Archive for September, 2015

Disease risks lie in ancient poo? Not really.

30 September, 2015

Defrosting ancient poo could reintroduce some age-old bugs to the modern world, scientists say.

Defrosting ancient poo could reintroduce some age-old bugs to the modern world, scientists say.

An extremely infectious and deadly ancient virus, released from a frozen slumber by warming climates, could play havoc with immune systems that have no experience of such germs.

A team of international biologists, including the University of Canterbury’s Arvind Varsani, has proven that such an incident is theoretically possible, after they resurrected an ancient virus from the 700-year-old frozen droppings of Canadian caribou.

With a little reconstruction, the DNA virus, christened the “caribou faeces-associated virus”, has gone on to infect modern-day plants, according to a paper published yesterday in Proceedings of the National Academy of Science.

Varsani said the team had proved ancient viruses were as worthwhile to study as today’s versions – as both may make up tomorrow’s germs

Sourced through from:

Arvind Varsani, again! He’s everywhere B-)

…and some scientists pooh-pooh such statements [sorry!], because – as with the Giant Killer Viruses From Tundra! sensationalism, there is NO proof that (a) there are myriad killer viruses in permafrost, (b) very little proof that they will infect anything outside of a lab.

Seriously: the French team that found pitho- and molliviruses had to use lab-cultured amoebae to resurrect them; Arvind and crew had to make agroinfectious partially dimeric clones of their virus and inject them into lab plants to make them infectious.

And there’ll be precious little of that going in in clearings in the tundra.

See on Scoop.itVirology News

So, viruses: living or dead?

29 September, 2015

This question has come up in my life innumerable times in the last 40 years that I have been interested in viruses – and I find that debate on it often becomes theological in its intensity, with proponents muttering things like “They’re just intracellular parasitic molecules!”, or “Of course they’re alive – they evolve, don’t they?”

And as happens when I hear theological arguments, my eyes glaze over, and I think of other things.

Because it’s really quite simple: as I have been patiently explaining to students for over thirty years now, viruses are simply acellular organisms – which find their full being inside host cells, where some measure of essential support services are offered in order to keep the virus life cycle turning.  What everybody sees as “viruses” are in fact virions, the particles that viruses cause to be made in order to transport their genomes between cells, and to preserve them while doing so.  Thus, in a very real sense a virus IS the cell it infects – because it effectively takes the latter over, and uses it to make portable versions of the genome that can infect other cells.

Back in 1995 or so, I wrote the following for my first teaching pages:

The concept of a virus as an organism challenges the way we define life:

  • viruses do not respire,
  • nor do they display irritability;
  • they do not move
  • and nor do they grow,
  • however, they do most certainly reproduce, and may adapt to new hosts.

By older, more zoologically and botanically biased criteria, then, viruses are not living. However, this sort of argument results from a “top down” sort of definition, which has been modified over years to take account of smaller and smaller things (with fewer and fewer legs, or leaves), until it has met the ultimate “molechisms” or “organules” – that is to say, viruses – and has proved inadequate.

If one defines life from the bottom up – that is, from the simplest forms capable of displaying the most essential attributes of a living thing – one very quickly realises that the only real criterion for life is:

The ability to replicate

In fact, I have just uncovered something I started writing in 2005 on the same subject:

Fruits of the Bushes of Almost-Life: A Natural History of Viruses


It is an amazing thing that when people speak or write of “life”, they generally miss out one of the most interesting and diverse facets of it: viruses…!

Viruses are like the black sheep of the family of life: they are everywhere, they infect everything, they are the most diverse organisms on our planet, and yet most biologists either do not mention them, or simply dismiss them as “parasites that you can’t even see with a microscope”.

Consider this: of the seven different kinds of genetic material shared by all organisms, all cellular life has only one – and viruses have all seven.

And this: the most abundant and genetically diverse organisms in the oceans, and therefore probably on the planet, are viruses.

Or this: viruses may be the only bridge left to understanding how our DNA-dominated cellular world came to be, from primitive RNA-genomed ancestors.

Let’s face it, viruses generally get a bad press: if it’s not “Will avian flu kill us all?”, it’s “Marburg virus outbreak threatens Luanda”, or “Is SARS coming back?” leaping out at us from our local newspapers – and that’s all just this year.  We even have speculation that global warming could unleash long-frozen plagues on us, as viruses thaw out of the Greenland icecap – and while all of this represents media hype, there are grains of truth in all of it,  Yes, the H5N1 influenza virus epidemic in poultry is a matter for very serious concern; yes, there was a chance that Marburg virus – an equally nasty relative of the dreaded Ebola – could have devastated Angola’s capital as recently as a few months ago; yes, epidemiologists are worried that SARS coronavirus may again leap out of its animal or even possibly human reservoirs and into the world and kill thousands; yes, long-frozen viruses may yet represent an unexpected and unwelcome disease threat to humanity, its crops and its livestock.

However, all of these concerns highlight only one facet of the complex phenomenon that is viruses: that is, the “viruses as ogre” side of these organisms.  Not that this is not amply justified: the single biggest killer of humans this year will probably be either diarrhoea-causing viruses or HIV; the legendary Black Plague that repeatedly decimated medieval Europe may well have been a haemorrhagic fever virus rather than a bacterial disease, and the “Spanish Flu” pandemic of 1918-1922 is now known to have killed more than 60 million people.  But viruses also possibly gave us the ability to develop a placenta and develop away from marsupials to become mammals – and viruses probably also regulate the lifetimes of algal blooms, cholera epidemics, aphids, moths that attack conifers, and possibly every living thing in the seas.

In short, viruses are intimately intertwined into every ecological web on this planet, whether we know it or not – and we find out more and more how much this is true the more we look.

What are Viruses?

The very nature of viruses severely taxes all conventional notions of what is an organism, or even of what is life.  While the debate on whether viruses are living or are indeed organisms gets almost theological in its intensity in certain biological circles, there is a very simple way around the problems – and that is to regard them as a particle/organism duality, much as physicists have learned to do with the dual wave/particle nature of light.

Quite simply, viruses are obligate intracellular parasites which use the resources of living cells to multiply their genetic material, and to make specialised particles which serve to protect and transport the genetic material, or genome, to other susceptible cells.  Their dual nature is defined by the two ends of their life cycle: the virus as organism is inextricably mixed into infected cells, integrated into pathways of nucleic acid and protein synthesis; the virus as particle can be purified away from all cellular components and kept in a bottle like a chemical, totally inert, until you decide to reintroduce it to its host cells.

I find I am not alone in this: while Vincent Racaniello of Virology Blog is possibly not a believer, his 2010 post mentions that

“The idea that virus and virion are distinct was first proposed by Bandea in 1983. He suggested that a virus is an organism without a cohesive morphological structure, with subsystems that are not in structural continuity…Viruses are presented as organisms which pass in their ontogenetic cycle through two distinctive phenotypic phases: (1) the vegetative phase and (2) the phase of viral particle or nucleic acid. In the vegetative phase, considered herein to be the ontogenetically mature phase of viruses, their component molecules are dispersed within the host cell. In this phase the virus shows the major physiological properties of other organisms: metabolism, growth, and reproduction”

OK, I think I said pretty much the same thing in teaching in 1981, but less elegantly, and I have no proof other than ooooold overhead projection slides B-)  He goes on, though, to mention in the context of mimiviruses, that

“Claverie suggested that the viral factory corresponds to the organism, whereas the virion is used to spread from cell to cell.”

This crystallises things nicely: viruses are acellular parasites which take over a cell, and make specialised particles (virions) to spread their genomes.  Qualitatively, this is exactly what seeds and spores of plants and fungi do: they make specialised vehicles that preserve their genomes, and which can respond to changes in their environment to initiate a new organism.

However, it’s in his last point that Racaniello gets sufficiently theological to silence some of the doubters.  He writes:

“Raoult and Forterre have therefore proposed that the living world should be divided into two major groups of organisms, those that encode ribosomes (archaea, bacteria and eukarya), and capsid-encoding organisms (the viruses).”

I like that.  I like it a lot.  It makes a lot of sense.  And in the light of my last two posts in ViroBlogy – on “The Bushes of Life“, and Deep Evolution of Viruses – I can see that the time has come to spread The True Gospel of Virology.

Which is that viruses are alive.  You OK with that?!

Deep evolution of viruses

28 September, 2015

Ian Mackay of Virology Down Under fame (or notoriety B-) today alerted me to a new paper on the evolution of viruses – which is being touted via press releases as being something that “…adds to evidence that viruses are alive”.

To my mind at least, it does nothing of the sort: what it does do is provide evidence via the medium of comparison of protein folds that “…implies the existence of ancient cellular lineages common to both cells and viruses before the appearance of the “last universal cellular ancestor” that gave rise to modern cells”.

Arshan Nasir and Gustavo Caetano-Anollés took advantage of the fact that protein structure is at least 3 to 10 times more conserved than sequence, and analysed all of the known folds in 5080 organisms, including 3460 viruses. They identified 442 protein folds shared between cells and viruses, and 66 that are unique to viruses – indicating that virus proteomes truly are more diverse than cellular proteomes.

The press release is rather annoying in places, such as in this excerpt:

“Some giant viruses also have genes for proteins that are essential to translation, the process by which cells read gene sequences to build proteins, Caetano-Anollés said. The lack of translational machinery in viruses was once cited as a justification for classifying them as nonliving, he said.

“This is no more,” Caetano-Anollés said. “Viruses now merit a place in the tree of life. Obviously, there is much more to viruses than we once thought.””

Well, some of us have thought a lot more of viruses for a lot longer, obviously!  I have taught for years, for example, that viruses are alive – and just last week this blog has a post on how “The” Tree of Life should in fact be a garden, with a tree and a whole lot of bushes.

I do like this bit from the paper itself, however:

“The most parsimonious hypothesis inferred from proteomic data suggests that viruses originated from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells.”

The authors have come up with a REAL Tree of Life, as well – one that includes viruses.  Smart folk B-)


The tree of life should be a garden. With bushes.

21 September, 2015

Biologists like to talk of and depict, “the” tree of life. This is shown here as in most places, with a bacterial and an archaeal bifurcation coming off a LUCA base, and then another bifurcation of archaea into modern archaea and eukaryotes.

Of course, there are also the anastomoses: an early intracellular colonisation of a eukaryote ancestor by a bacterium, which gave rise to mitochondria, and then another later event, where a cyanobacterium became chloroplasts in the ancestor of green plants and algae.

What is not generally appreciated is that the latter occurred more than once – with different photosynthetic bacteria providing distinctly different types of chloroplasts in the various lineages of algae, The situation then becomes more complicated, with minor and more complex anastomoses among eukarya, with unicellular eukaryotic algae becoming intracellular symbionts and then complex organelles – with evidence in some cases that this happened more than once, as evidenced by multiple layers of membranes surrounding chloroplasts in photosynthetic organisms whose closest relatives are non-photosynthetic.

Thus,”the” Tree of Life already has some internal interconnections that make parts of it more a reticulated network than a bifurcating tree – but this complication pales into insignificance when one takes into account the fact that “the” Tree does not take into account the wildly bushy garden of shrubs that would be viruses.

Seriously: despite repeated urging by folk like me, the multitude of Tree designers have consistently ignored the majority of organisms on this planet. Indeed, in a comment in a recent Twitter exchange on a new Tree, answering my comment that it took no notice of viruses, @phylogenomics: wrote “it does say tree of “Life” not tree of weird parasites of still unknown origin ….”

So I just HAD to reply ” …that happen to be life forms in good standing. In everyone B-) And [which] outnumber everything else.”

A good-natured exchange followed, which prompted the writing of this post – because, really, the Tree of Life SHOULD be a Garden of Life, with one tree and a collection of distinct bushes, some pretty big, representing different virus lineages. The biggest bushes would probably be the so-called megaviruses, and collections of viruses dignified by being grouped into taxonomic Orders, such as the tailed phages in the order Caudovirales and the ssRNA(-) viruses grouped as Mononegavirales.

And of course, some components of those bushes meet up with some of the roots of the tree – in the form of specific genes like DNA polymerases, which may well have a common origin with cellular genes.

Some of those bushes also inerconnect underground, like some of the reverse transcriptase-dependent viruses which have nothing else in common; the RNA viruses which share RNA-dependent RNA pol enzymes, but with other components from different origins – the okapi-like viruses, as they were termed by Rob Goldbach.

Some bushes in fact parasitise the tree, just like parasitic plants grow on other plants: the polydnaviruses of wasps, for example, are effectively genome components, and are used by their hosts to aid in parasitising their target hosts.

So, a garden – and one that it would be challenging to portray.

Which I would like to leave up to someone with far more artistic ability than me B-)

New header graphic: something old, something new; something borrowed – and something blue

8 September, 2015

That’s right: a new header graphic after lo, these many years.

Something old: Maize streak virus, in all its geminate glory, on the left. Picture taken by RG (Bob) Milne in Cape Town, 1978.

Something new: unidentified phycodnaviruses, middle right. Picture by Hendrik Els, 2015.

Something borrowed: T4-like phage particles, right. Picture by Mohammed Jaffer, 2005.

Something blue: Bluetongue orbivirus particles, centre left. Picture by Ayesha Mohamed, 2015.

Emerging Infectious Diseases 20-year Timeline – Emerging Infectious Disease journal – CDC

7 September, 2015

Emerging Infectious Diseases 20-year Timeline

Sourced through from:

It is well worth remembering that the CDC’s EID has been in the forefront of reliable reporting on emerging viral diseases – as well as others, of course – for a quarter century now.

And I’ve been getting it that long…they used to send it out for free, AND it was available on the Web from very early on, so I used to regularly use articles from it for teaching 3rd year students.

It is a great institution, and I wish it well!

See on Scoop.itAquatic Viruses