Viruses and the tree of life




1. Viruses are not alive

2. Viruses are polyphyletic

3. There are no ancestral viral lineages


5. Viruses don’t have a structure derived from a common ancestor

6. Viral metabolic genes originate from cells

7. Viral translation genes originate from cells

8. Viruses steal genes from cells

9. Most gene transfer goes from viruses to cells





Comments on this entry are closed.

  • PaperHand 19 March 2009, 8:29 am

    I've never really understood the “are viruses alive or not?” debate. Life isn't a simple binary function. Whether you count viruses as alive or not depends on your definition of life, it seems to me. So, really, isn't the debate more “Is a definition of life that includes viruses useful or not?”? Framing the debate as “are viruses alive or not?” implies that there is an already-established definition of “life” allowing a debate over whether viruses fall in that established category.

  • Dave UH 19 March 2009, 12:55 pm

    I thought that the line of reasoning was very cogently presented. I, as a supporter of viruses being alive and having a deep root in evolutionary history will have to rethink my previously held hypothesis, in light of recent discoveries. I believe that at this time there is not enough evidence to assert the view that viruses are remnants from the “RNA World”.

  • foop 19 March 2009, 2:06 pm

    Seems to me that they can become alive in the right environments.

  • bill_mcculley 30 March 2009, 8:34 am

    Hello Dr. Racaniello,

    Great questions for discuss. I hope you don't mind laypersons (electrical engineers like myself) in asking a few questions I've been thinking about! One recommendation is perhaps a you can setup a general discussion area on this website for oddball questions like mine or others that aren't easily catagorized.

    This thread is about as broad as any other, so here are a couple of unconventional ideas I've had –

    1. Did you ever think, at a more primary fundamental level, perhaps proteins/amino acids themselves were the actual “intelligence” rather than DNA “driving the show”. Perhaps DNA is merely just a scoffolding which the amino acids decide to hang their hats. Perhaps there is something beyond the interaction between amino acids – beyond mere biochemstry? (Perhaps it sounds really strange)

    2. Did you ever wonder if, by the broad use of vaccines, we are exerting an artificial stress on the ecology of a virus, thereby essentially resulting in a stronger virus to be selected down the road? Sort of like the National forest park policy of preventing fires for for so many decades, thus creating conditions in which much larger, horrendous forest fires can now occur.

    Like I said, I'm interested about learning more. So I hope you don't mind my lack of exact terminology or my understanding in terms of the basic concepts of virology

    – Bill

  • profvrr 1 April 2009, 10:55 am

    Hi Bill,

    Don't apologize for questions – here at virology blog there aren't any bad questions. We want to teach virology so all inquiries are welcome. In fact your questions are excellent.

    Having a discussion board is a great idea. I'll look into the software to run it. As for your questions:

    1. Chromosomes were known for many years to be composed of both protein and DNA, and scientists didn't know which was the genetic material. A key experiment was done in 1944 when Avery, McLeod and McCarty showed that DNA could induce a change in bacterial phenotype. In 1952 Hershey and Chase provided further support for DNA as genetic material, by showing that the DNA, and not protein, enters cells during a viral infection.

    2. Vaccines mimic (although not always perfectly) what happens in a natural infection – the production of immunity to the virus. This immune response clearly exerts selective pressure on the virus. A perfect example is the yearly antigenic change of influenza virus that is selected each year by population immunity. Some viruses, like poliovirus, are not antigenically variable and probably not subject to such selective forces.

  • jerryclatham28 8 June 2009, 12:09 am

    Viral translation genes originate from cells The mimivirus genome harbors genes encoding elements of the protein synthesis machinery. This observation has been interpreted to mean that viruses did not always rely on cells for translation. However, sequence analysis indicates that these genes are derived from cells by horizontal gene transfer.Viruses steal genes from cells Viral genomes encode many genes that have no homologues in cells. It has been suggested that viruses influence evolution of cells by donating new genes. Sequence analysis has failed to provide support for this hypothesis. Viruses are ‘gene robbers, not gene inventors and massive gene suppliers’.

  • Anonymous 8 June 2009, 4:29 pm

    I do continue to have questions about point 4, and if anyone can assist in clarifying I would be much appreciated. The ODE is very serious about keeping the editorial control of the paper out of the publishers hands, but Steve Smith’s recommendation and (this is the point I need clarification on) proposed contract had language that separated editorial control of the paper from the publisher and, as far as I can tell, give the publisher a higher rank in business matters only.

  • Xelo 21 June 2009, 12:39 pm

    I will agree that when outside a cell that the virion is not living or more aptly put dormant. However every organism is built to reproduce and pass on its genetic material from one generation to another. Once in side a host cell viruses reproduce and can use cellular energy to create more of themselves. Also they evolve, they respond to pressures from their biotic environment. Simply put, viruses evolve and reproduce, two characteristics that inanimate matter, should not posses.

  • Chelsea 4 July 2009, 8:51 pm

    i was pondering about all of this and is it possible that the reason, in #9, “This conclusion is paradoxical because viral genomes are the most abundant on earth.” is because all life could have been created from different 'viruses'?

  • Chelsea 4 July 2009, 9:01 pm

    my mother is greatly against vaccine use, and i have never once been vaccinated and have many health benefits due so..

    our race is so hideously fixated on saving EVERYONE that we do not take in account the future

    we are AFRAID of natural selection.

  • Chelsea 5 July 2009, 3:53 am

    YES YES YES!!!!!!!!!

  • Traveller 2 August 2009, 4:39 am

    This is quite impressive, I am pleased to read this post, keep posts like this coming, you totally rock!Cheers,Blog Review

  • Prophage 22 August 2009, 3:37 pm

    Virses are living entities! They are obligate parasites which means that they need a host to replicate, otherwise they are dormant.

    They discovery of Sputnik- a virus that infects a virus also adds weight to this argument.

    Any genetic material capable of replicating can be considered “living”. It will only be a matter of time, loss of old dogma and a broader view of life sciences that will result in this idea becoming universal…

  • yoyo123a 7 October 2009, 10:20 pm

    Your blog is nice,i like it.

  • tumblemark 17 December 2009, 8:01 am

    On the matter of virus monophylogeny, consider that their origin in the three kingdom tree of life has been established in the computational biology paper:

    Sun F-J, Caetano-Anolle´s G (2008) Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses. PLoS
    Comput Biol 4(3): e1000018. doi:10.1371/journal.pcbi.1000018

  • E.I. 30 January 2010, 11:16 pm

    Yes, it is true that viruses do not fit into the cellular tree of life, but viruses are capable of forming phylogenetic trees of their own. These trees show relatedness among viruses of a particular domain (eukaryotic viruses, archaeal viruses, etc.) and do suggest a common viral ancestor. The fact that we know so little about viruses complicates these phylogenetic comparisons.

    As for the argument that viruses don't share a common structure… Viruses rapidly evolve; it's one of the major reasons for their tremendous success. This rapid evolution makes it difficult to say that viruses don't share things in common. We have little idea what the early earth was like, but it is obvious that conditions have changed since the origin of “life.” As viruses adapted to new hosts they altered their genetic makeup to make them better equipped for a certain host.

    The fact that there is not a common ancestor does not mean that it never existed. That is just illogical and completely unsupported. Cellular life leaves fossilized evidence. We are learning that viruses do as well, but it is much (MUCH) more difficult to collect this data (viruses are much smaller than cells).

  • ductub 24 April 2010, 6:51 am

    Prof. Racaniello,
    1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?
    2. If viruses are not alive, why some viral vaccines contain live viruses?
    3. Do you think that obligate intracellular bacteria are not alive either? They can't replicate without host cells, same as viruses.
    4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the “organismic” structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.

  • ductub 24 April 2010, 1:51 pm

    Prof. Racaniello,

  • Liz 10 January 2011, 3:51 pm

    It is just plain scary that people like you, who have no clue about this stuff are making vaccines.

  • Chris Stacy 25 March 2011, 2:21 pm

    Someone already answered you generally about proteins vs. DNA, but you ought to google these terms for more information on a tangent you would be interested in: “epigenetics” and “RNA world”. There are probably decent Wikipedia articles to get you started.

    Moreover,everything about DNA is subject to what is broadly called “regulation”. The story that DNA ultimately codes for proteins is an extraordinarily simplistic explanation. There is so much more to it, most of which we do not understand.

  • Dan, Tx 7 February 2012, 5:43 pm

    I consider viruses to be alive, they have a genome, they use the genome to direct transcription, translation, and protein synthesis (except for viroids).  But even naked RNA strands of viroids are capable of replication in the correct environment (host cell).  What living organism can reproduce in the absence of nutrients? None. Viruses are no different, they require a very special set of nutrients. They are obligate parasites – many organisms are known that can not grow or replicate outside of their hosts, but can survive in a resting state. So, I see viruses as living. The flu is not cause by a toxin, it is caused by a pathogen that replicates and causes symptoms in its host.  Viruses probably have arisen many times as degenerated bits from other living forms and have been cobbled together from bits picked up along the way. So, they are very different from organisms that we think of in the tree (usually). However, over short periods of time populations clearly can evolve.  You seem hung up on the fact that the virus only is actively living when it inhabits a host cell. This is quite a prejudice.  Perhaps the earth could view us as viruses? After all, we don’t make our own planets, we just live off of ones that are already there.  Prions are the example of a non-living infectious agent.  I do draw the line at prions, because they do not possess a genome and are simply proteins that are unable to specify their own.

  • Ramsy 9 February 2012, 5:37 am

    I personally think that viruses are non-living and living, because of the fact that they sought of become alive when they enter a living cell. Another thing that boggles me is how do viruses know how to do their thing, how do they find a cell……?

  • Ifaithway 17 March 2012, 12:37 pm

    how can you depend that virus is nonliving, when they say that when the virus attach in a living cell,the virus become living???

  • lunarlander 18 March 2012, 10:54 pm

    Amen. You couldn’t have said it better. My sentiments exactly. Biological reality is fuzzy and humans like to stick things in dichotomous groups to understand them. Then they mistakenly assume that the groups are a property of reality itself and don’t see that the essence of what is being debated is only the arbitrary inclusion or exclusion of something based on a particular human construct. The real question, like you said is: What is your motivation for arbitrarily deciding to chop up reality as you did? For what functional reason should I be define something one way versus the many other ways in which it could be validly defined? Certain metaphors constructed by certain definitions may be more useful than others depending on context.
    What about organisms which were once freely reproducing and then became completely unable to replicate on their own without a host cell, like mitochondria and chloroplasts? Are my mitochondria alive? Are they as alive as my gut bacteria are? Are they part of my organism?- or are they an independent organism? Were they once an organism and now are not? Were they once alive and now are not? If not, exactly at what point in evolutionary history did they become “not an organism” or “not alive”? 
    What about our white blood cells which essentially move around and act just like amoebae but would not be considered an independent life form because they are a part of a larger organism? We could have a debate about all these things until the cows come home and there are no cut and dry answers to many of them but some of the debates are not very useful because they are only pointing out over and over again that neat boxes don’t map perfectly onto the seemingly endless continuum of biological reality. These debates highlight the awkward areas left over when trying to square the circle of reality so to speak; This exact type of debate can be had over what is an “organism”, “species”, “gene”, etc.? ad infinitum. I believe these debates can be fun, and can even be beneficial for refining classification and thinking about the world in different ways but they do nothing to change biological reality which ultimately defies this binary type of categorization we desperately attempt to apply to it. Metaphor is wonderfully useful for understanding natural phenomena but it should be recognized as such rather than an intrinsic property of reality itself.

  • Kupfernick 30 April 2012, 11:17 am

     Absolutely. The question is what is important, not the answer. The question helps frame the larger debate “What is life?” but in science we look for facts, not truths.
    “If it’s truth you’re looking for, Dr. Tyree’s philosophy class is right down the hall (Dr. Henry (Indiana) Jones, Jr.)”

  • haho 8 September 2012, 1:46 pm

    For me it is irrelevant if viruses are alive or not; they have DNA and this mutates, they evolve so there can be drawn an evolutionary tree from the differences between their DNA. HIV viruses also continuously evolve and occur in different strains. It would be interesting to see the (many) evolutionary trees of viruses groups and any possible connections with the bacteria. Maybe viruses and their ancestors crossed the boundary of life many times in both directions and viruses might have bacterial ancestors?
    In any case, it might be assumed that viruses are as old as bacteria and have some 3 billion years of evolution behind them. However, since the DNA of viruses is very short and large parts of it will have evolved parallel to their host bacteria, the parts of the virus DNA from which an evolutionary tree can be constructed will probably be very limited.

  • cormac 30 September 2012, 7:11 pm

    dead means they were at one point alive and no longer are. if something was never alive, its considered nonliving. live just means they’re contagious. and because something can adapt and evolve does not mean it is alive, that is one of many characteristics of life

  • muskan 5 June 2013, 1:19 am


  • muskan 5 June 2013, 1:20 am

    kya kr rhe ho

  • muskan 5 June 2013, 1:21 am


  • Arthfael 10 March 2014, 8:31 am

    I believe that several arguments against viruses being alive cited here are irrelevant, namely those of an evolutionary order. Being alive has nothing to do with how you came to be alive. May I remind you that we acquired a great part of our metabolism through horizontal gene transfer?
    As for lack of structure conservation, virus evolution is known to be faster (as should be expected) than that of other organisms. Simpler genomes, much higher populations, exposure to other genomes in the same compartment (cellular, other viruses), higher plasticity (esp. for RNA viruses). No surprise it’s difficult to see sequence or even structure conservation. Viruses may even have evolved independently several times and have converged to look superficially similar, just like algae have evolved independently several times (though in each case their photosynthesis was inherited directly or not from cyanobacteria).
    I believe that the question of being alive in the sense of life forms as we know them on earth comes back to the question of genetic information, a nucleic acid genome – or set of genes/nucleic acid sequences interpretable as information coding for at least a dissemination form – which have for a moment put their lot together and are attempting to perpetuate themselves. The means of replication/perpetuation are irrelevant, as long as the genome manages to perpetuate itself. For all genetic information, on earth, perpetuation appears to require a cellular life form, and viruses exist as cellular life forms – the so called viral factories in infected, usurped cells….

  • Zekava 5 June 2014, 1:09 pm

    As a rebuttal to your final point, life started as complex molecules that made copies of themselves, and viruses are barely more than that, just using a convenient cell as means of reproduction.

  • Esteban Vilahu 1 October 2014, 7:21 am

    In my opinion, we NEED TO KNOW what is the incentive for viruses to survive and flourish? Who or what motivates in their quest for SURVIVAL??

  • Esteban Vilahu 1 October 2014, 7:34 am

    MY POINT; Based on current hypotheses of Evolution, a virus will NEVER evolve into human.

  • Esteban Vilahu 1 October 2014, 7:36 am

    GOD is NOT the answer.

  • Yo mama 7 April 2015, 10:58 am

    Yo mama

  • Valhala 16 April 2015, 3:29 pm

    Actually, the probability of any living thing at all ( including chimps, which have 98% DNA sequence similiarity with us) evolving into a human is negligible and I’d bet that it won’t happen even in another 4.5 billion

  • Ravindra Bahl 30 June 2015, 11:08 pm

    I agree the virus are alive or not depends upon our definition of being live.

  • Ravindra Bahl 30 June 2015, 11:11 pm

    Is it possible EBOLA has evolved form Influenza

  • Ravindra Bahl 30 June 2015, 11:14 pm

    Dear Dan,Tx What you accept as resting state can be non alive state in virus.(A state with no or very little activity)

  • Eugene Ioanid 4 September 2015, 11:10 pm

    As a neurobiologist virology is not my thing. Yet, I asked in a class on molecular biology where the viruses fit on the “Tree of Life,” and I got the same glib answer as that of the High Priests on this page. But then I asked: “Well, do you consider them as leaves that fall off the Tree of Life and so at which point do viruses appear on the branches? Which and when and what’s the TEMPORAL order of viruses? I got the usual: IT ain’t alive so it ain’t on the tree!”

    Ah, but lets think abut it. Most of what we know about “life” we know from CURRENT organisms and the rest is philosophy!

    Like cosmology, geology and archaeology work by sets of assumptions. I can hear the retort now: So, you claim these are wrong?
    No, absolutely not. But 55 years of tooling in biosciences and dabbling in physical sciences has brought me to a late (not mid) life crisis as I can no longer distinguish between what comes from the experimental learning and what provenes from “principle’….what ever that means. We are in tough times. Money for groping in the dark is log dried up and money for proving that the NIH/NSC search committee reviewers seems all that’s left. worst still, only a few have a lot of the available equipment and they’re not about to make it available to someone who’s not above wacking at the pat theories that got that famous big name the equipment to begin with. I other words, when science has to do more with less it usually does LESS!

    So, I propose that philosophers ought to get in here and say: “Let’s start looking at how you set up your terms; are they support beams for your premises?

    I would suggest that a lot we take for granted about evolution in times long ago should go the way of a lot we take for granted about things far, far away. Philosophers should scrutinize how, not Science, but scientists get at “truths.” The “evolution” of viruses thus fits into this schema of the evolution of the Big Bang: how much is royal,” ie. big shots’ speculation and how much is inescapable data momentum?

    I, personally, am in a sort of crisis about “chicken and egg”: which came first, the nuclear blue prints or the cytosomal entities? We know that mitochondria are “things” that “blobs” ate and voila, we’ze got metabolism!

    Was it all at once, or was it in steps?

    Recall please that I metaphorically referred to viruses as leaves that fall off the Tree of Life. As we approach Fall, none of us doubts that the beautiful foliage we all go to the mountains to admire is NOT ALIVE. It ain’t green, it ain’t alive, n’est pas? But, are the dead leaves biologic entities? Indeed they are, like bones in an ancient grave site. Yet, these dead bones have been our clues to life for a couple of centuries. Viruses evolve…viruses become through evolution ever more complex. Do they do so until they become living things by the definition biologists use: WE HAVE NO WAY OF KNOWING FOR IF THEY BECOME LIVING THINGS THEY ARE IPSO FACTO NO LONGER VIRUSES, by definition!

    And yet, they appear somewhere on the branches of the tree of life and “evolve.” Are they the remaining fragments of once living things, or are they the “feces of life”? TRANSPOSONS are weird for someone trying to learn to drive on the highway of mol-bio without getting a ticket from the instructors serving as cops for the Genomic Dogma of life. Which came first, the cytoplasmic proteins or the nuclear nucleotides? Did virus precede life as trial balloons that went flat, or are they garbage produced in evolution of the Tree of Life?

    In conclusion, to say that viruses are not living things is to walk into the mine-field of where fits in what is both a parallel and most effective evolution, for viruses may well be what snuffs out the “life” within us massive cellular communities. Viruses certainly are a part of life, a part that keeps evolving so that it can, truly be said to DWELL WITHIN IT. So if viruses are leftover nuts and bolts, how do evolutionists relate their existence relative to the evolution of life? Could life have “happened,” flourished and, indeed, evolved without viruses around? Did reproduction precede viruses? Were they “junk” (as we so imprudently said about 70%+ of the DNA when collecting big cash for the Genome Project?

    Demi-god Ventner created life by putting home-made DNA into “a bag of chemicals.” Had he put the home-made DNA into a capside and it would then attack cells, forcing them to make more of IT until the cells burst, would we then also say that he produced life?

    If viruses are not life, do they come as roots or leaves of the tree of life?

  • eugnid 8 September 2015, 4:11 pm

    The issue of dead or alive is much like a little pregnant or a lot. A lot, I guess is near gestational, a little is early in the oven, I assume. Viruses may not be branches on the Tree of Life but they may well be roots or falling leaves. One way or another– under or falling off– viruses are OF the tree of life. A sperm and an egg fertilized on a table top is not only not much fun but is totally non-viable as a fetus. Is a sperm a cell? Are polar bodies cells? Are we looking at life with a stick drawing a line between life and non-life? If so, do we know enough about the mechanisms of the realm of biology to impose upon it definitions and distinctions we dream up? I am sort of a vitalist and a spiritualist so I feel great guilt over every monkey cat and rat I operated and experimented on. But where that guilt stops I don’t know. Even when I crashed my car….as soon as I realized that I got out alive I felt like a murderer. And when I get my flu shots I am expecting as much from my new IgGs as I do from my T cells in protecting me (each in his own way). So, is my immune SYSTEM ALIVE, made up of cells and non-cells fighting part cells. As an old physiologist I defer to you young molecular biologists, to be sure, but remember that it is you guys that constantly muddle the border between organic and biochemistry.

  • eugnid 8 September 2015, 5:34 pm

    One last thought, if I may, please. We really should take time from the busy schedules of our prospective MDs and PhDs to discuss these issues that philosophers ponder because we are making very big distinctions that hem-in our experimental designs and restrict the flight of thought of our budding researchers. NIH has had its budget viciously cut at a time when good scientists were becoming very hard to distinguish from bad ones, given how almost 1/3 of published papers had to be retracted because of desperate attempts to rise or not to fall off the research funds ladder. Looking at how medicine depends of clinical statistical studies and basic science on esoteric physicochemical computations, a giant chasm separates the good from the bad and desperate “must do” clinical and research institutions are sinking in a morass of dogmatisms that they can’t afford to query because you just can’t get your next grant questioning your previous one in these tight times when for profit has encroached on the pristine arena of pure science. Our only defense– as in a courtroom– is the argument. We need a new 1960s UC Berkley “Free Speech Movement” questioning the authority of the Establishment. As one who was there let me tell you, despite all the infantile affectations and revolutionary crap, there was incredible “MEANINGFUL DIALOGUE,” of the kind that would now bend and even break the monstrous cathedrals of textbook writers and grant review committees….and it would cost us nothing but time. Back then at UC Berkley Red lions lay with conservative lambs (or the other way around) seeking a medium on which iconoclasm could flourish. It hounds my nightmares that within two short years the FSM devolved from free speech as essential to the intellectual’s fulfillment of his/her’s social and moral obligation as a citizen to freedom of hedonism and nihilism, just before it moved to th Vietnam War issue. Today science is corrupt; that’s inevitable given how desperate it is. Its high priests are the very student revolutionaries of the 60s– now all comfortably tenured. As Society for Neuroscience Conventions I marveled at how the High Priests of neuroscience dominated with their facile psychiatric theories. Then came the world of the GENOME. Now we knew everything! And yet, here we are debating the distinction between proteins, nucleotides and life. Responsible debates like this are our only salvation. By never resolving but ever sophisticating our arguments we will become great communicators which will allow the great wise American public to put its money where our mouths are. With line in the sand dogmatism and tsk-tsking errors and flaws in the thinking of debators we will only produce the Aristotilian rigidity that ended the Golden Era of Thought instead of the Socratic quest that made mature so many young inquisitive lives. Molecular Biology has all but smeared the line distinguishing life from non-life and that may be a stmptom from which we need chaos to save us through wild debates that seem pointless and endless.

    PS I read through Flint’s Principles of Virology and STILL don’t feel I know the answer to our discussion so thank you all for debating it!