Redefining viruses: lessons from Mimivirus
Viruses are the most abundant living entities and probably had a major role in the evolution of life, but are still defined using negative criteria. Here, we propose to divide biological entities into two groups of organisms: ribosome-encoding organisms, which include eukaryotic, archaeal and bacterial organisms, and capsid-encoding organisms, which include viruses. Other replicons (for example, plasmids and viroids) can be termed 'orphan replicons'. Based on this suggested classification system, we propose a new definition for a virus — a capsid-encoding organism that is composed of proteins and nucleic acids, self-assembles in a nucleocapsid and uses a ribosome-encoding organism for the completion of its life cycle.
What makes a virus a virus?
In a recent review, Raoult and Forterre (Redefining viruses: lessons from mimivirus. Nature Rev. Microbiol. 6, 315–319 (2008)1) proposed a dichotomy of the biological world, dividing it into 'organisms', those entities that encode a functional translational machinery, and viruses, those entities that have capsid shells instead. The implied definition of viruses, although highly relevant, does not rely on the most fundamental aspect of what makes a virus a virus: it breaks up and loses its bodily integrity, with its progeny becoming reconstituted after replication from newly synthesized parts. We propose that the defining attribute of all viruses is their disintegration and reconstitution, from the tiny geminiviruses (15–20 nm diameter; 2.5 kb DNA genome) to the colossal Mimivirus (400 nm diameter; 800 kb DNA genome). Importantly, disintegration and reconstitution are totally independent of time, with reconstitution occurring minutes, days, years or centuries after disintegration.
What makes a virus a virus: reply from Raoult and Forterre
The correspondence on our Opinion article (Redefining viruses: lessons from mimivirus. Nature Rev. Microbiol. 6, 315–319 (2008)1) by Wolkowicz and Schaechter (What makes a virus a virus? Nature Rev. Microbiol. 16 July 2008 (doi:10.1038/nrmicro1858-c1)2) has allowed us to clarify some of the elements of our virus definition1. The authors rightly insist that the phenomenon of disappearance and reappearance of a virus (eclipse phase) is a major characteristic of viruses. They then go a step further, however, to suggest that it is the most fundamental aspect of a virus and propose to use this feature, instead of the capsid, to define viruses. Although the eclipse phase is informative in terms of virus description and could be added to our virus definition, we think that such a feature cannot be solely used to define viruses, because it is a phenotypic trait that cannot readily be assigned to a particular gene or set of genes (unlike the capsid) in the viral genome. Consequently, a definition of viruses that is based only on such properties would have a pre-Darwinian flavour (similar to the prokaryote or eukaryote classification system).
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