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The role of viruses as a gray area between living and nonliving is discussed. A research by Stanley and others established that a virus consist of nucleic acids (DNA or RNA) enclosed in protein coat that may also shelter viral proteins involved in infection. It is found that viruses depend on the host cell for the raw materials and energy necessary for nucleic acid synthesis, protein synthesis, processing, and transport. Viruses are simply nonliving parasites of living metabolic systems but a spectrum exists between what is certainly alive and what is not.
Are Viruses Alive?
LUIS P. VILLARREAL is director of the Center for Virus Research
at the University of California, Irvine. He was born in East Los
Angeles. He received his doctorate in biology from the University
of California, San Diego, and did postdoctoral research in
virology at Stanford University with Nobel laureate Paul Berg.
He is active in science education and has received a National
Science Foundation Presidential Award for mentoring. In his current
position, Villarreal has established programs for the rapid
development of defenses against bioterrorism threats. He has
two sons and enjoys motorcycles and Latin music. A
In an episode of the classic 1950s television comedy The Honeymooners,
Brooklyn bus driver Ralph Kramden loudly explains to his wife, Alice,
“You know that I know how easy you get the virus.” Half a century ago
even regular folks like the Kramdens had some knowledge of viruses—as
microscopic bringers of disease. Yet it is almost certain that they did not
know exactly what a virus was. They were, and are, not alone.
For about 100 years, the scientific community has repeatedly changed its
collective mind over what viruses are. First seen as poisons, then as life-forms,
then biological chemicals, viruses today are thought of as being in a gray area
between living and nonliving: they cannot replicate on their own but can do so
in truly living cells and can also affect the behavior of their hosts profoundly.
The categorization of viruses as nonliving during much of the modern era of biological
science has had an unintended consequence: it has led most researchers
to ignore viruses in the study of evolution. Finally, however, scientists are
beginning to appreciate viruses as fundamental players in the history of life.
it is easy to see why viruses have been diffi cult to pigeonhole. They
seem to vary with each lens applied to examine them. The initial interest in
viruses stemmed from their association with diseases—the word “virus” has
its roots in the Latin term for “poison.” In the late 19th century researchers
realized that certain diseases, including rabies and foot-and-mouth, were
caused by particles that seemed to behave like bacteria but were much smaller.
Because they were clearly biological themselves and could be spread from one
victim to another with obvious biological effects, viruses were then thought
to be the simplest of all living, gene-bearing life-forms.
Their demotion to inert chemicals came after 1935, when
Wendell M. Stanley and his colleagues, at what is now the
Rockefeller University in New York City, crystallized a virus—
tobacco mosaic virus—for the first time. They saw that it
consisted of a package of complex bio-chemicals. But it lacked
essential systems necessary for metabolic functions, the biochemical
activity of life. Stanley shared the 1946 Nobel Prize—
in chemistry, not in physiology or medicine—for this work.
Further research by Stanley and others established that a
virus consists of nucleic acids (DNA or RNA) enclosed in a
protein coat that may also shelter viral proteins involved in infection.
By that description, a virus seems more like a chemistry
set than an organism. But when a virus enters a cell (called
a host after infection), it is far from inactive. It sheds its coat,
bares its genes and induces the cell’s own replication machinery
to reproduce the intruder’s DNA or RNA and manufacture
more viral protein based on the instructions in the viral nucleic
acid. The newly created viral bits assemble and, voilà, more
virus arises, which also may infect other cells.
These behaviors are what led many to think of viruses as
existing at the border between chemistry and life. More poetically,
virologists Marc H. V. van Regenmortel of the University
of Strasbourg in France and Brian W. J. Mahy of the Centers
for Disease Control and Prevention have recently said that with
their dependence on host cells, viruses lead “a kind of borrowed
life.” Interestingly, even though biologists long favored the view
that viruses were mere boxes of chemicals, they took advantage
of viral activity in host cells to determine how nucleic acids
code for proteins: indeed, modern molecular biology rests on
a foundation of information gained through viruses.
Molecular biologists went on to crystallize most of the essential
components of cells and are today accustomed to thinking
about cellular constituents—for example, ribosomes, mitochondria,
membranes, DNA and proteins—as either chemical
machinery or the stuff that the machinery uses or produces.
This exposure to multiple complex chemical structures that
carry out the processes of life is probably a reason that most
molecular biologists do not spend a lot of time puzzling over
whether viruses are alive. For them, that exercise might seem
equivalent to pondering whether those individual subcellular
constituents are alive on their own. This myopic view allows
them to see only how viruses co-opt cells or cause disease. The
more sweeping question of viral contributions to the history
of life on earth, which I will address shortly, remains for the
most part unanswered and even unasked.
the seemingly simple question of whether or not
viruses are alive, which my students often ask, has probably
defi ed a simple answer all these years because it raises a fundamental
issue: What exactly defines “life?” A precise scientifi
c defi nition of life is an elusive thing, but most observers
would agree that life includes certain qualities in addition
to an ability to replicate. For example, a living entity is in a
state bounded by birth and death. Living organisms also are
thought to require a degree of biochemical autonomy, carrying
on the metabolic activities that produce the molecules
and energy needed to sustain the organism. This level of autonomy
is essential to most definitions.
Viruses, however, parasitize essentially all biomolecular
aspects of life. That is, they depend on the host cell for the
raw materials and energy necessary for nucleic acid synthesis,
protein synthesis, processing and transport, and all other biochemical
activities that allow the virus to multiply and spread.
One might then conclude that even though these processes
come under viral direction, viruses are simply nonliving parasites
of living metabolic systems. But a spectrum may exist
between what is certainly alive and what is not.
A rock is not alive. A metabolically active sack, devoid of
Overview/A Little Bit of Life
“ ‘Life’ and ‘living’ are words
that the scientist has borrowed
from the plain man. The loan
has worked satisfactorily until
comparatively recently, for the
scientist seldom cared and certainly never knew
just what he meant by these words, nor for that
matter did the plain man. Now, however, systems
are being discovered and studied which are neither
obviously living nor obviously dead, and it is
necessary to defi ne these words or else give up
using them and coin others.”
—British virologist Norman Pirie, c. 1934
“You think that life is nothing but not being
stone dead.”
—George Bernard Shaw, St. Joan, 1923
genetic material and the potential for propagation, is also not
alive. A bacterium, though, is alive. Although it is a single cell,
it can generate energy and the molecules needed to sustain itself,
and it can reproduce. But what about a seed? A seed might not
be considered alive. Yet it has a potential for life, and it may be
destroyed. In this regard, viruses resemble seeds more than they
do live cells. They have a certain potential, which can be snuffed
out, but they do not attain the more autonomous state of life.
Another way to think about life is as an emergent property of
a collection of certain nonliving things. Both life and consciousness
are examples of emergent complex systems. They each
require a critical level of complexity or interaction to achieve
their respective states. A neuron by itself, or even in a network
of nerves, is not conscious—whole brain complexity is needed.
Yet even an intact human brain can be biologically alive but
incapable of consciousness, or “brain-dead.” Similarly, neither
cellular nor viral individual genes or proteins are by themselves
alive. The enucleated cell is akin to the state of being brain dead,
in that it lacks a full critical complexity. A virus, too, fails
to reach a critical complexity. So life itself is an emergent, complex
state, but it is made from the same fundamental, physical
building blocks that constitute a virus. Approached from this
perspective, viruses, though not fully alive, may be thought of
as being more than inert matter: they verge on life.
In fact, in October, French researchers announced findings
that illustrate afresh just how close some viruses might
come. Didier Raoult and his colleagues at the University of
the Mediterranean in Marseille announced that they had
sequenced the genome of the largest known virus, Mimivirus,
which was discovered in 1992. The virus, about the
same size as a small bacterium, infects amoebae. Sequence
analysis of the virus revealed numerous genes previously
thought to exist only in cellular organisms. Some of these
genes are involved in making the proteins encoded by the
viral DNA and may make it easier for Mimivirus to co-opt
host cell replication systems. As the research team noted in
its report in the journal Science, the enormous complexity
of the Mimi-virus’s genetic complement “challenges the
established frontier between viruses and parasitic cellular
Impact on Evolution debates over whether to label viruses as living lead
naturally to another question: Is pondering the status of viruses
as living or nonliving more than a philosophical exercise,
the basis of a lively and heated rhetorical debate but with
little real consequence? I think the issue is important, because
how scientists regard this question infl uences their thinking
about the mechanisms of evolution.
Viruses have their own, ancient evolutionary history, dating
to the very origin of cellular life. For example, some viral-
repair enzymes—which excise and re-synthesize damaged
DNA, mend oxygen radical damage, and so on [see box below]—
are unique to certain viruses and have existed almost
unchanged probably for billions of years.
Nevertheless, most evolutionary biologists hold that because
viruses are not alive, they are unworthy of serious consideration
when trying to understand evolution. They also
look on viruses as coming from host genes that somehow
escaped the host and acquired a protein coat. In this view, viruses
are fugitive host genes that have degenerated into parasites.
And with viruses thus dismissed from the web of life,
important contributions they may have made to the origin
of species and the maintenance of life may go unrecognized.
Because viruses occupy a netherworld between life
and non-life, they can pull off some remarkable feats.
Consider, for instance, that although viruses ordinarily
replicate only in living cells, they also have the capacity to
multiply, or “grow,” in dead cells and even to bring them back to
life. Amazingly, some viruses can even spring back
to their “borrowed life” after being destroyed.
A cell that has had its nuclear DNA destroyed
is dead: the cell lacks the genetic instructions for
making necessary proteins and for reproduction.
But a virus may take advantage of the cellular
machinery in the remaining cytoplasm to replicate.
That is, it can induce the machinery to use the
virus’s genes as a guide to assembling viral
proteins and replicating the viral genome. This
capacity of viruses to grow in a dead host is most
apparent in their unicellular hosts, many of which
live in the oceans. (Indeed, an almost unimaginable
number of viruses exist on the earth. Current estimates hold
that the oceans alone harbor some 1030 viral particles, either
within cellular hosts or floating free.)
In the cases of bacteria, as well as photosynthetic
cyanobacteria and algae, the hosts are often killed when
ultraviolet (UV) radiation from the sun destroys their
nuclear DNA. Some viruses include or encode enzymes that
repair various host molecules, restoring the host to life. For
instance, cyanobacteria contain an enzyme that functions
as the photosynthetic center, but it can be destroyed by too
much light. When this happens, the cell, unable to carry on
photosynthesis and subsequent cellular metabolism, dies.
But viruses called cyanophages encode their
own version of the bacterial photosynthesis
enzyme—and the viral version is much more
resistant to UV radiation. If these viruses infect a
newly dead cell, the viral photosynthesis enzyme
can take over for the host’s lost one. Think of it as
lifesaving gene therapy for a cell.
Enough UV light can also destroy cyanophages.
In fact, UV inactivation is a common laboratory
method used to destroy viruses. But such viruses
can sometimes regain form and function. This
resurrection comes about through a process
known as multiplicity reactivation. If an individual
cell harbors more then one disabled virus, the viral genome can
literally reassemble from parts. (It is exactly such a reassembly
capacity that allows us to create artifi cial recombinant viruses
in the laboratory.) The various parts of the genome can also
sometimes provide individual genes that act in concert
(called complementation) to reestablish full function without
necessarily re-forming a full or autonomous virus. Viruses
are the only known biological entity with this kind of “phoenix
phenotype”—the capacity to rise from their own ashes. —L.P.V.
Distracted by Cells
“Attention of biologists was
distracted for nearly a century
by arguments over whether
viruses are organisms. The
disagreement stems largely
from the generalization put
forth in the latter half of the nineteenth century
that cells are the building blocks of all life. Viruses
are simpler than cells, so, the logic goes, viruses
cannot be living organisms. This viewpoint seems
best dismissed as semantic dog wagging by
the tails of dogma.”
—American evolutionary biologist Paul Ewald, 2000
Tobacco mosaic virus
T4 bacteriophage
(Indeed, only four of the 1,205 pages of the 2002 volume The
Encyclopedia of Evolution are devoted to viruses.)
Of course, evolutionary biologists do not deny that viruses
have had some role in evolution. But by viewing viruses as inanimate,
these investigators place them in the same category
of infl uences as, say, climate change. Such external infl uences
select among individuals having varied, genetically controlled
traits; those individuals most able to survive and thrive when
faced with these challenges go on to reproduce most successfully
and hence spread their genes to future generations.
But viruses directly exchange genetic information with living
organisms—that is, within the web of life itself. A possible
surprise to most physicians, and perhaps to most evolutionary
biologists as well, is that most known viruses are persistent
and innocuous, not pathogenic. They take up residence in
cells, where they may remain dormant for long periods or take
advantage of the cells’ replication apparatus to reproduce at
a slow and steady rate. These viruses have developed many
clever ways to avoid detection by the host immune system—
essentially every step in the immune process can be altered or
controlled by various genes found in one virus or another.
Furthermore, a virus genome (the entire complement of
DNA or RNA) can permanently colonize its host, adding viral
genes to host lineages and ultimately becoming a critical
part of the host species’ genome. Viruses therefore surely have
effects that are faster and more direct than those of external
forces that simply select among more slowly generated,
internal genetic variations. The huge population of viruses,
combined with their rapid rates of replication and mutation,
makes them the world’s leading source of genetic innovation:
they constantly “invent” new genes. And unique genes of viral
origin may travel, fi nding their way into other organisms and
contributing to evolutionary change.
Data published by the International Human Genome Sequencing
Consortium indicate that somewhere between 113
and 223 genes present in bacteria and in the human genome
are absent in well-studied organisms—such as the yeast Saccharomyces
cerevisiae, the fruit fl y Drosophila melanogaster
and the nematode Caenorhabditis elegans—that lie in
between those two evolutionary extremes. Some researchers
thought that these organisms, which arose after bacteria
but before vertebrates, simply lost the genes in question at
some point in their evolutionary history. Others suggested
that these genes had been transferred directly to the human
lineage by invading bacteria.
My colleague Victor DeFilippis of the Vaccine and Gene
Therapy Institute of the Oregon Health and Science University
and I suggested a third alternative: viruses may originate
genes, then colonize two different lineages—for example, bacteria
and vertebrates. A gene apparently bestowed on humanity
by bacteria may have been given to both by a virus.
In fact, along with other researchers, Philip Bell of Macquarie
University in Sydney, Australia, and I contend that the
cell nucleus itself is of viral origin. The advent of the nucleus—
which differentiates eukaryotes (organisms whose cells
contain a true nucleus), including humans, from prokaryotes,
such as bacteria—cannot be satisfactorily explained solely by
the gradual adaptation of prokaryotic cells until they became
eukaryotic. Rather the nucleus may have evolved from a persisting
large DNA virus that made a permanent home within
prokaryotes. Some support for this idea comes from sequence
data showing that the gene for a DNA polymerase (a DNA copying
enzyme) in the virus called T4, which infects bacteria,
is closely related to other DNA polymerase genes in both eukaryotes
and the viruses that infect them. Patrick Forterre of
the University of Paris-Sud has also analyzed enzymes responsible
for DNA replication and has concluded that the genes for
such enzymes in eukaryotes probably have a viral origin.
From single-celled organisms to human populations, viruses
affect all life on earth, often determining what will survive.
But viruses themselves also evolve. New viruses, such as
the AIDS-causing HIV-1, may be the only biological entities
that researchers can actually witness come into being, providing
a real-time example of evolution in action.
Viruses matter to life. They are the constantly changing
boundary between the worlds of biology and biochemistry. As
we continue to unravel the genomes of more and more organisms,
the contributions from this dynamic and ancient gene
pool should become apparent. Nobel laureate Salvador Luria
mused about the viral influence on evolution in 1959. “May
we not feel,” he wrote, “that in the virus, in their merging with
the cellular genome and reemerging from them, we observe
the units and process which, in the course of evolution, have
created the successful genetic patterns that underlie all living
cells?” Regardless of whether or not we consider viruses to be
alive, it is time to acknowledge and study them in their natural
context—within the web of life.
Viral Quasi-species. Manfred Eigen in Scientific American, Vol. 269,
No. 1, pages 42–49; July 1993.
DNA Virus Contribution to Host Evolution. L. P. Villarreal in Origin and
Evolution of Viruses. Edited by E. Domingo et al. Academic Press, 1999.
Lateral Gene Transfer or Viral Colonization? Victor DeFilippis and Louis
Villarreal in Science, Vol. 293, page 1048; August 10, 2001.
Viruses and the Evolution of Life. Luis Villarreal. ASM Press (in press).
All the Virology on the WWW is at
“The very essence of the virus is
its fundamental entanglement
with the genetic and metabolic
machinery of the host.”
— American Nobel laureate Joshua Lederberg, 1993
“Whether or not viruses should be regarded as
organisms is a matter of taste.”
— French Nobel laureate André Lwoff, 1962
“A virus is a virus!”
—Lwoff, 1959
Bluetongue virus
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Disease transmission is a fruitful domain in which to examine how scientific and folk theories interrelate, given laypeople’s access to multiple sources of information to explain events of personal significance. The current paper reports an in-depth survey of U.S. adults’ ( N = 238) causal reasoning about two viral illnesses: a novel, deadly disease that has massively disrupted everyone’s lives (COVID-19), and a familiar, innocuous disease that has essentially no serious consequences (the common cold). Participants received a series of closed-ended and open-ended questions probing their reasoning about disease transmission, with a focus on causal mechanisms underlying disease contraction, transmission, treatment, and prevention; non-visible (internal) biological processes; and ontological frameworks regarding what kinds of entities viruses are. We also assessed participants’ attitudes, such as their trust in scientific experts and willingness to be vaccinated. Results indicated complexity in people’s reasoning, consistent with the co-existence of multiple explanatory frameworks. An understanding of viral transmission and viral replication existed alongside folk theories, placeholder beliefs, and lack of differentiation between viral and non-viral disease. For example, roughly 40% of participants who explained illness in terms of the transmission of viruses also endorsed a non-viral folk theory, such as exposure to cold weather or special foods as curative. Additionally, participants made use of competing modes of construal (biological, mechanical, and psychological) when explaining how viruses operate, such as framing the immune system response (biological) as cells trying to fight off the virus (psychological). Indeed, participants who displayed greater knowledge about viral transmission were significantly more likely to anthropomorphize bodily processes. Although comparisons of COVID-19 and the common cold revealed relatively few differences, the latter, more familiar disease elicited consistently lower levels of accuracy and greater reliance on folk theories. Moreover, for COVID-19 in particular, accuracy positively correlated with attitudes (trusting medical scientists and taking the disease more seriously), self-protective behaviors (such as social distancing and mask-wearing), and willingness to be vaccinated. For both diseases, self-assessed knowledge about the disease negatively predicted accuracy. The results are discussed in relation to challenges for formal models of explanatory reasoning.
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Influenza is still a frequent seasonal infection of the upper respiratory tract, which may have deadly consequences, especially for the elderly. This is in spite of the availability of vaccines suggested for persons above 65 years of age. Two types of conventional influenza vaccines are currently licensed for use—live attenuated and inactivated vaccines. Depending on local regulatory requirements, live attenuated vaccines are produced by the reverse genetics technique or by classical reassortment in embryonated chicken eggs. Sometimes, the efficiency of classical reassortment is complicated by certain properties of the wild-type parent virus. Cases of low efficacy of vaccines have been noted, which, among other reasons, may be associated with suboptimal properties of the wild-type parent virus that are not considered when recommendations for influenza vaccine composition are made. Unfortunately, knowledge surrounding the roles of properties of the circulating influenza virus and its impact on the efficacy of the reassortment process, vaccination efficiency, the infectivity of the vaccine candidates, etc., is now scattered in different publications. This review summarizes the main features of the influenza virus that may dramatically affect different aspects of the preparation of egg-derived live attenuated vaccine candidates and their effectiveness. The author expresses her personal view, which may not coincide with the opinion of other experts in the field of influenza vaccines.
The debate over whether viruses are living organisms tends to be paradigmatically determined. The metabolic paradigm denies that they are, while new research evidences the opposite. The purpose of this paper is to deliver a generic model for viral contexts that explains why viruses are alive. It will take a systems biology approach, with a qualitative part (using metacybernetics) to provide deeper explanations of viral contexts, and a quantitative part (using Fisher Information deriving fromthe variational principle of Extreme Physical Information) which is in principle able to take measurements and predict outcomes. The modelling process provides an extended view of the epigenetic processes of viruses. The generic systems biology model will depict viruses as autonomous entities with metaphysical processes of autopoietic self-organisation and adaptation, enabling them to maintain their physical viability and hence, within their populations, mutate and evolve. The autopoietic epigenetic processes are shown to describe their capability to change, and these are both qualitatively and quantitatively explored, the latter providing an approach to make measurements of physical phenomena under uncertainty. Viruses maintain their fitness when they are able to maintain their stability, and this is indicated by information flow efficacy. A brief case study is presented on the COVID-19 virus from the perspective that it is a living system, and this includes outcome predictions given Fisher Information conditions for known contexts. (
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Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: (1) means reification (phenomena-to-object), when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and (2) target reification (object-to-phenomena), when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used.
For Black American youth and their families, the racial terror that claimed the life of George Floyd in May 2020 is nothing new, as stories of people who look just like them have been part and parcel of their lived experience in the United States. Beyond state-sanctioned murder, Black youth were also witnessing the disproportionate transmission, treatment, and travesty plaguing their community with COVID-19 – all predictable outcomes given the inequitable systems supporting the American pipeline from cradle to grave. Why, then, were so many White Americans just coming into awareness of this deadly disease of individual and systemic racism that has ravaged Black American communities for centuries? In this work, we seek to explain in what ways racism is tantamount to a social virus and how its permeation is endemic to the American body, rather than an emerging threat, like a pandemic. We will also address how better conceptualizing racism as a virus allows for more accurate, precise, and feasible treatments for transmitters and targets of racism with respect to prevention (e.g., inoculation) and intervention (e.g., healing and vaccination). Finally, we will describe clinical therapeutic trials that will help to decipher whether our treatment of this social disease is effective, including family-level interventions and systemic shifts in prevention through clinical training.
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We argue for multiple forms of life realized through multiple different historical pathways. From this perspective, there have been multiple origins of life on Earth—life is not a universal homology. By broadening the class of originations, we significantly expand the data set for searching for life. Through a computational analogy, the origin of life describes both the origin of hardware (physical substrate) and software (evolved function). Like all information-processing systems, adaptive systems possess a nested hierarchy of levels, a level of function optimization (e.g., fitness maximization), a level of constraints (e.g., energy requirements), and a level of materials (e.g., DNA or RNA genome and cells). The functions essential to life are realized by different substrates with different efficiencies. The functional level allows us to identify multiple origins of life by searching for key principles of optimization in different material form, including the prebiotic origin of proto-cells, the emergence of culture, economic, and legal institutions, and the reproduction of software agents.
To understand 2020’s pandemic is to see virus as a language we can use. By drawing on viral principles—viruses are infections through information, viruses can be understood only through percentages and exponentials, and viruses are zombies from outer space—the dynamics of our twenty-first-century virus crisis can be discerned, even influenced. The crisis isn't just biological, it is about ideas and how they propagate through, for example, conspiracy theories and inflammatory actions. Viral emotions are integral to what is happening, as attention to both the virus of fascism and fear-based reactions to COVID-19 make clear. The opposite of fear, or perhaps the product of fear sometimes, is bravery. Hope is beyond that. Viruses spread because of their intrinsic properties and the relevant vectors, catalysts, growth mediums, and controls. Our future will be shaped by a wide range of viruses. We know it will be abnormal, but viruses will not act alone. Much of nature, and thus human culture, is beyond the viral. The key issue is control and just what mix of authoritarian control, self-control, and out-of-control (in both senses) we will end up living with.
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The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used to obtain the nucleotide sequences; In the first one, chunks of equal length (four nucleotides) are considered. In the second approach, the whole RNA genome is divided into parts by adenine or the most frequent nucleotide as a “space”. Rank–frequency distributions are studied in both cases. The defined nucleotide sequences are signs comparable to a certain extent to syllables or words as seen from the nature of their rank–frequency distributions. Within the first approach, the Pólya and the negative hypergeometric distribution yield the best fit. For the distributions obtained within the second approach, we have calculated a set of parameters, including entropy, mean sequence length, and its dispersion. The calculated parameters became the basis for the classification of viruses. We observed that proximity of viruses on planes spanned on various pairs of parameters corresponds to related species. In certain cases, such a proximity is observed for unrelated species as well calling thus for the expansion of the set of parameters used in the classification. We also observed that the fifth most frequent nucleotide sequences obtained within the second approach are of different nature in case of human coronaviruses (different nucleotides for MERS, SARS-CoV, and SARS-CoV-2 versus identical nucleotides for four other coronaviruses). We expect that our findings will be useful as a supplementary tool in the classification of diseases caused by RNA viruses with respect to severity and contagiousness.
Many viral infections have a profound impact on host fitness and survival and thus affect host evolution. DNA viruses have a tendency to establish lifelong and inapparent persistent infections. This chapter reviews the theoretical and observed relationships between the DNA virus and its host, and the persistent infections caused by DNA viruses that provide an important contribution to host evolution, such as being the likely source of host DNA replication genes. The apparent genetic stability of DNA viruses makes them appear to evolve slowly. As host genomes are DNA and as DNA replication is tightly regulated, DNA viruses must either parasitize this host DNA replication apparatus, or override host regulation with viral replication proteins.