimated to be around 10 31.
A phage weighs about one femtogram (10-15) and has a length of about 125nm. Phage biomass on
earth: 1016 grams. (>1OOO-fold the biomass of elephants). The length, head to tail of all phages is
> 1000 million light years.
− Viruses are also present in the water. Marine caliciviruses in oceans infect zooplanktons and
whales and other marine organisms. It infect to very high numbers and is the origin of human
viruses like hepatitis E virus. Whales excrete >106 caliciviruses per gram of feces -> 1013 caliciviruses
daily. Marine caliciviruses remain viable more than 14 days in 15°C seawater. => exceptional
because the virus needs to be able to infect another host
− There are more RNA viruses than DNA viruses. DNA viruses has polymerases with proofreading so
there will be less mutations. RNA viruses doesn’t have proofreading, so makes a lot of errors.
− Unlike cell-based life forms, viruses don’t have a single common ancestor, which make it
impossible to create a phylogenetic tree. Instead the International committee on taxonomy of
viruses recognizes six realms, defined by similarities in their members genes and proteins, each
arising from a different common ancestor.
− Most viruses just pass through us. We ingest many non-animal viruses regularly with foods. Most
RNA virus sequences (91%) in human feces are similar to plant viruses. The most abundant human
fecal virus is the pepper mild mottle virus, they are extremely stable. This is a kind of fecal indicator.
It is used to know how many coronavirus is spreading in a certain
region by measuring the RNA of pepper mold mottle virus and of
coronavirus in waste water.
− Viruses come in all shapes and sizes.
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,− Viruses can cause human disease! The main reason!
o Even with constant exposure to viruses everywhere, the vast majority of viruses that infect
us have little or no impact on our health or well-being
o This relative safety depends on our elaborate immune defense systems, which have
evolved to fight microbial infection
o When these defenses are compromised, even the most common infection can be lethal.
o Despite the immune system, some of the most devastating human diseases have been or
still are caused by viruses; these diseases include smallpox, yellow fever, poliomyelitis,
influenza, measles, and AIDS
o Viral infections can lead to life-threatening diseases that impact virtually all organs,
including the lungs, liver, central nervous system, and intestines
o Viruses are responsible for ± 20% of the human cancer burden
o Viral infections of the respiratory and gastrointestinal tracts kill millions of children in the
developing world each year because they have a lower immune system
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,− Viruses infect all living things.
We haven’t found a single
organism that does not
have any virus.
− Viruses can be beneficial => they are catalyst for biochemical cycling.
o Despite the appalling statistics from human and agricultural epidemics, it is important to
realize that viruses can also be beneficial
o In marine ecology, virus particles are the most abundant biological entities
▪ 94% of all nucleic acid-containing particles in the oceans
▪ 15 times more abundant than the Bacteria and Archaea
▪ Viral infections in the ocean kill 20 to 40% of marine microbes daily
release essential nutrients that supply phytoplankton
Release carbon dioxide and other gases that affect the climate of the earth
o Pathogens can also influence one another, and infection by one virus can have an
ameliorating effect on the pathogenesis of a second virus or even bacteria
▪ human immunodeficiency virus-infected AIDS patients show a substantial
decrease in their disease progression if they are persistently infected with
hepatitis G virus
▪ 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
o As the world’s human population continues to expand and impinge on the wilderness,
cross-species (zoonotic) infections of humans are occurring with increasing frequency
o In addition to the AIDS pandemic, the highly fatal Ebola hemorrhagic fever and the SARS
and SARS-CoV-2 are recent examples of viral diseases to emerge from zoonotic infections
▪ SARS-COV-2 transmits easier then SARS.
o Current pandemic of influenza virus H5N1 in avian -> frightening possibility of transmission
to humans of a highly pathogenic strain. It is already been seen but the virus is not well
adapted. So it is a death end transmission.
− We are viruses – viruses are us – 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
o Most are inactive, fossil remnants from infections of germ cells that have occurred over
millions of years during our evolution
o Some of them are suspected to be associated with specific diseases
o Protein products of other endogenous retroviruses are essential
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, o Retrotransposons (Class I transposable
elements or transposons via RNA
intermediates) type of genetic component
that copy and paste themselves into
different genomic locations (transposon)
by converting RNA back into DNA through
the process reverse transcription using an
RNA transposition intermediate
o Transposable elements (TEs)
▪ discrete pieces of DNA that can
move from site to site within (and sometimes between) genomes
▪ Also known as “jumping genes”
o TE discovery dates back to the 1940s, yet it took about half a century before we
understand the importance
o A crucial stage was reached with the completion of the first human genome sequence
➔ nearly half of our genome is derived from TE
o SINEs and LINEs are short and long interspersed retrotransposable elements, respectively,
that invade new genomic sites using RNA intermediates
o SINEs and LINEs are found in almost all eukaryotes (although not in Saccharomyces
cerevisiae) and together account for at least 34% of the human genome
o Viruses have been part of all of human history: they were present long before Homo
sapiens evolved, and the majority of human infections were likely acquired from other
animals (zoonoses)
o Epidemics most likely have shaped which species and populations have been succesfull 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 remains incomplete
Protein products of endogenous retroviruses are essential for who we are as a species
o 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
o 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 ago
The disappearance of viruses would impact the evolutionary potential for all life on the planet
– including Homo sapiens
o Because viruses are constantly replicating and mutating, viruses also hold a massive
repository of genetic innovation that other organisms can incorporate
o Viruses replicate by inserting themselves into host cells and hijacking their replication
tools. If this happens in a germline cell (eggs and sperm), the viral code can be passed on
to the next generation and become permanently integrated
o The insertion of new DNA into genomes is a major mode of evolution. The disappearance
of viruses, in other words, would impact the evolutionary potential for all life on the planet
– including Homo sapiens
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