Viruses are cellular organisms

It has been realized that viral particles are by far the most abundant biological entities on our planet.

A typical virus replication cycle
picture thankfully shared from wikipedia.org

Some bacteriophages inject their
genomes into bacterial cells (not to scale)
*picture thankfully shared from wikipedia.org

If you get sick with the flu, for example, every infected cell in your airway produces about 10,000 new viruses. The total number of flu viruses in your body can rise to 100 trillion within a few days. That’s over 10,000 times more viruses than people on Earth.

If there can be so many viruses in a single person, how many viruses are there in total on our planet? I’ve hunted around for a number, and the one I’ve seen most often is 10³¹. As in, 10000000000000000000000000000000. As in over 10 million times more viruses than there are stars in the universe. As in, if you were to stack one virus on top of another, you’d create a tower that would stretch beyond the moon, beyond the sun, beyond Alpha Centauri, out past the edge of the Milky Way, past neighboring galaxies, to reach a height of 200 million light years.  

*by Carl Zimmer

Noroviruses. Photo by Charles D. Humphrey,
Centers for Disease Control and Prevention

Times are changing and viruses, once only considered as side-products of cellular evolution, are now at the center of many debates on the early evolution of life on our planet

The recent studies have confirmed that:

• Viruses have played and still playing a major innovative role in cellular organisms.
• Their position in the universal tree of life.
• Viruses are no more confused with their virions, but can be viewed as a complex living entities that transform the infected cell into a novel organism - the virus - producing virions.

Viruses and their relation to cellular organism:

Now living organisms are divided into three primary lineage (Woese and Fox 1977);

Three cellular domain concept          Old dichotomy of virus

from the virus perspective                  1. Prokaryotes
1. Bacteria (Eubacteria)                                       (Bacteriophages)

(Bacterioviruses)                                              2. Eukaryotes           

2. Archaea (Archaebacteria)                                 (Viruses)
(Archaeoviruses)
3. Eukarya (Eukaryotes)
(Eukaryoviruses)

This trinity concept has now been corroborated by comparative biochemistry and comparative genomics.

Viruses are ancient:

The ubiquitous existence of viruses infecting members of the three cellular domains strongly suggests that viruses originated before LUCA, when cells still had genomes made of RNA and not DNA (DNA, which is a chemically modified form of RNA, could have appeared only after the emergence of complex proteins capable of modifying RNA,

Some archaeoviruses, bacterioviruses and eukaryoviruses share homologous capsid proteins and/or ATPases for protein packaging, suggesting that they all evolved from a common virus that existed at the time of LUCA of even before.

Viruses are therefore very ancient.

Major role in biological evolution: 

The idea that viruses are very ancient and have co-evolved with the three cellular lineages from the time of LUCA and even before has recently led to several hypotheses posing that viruses have played a major role in several critical evolutionary transitions. For instance:

it has been suggested that DNA and DNA replication machineries first originated in the viral world (Forterre 1999; Villarreal and DeFilippis 2000; Forterre 2002), that virus-induced transition of cells with RNA genomes into cells with DNA genomes triggered the emergence of the three cellular domains (Forterre 2006), that the nucleus of eukaryotic cells originated from a large DNA virus (Takemura 2001; Bell 2001), or even that the selection pressure to prevent the entry of virions promoted the evolution of cell walls (Jalasvuori and Bamford 2008). All these hypotheses are not easily testable, but recent findings make them reasonable. Indeed, it has been shown that cellular proteins playing very important roles in modern organisms may have a viral origin. For instance, phylogenetic analyses have revealed that the RNA polymerase, DNA polymerase and DNA helicase that transcribe and replicate DNA in modern mitochondria were recruited from a virus that was originally integrated into the genome of the bacterium at the origin of the mitochondria (Filée and Forterre 2005). More recently, it has been shown that placentation in mammals is initiated by a protein, syncitin, encoded by a retrovirus integrated in mammalian chromosomes (De Parseval and Heidmann 2005; Prudhomme et al. 2005). There are many other examples of the role that viruses have played in recent cellular evolution (for reviews, see Ryan 2007; Brosius 2003; Villarreal 2005). Brosius wrote, for instance, that “the interaction of hosts with retroviruses, retrotransposons and retroelements is one of the eternal conflicts that drive the evolution of life” (Brosius 2003). Prangishvili and myself have recently extended his argument, concluding that the conflict between cells and viruses has been (and still is) the major engine of life evolution (Forterre and Prangishvili 2009).

*thankfully shared from: Defining life: The virus viewpoint by Patrick Forterre in NCBI article: Published online 2010 March 3

Nature of virus:

the intracellular phase of the virus life cycle is the ontogenetically mature phase of viruses, where it shows the major physiological properties of oher organisms: metabolism, growth and reproduction. 

Eukaryotic viruses that replicate in the cytoplasm form complex localized viral factories to replicate their genome and produce virion. The viral factory corresponds to the real viral organism, whereas the virion corresponds to the mechanism used by the virus to spread from one cell to others.

If infected archaea and bacteria are indeed transformed into bona fide viruses, one can conclude that infected eukaryotic cells in which viral factories have taken control of the cellular machinery became viruses themselves, the viral factory being in that case the equivalent of the nucleus. By adopting this viewpoint, one should finally consider viruses as cellular organisms. They are of course a particular form of cellular organism, since they do not encode their own ribosomes and cell membranes, but borrow those from the cells in which they live.

To take into account the idea that viruses represent a bona fide form of life, Didier Raoult and myself have recently proposed to divide the living world into two major groups of organisms, ribosome encoding-organisms (the descendants of LUCA, archaea, bacteria and eukarya) and capsid-encoding organisms (the viruses) (Raoult and Forterre 2008).

Now newer perspective in defining:  

Life: Mode of existence of ribosomes encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors.

Organism: An ensemble of integrated organs (molecular and cellular) producing individuals evolving through natural selection.

Viruses encode two different "organs": 
1. replicon: allowing genome replication,
2. capsid

Virus structure:

*pictures thankfully shared from; http://www.twiv.tv/virus-structure/

Helical Symmetry

Icosahedral Symmetry

Enveloped with helical nucleocapsid (influenza virus)

Enveloped with icosahedral nucleocapsid (herpesvirus)

Complex symmetry (poxvirus)