Environmental Microbiology article asks: How many different types of viruses, how many independent origins?
It is estimated that there are from 10 to 100 virus particles for every living cell, making viruses the most abundant biological entities on Earth.
It is estimated that there are from 10 to 100 virus particles for every living cell, making viruses the most abundant biological entities on Earth.
While it was once assumed that all viruses descend from a single common ancestor, advances in the techniques for analyzing genomes make it likely that this cannot be the case, simply because there is no single conserved gene across all viral realms.
In addition, new discoveries have turned up many species that do not fit into the six realms (the highest rank of classification) traditionally used to describe viruses.
An editorial published Sept. 12 in the online journal Environmental Microbiology asks about the global virome: “How much diversity and how many independent origins?”
Vast number of viral species
“To the best of our current understanding,” the authors of the editorial write, “all organisms on Earth are hosts to multiple viruses, with the possible exception of some endosymbiotic bacteria.”
Viral genomes are also extremely diverse, they point out, “and the ongoing metagenomic-metatranscriptomic revolution reveals the vast scale of that diversity.”
Metagenomics is the study of the genes involved in transcription, that is the copying of a segment of DNA into messenger RNA that then guides protein production. Metatranscriptomics is a technique that identifies the active genes within a microbial community, rather than trying to identify specific organisms.
As one example the authors note a metatranscriptomic study of the RNA viruses found a twofold expansion of the number of known RNA viruses within a single microbial community rich in unicellular eukaryotes (algae, for example, or amoebas).
“Three independent subsequent studies exploring thousands of metatranscriptomes from diverse environments each led to further, several-fold increase in the number of known distinct RNA viruses,” the editorial notes.
Studies suggest that the case is similar for DNA viruses.
Using a back-of-the-envelope calculation that extrapolates from these remarkable discoveries, the authors estimate from 10 million to 1 billion distinct virus species.
This is compared to the mere 10 thousand viral species currently recognized.
Evidence for more than one origin of viruses
To examine the likelihood of a single origin of viruses, lead author Eugene Koonin, an expert in computational and evolutionary biology, draws on a concept he developed in earlier writings, the virus hallmark gene (VHG). These are the genes that encode the key proteins that are involved in virus replication and virus formation.
The study of these hallmark genes led to a hypothesis of viral origin known as the chimeric origin scenario. This involves hypothesized non-viral replicators (biochemical entities that would have preceded present-day life forms) capturing host proteins, which are repurposed to become components of the virus, in particular the proteins of the viral shell, or capsid.
Implied in this view is that before there was cellular life, there was a “viral world” containing organisms somewhat like the viruses we know today. However, according to the authors, there could not have been a single common origin of today’s viruses “simply because viruses do not share a single universally conserved gene.”
This raises the question of how many independent ancestors there are for the contemporary array of viruses known as the global virome?
In examining the four most expansive realms of viruses, Riboviria, Monodnaviria, Duplodnaviria, and Varidnaviria, the authors show the difficulty of attributing a common ancestor to the many and highly varied species within these realms.
Even when there is a hallmark gene common to all the members of a particular realm, they point out, one cannot attribute this commonality to the origins of the viruses themselves.
As an example they cite the realm of Ribovaria. The members of the two large subdivisions, or kingdoms, in this realm all share an enzyme for replication that is homologous, and therefore presumed to have come from a common ancestor.
However, the authors note, “the origins of the viruses themselves, resulting from the recruitment of distinct capsid proteins, were clearly independent.
An “even more striking” example, they argue, is found in the realm of Monodnaviria, which, they believe, contains members which evolved “on at least four independent occasions via parallel routes.”
These parallel routes were the capture by small rolling-circle plasmids (a genetic structure within a cell that can replicate independently of the chromosomes), of either a virus gene or a repurposed cellular gene capable of encoding a capsid protein.
Citing many other examples from the other now-recognized viral realms, the authors conclude, "Although new viruses do not emerge ‘every other day,’ there have been many points of virus origin. It is not inconceivable that, before we are done with the global virome, the number of distinct, independently evolving groups of viruses that, at least in principle, have to be classified as realms will far exceed the current six."
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E.V. Koonin et al. The global virome: how much diversity and how many independent origins? Environmental Microbiology (2022).
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