Archive for the ‘General’ Category
Maize streak Reunion virus (MSRV) is a member of the Mastrevirus genus in the family Geminiviridae. Of the diverse and increasing number of mastrevirus species found so far, only Wheat dwarf virus and Sweetpotato symptomless virus 1 have been discovered in China. Recently, a novel, unbiased approach based on deep sequencing of small interfering RNAs followed by de novo assembly of siRNA, has greatly offered opportunities for plant virus identification.
Image of a mastrevirus from Ed Rybicki
This is quite a big deal: there are very few cereal-infecting geminiviruses described from Eurasia, let alone symptomatic maize-infecting mastreviruses whose closest relatives come from Isle de la Reunion in the South Indian Ocean and Nigeria.
Mastreviruses are not seed-transmitted, so how did it get there? What is transmitting it? Is it possibly the elusive Bajra streak virus from India, that was described but never sequenced?
The authors say, in their conclusion:
“To date, other than MSV, MSRV is the only mastrevirus species that has ever been sampled from maize having maize streak disease symptoms. Interestingly, MSRV was also detected from wild grasses such as Setaria barbata and Rottboellia sp. in Nigeria, suggesting expanded host and geographical ranges for this virus . This first report of MSRV isolates in China reveals that this virus is likely to possess a far greater diversity and distribution than has been appreciated. Because 10 of 22 samples from Yunnan Province, China, were infected with MSRV-YN, for an infection rate of 45.5 %, further work on epidemics of MSRV-YN in China is needed.”
Absolutely! Maize streak, whether caused by MSV or potentially by MRSV, can be a devastating disease – and if this is expanding out of endeminicty in grasses thanks to leafhopper population expansion, or climate change, things could get interesting int hat part of the world.
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.
“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?!
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-)
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
Sourced through Scoop.it from: wwwnc.cdc.gov
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!
REGISTRATION IS NOW OPEN – VIROLOGY AFRICA 2015
On behalf of the Institute of Infectious Disease and Molecular Medicine of the University of Cape Town and the Poliomyelitis Research Foundation, we are pleased to invite you to Virology Africa 2015 at the Cape Town Waterfront.
VENUE AND DATES:
The conference will run from Tuesday 1st – Thursday 3rd December 2015. The conference venue is the Radisson Blu Hotel with a magnificent view of the ocean. The hotel school next door will host the cocktail party on the Monday night 30th November and in keeping with Virology Africa tradition, the dinner venue is the Two Oceans Aquarium.
Early Bird Registration closes – 30 September 2015
Abstract Submissions deadline – 30 September 2015
The ACADEMIC PROGRAMME will include plenary-type presentations from internationally recognised speakers. We wish to emphasise that this is intended as a general virology conference – which means we will welcome plant, human, animal and bacterial virology contributions. The venue will allow for parallel workshops of oral presentations. There will also be poster sessions. Senior students will be encouraged to present their research. We have sponsorship for students to attend the meeting and details will be announced later in the year.
A program outline has been added to the website
Our preliminary programme includes two workshops.
There is a hands-on workshop on “Plant cell packs for transient expression: Innovating the field of molecular biopharming”, with the contact person being Dr Inga Hitzeroth – Inga.Hitzeroth@uct.ac.za. This workshop will run at UCT one day before the conference, 30th November, and a second day, 4th December, after the conference.
The second workshop is on “”Viromics for virus discovery and viral community analysis”. The workshop at UCT will be on 4 and 5 December with the contact person being Dr Tracy Meiring – email@example.com.
Some of the workshop presenters will be integrated into the conference programme but the practical components will be run at University of Cape Town. Separate applications are necessary for each workshop.
If you are prepared to fund an internationally recognised scientist to speak at the conference or if you wish to organise a specialist workshop as part of the conference, please contact
Anna-Lise Williamson or Ed Rybicki.
For any enquiries please contact
Miss Bridget Petersen/ Email: firstname.lastname@example.org or phone: +27 21 486 9111
Ms Deborah McTeer/Email: email@example.com or +27 83 457 1975
I was reminded via Twitter by Vincent Racaniello, he of “virology blog” fame, of the problem of preserving stocks of old viruses.
Particularly, in his case, of stocks of a virus that may be eradicated in the wild in a few years, and then – according to him – will need to be destroyed.
Surely we need to at least preserve sequence information of these pathogens before we let them go into oblivion, the way variola and rinderpest viruses have already gone?
So I wrote this to him:
“Great that you have preserved these samples – but a longer-term strategy needs to be adopted, before completely irreplaceable specimens are lost forever, to you and to science in general.
I have the same problem: a colleagues’ samples of plant viruses; beautifully preserved in heat-sealed glass vials, dried over silica gel, dating back in some cases to the early 1960s. For that matter, I have about a thousand glass bottles of liquid plant virus samples at 4degC, dating back in some cases over 40 years – and still viable.
Surely there is a case to be made for preserving some of these viruses? Mining them for sequence in this metagenomic age is not that difficult; preserving their infectivity, however – another matter. Some of my plant viruses are probably bomb-proof; your poliovirus samples, on the other hand – probably slowly deteriorating as we watch.
A wider conversation is needed: I know of other archives, of old poxvirus collections for example, that will be lost forever in a few years. Should we not get an international effort going to log them, sequence them, preserve them?
I think so.
Want to join in?
If any of you out there have a similar problem, let’s hear from you – and maybe we can do something to at least preserve the genetic information in unique collections.
I would like to test the response to a Introduction to Virology ebook that I want to develop from my extant Web-based material, given that this is likely to disappear soon with our Web renewal project here at UCT.
Download the Virus Picture Book excerpt here. And then please tell me what you think / whether you would buy one (projected price US$15 – 20)? Ta!
In 2008–09, evidence of Reston ebolavirus (RESTV) infection was found in domestic pigs and pig workers in the Philippines. With species of bats having been shown to be the cryptic reservoir of filoviruses elsewhere, the Philippine government, in conjunction with the Food and Agriculture Organization of the United Nations, assembled a multi-disciplinary and multi-institutional team to investigate Philippine bats as the possible reservoir of RESTV.
Sourced through Scoop.it from: www.virologyj.com
I recall at the time of its discovery, thinking that the virus must have reservoir species back home in the East – and that the fact that no disease had ever been reported from there in humans, meant it was completely under the radar.
There was also the issue that the virus seemed to have been transmitted between monkeys in the Reston facility without any direct contact – and even between rooms, which would imply airborne transmission.
Which frightened the cr@p out of many people, and I am sure especially those primate centre workers who were found to be seropositive for the virus, in the absence of any symptoms – even though at teh time, unsanitary conditions and overcrowding were blamed (http://www.mcb.uct.ac.za/ebola/ebolair.html).
It is still something that needs to be looked at seriously: is Ebola Reston more transmissible than Zaire, Sudan and the rest – and if so, why?
Those interested can pick up on what happened at the time, here on the Ebola information pages I ran for a while: