Archive for the ‘General’ Category

VIGS in fungi – using TMV?!

5 March, 2014

See on Scoop.itVirology News

RNA interference (RNAi) is a powerful approach for elucidating gene functions in a variety of organisms, including phytopathogenic fungi. In such fungi, RNAi has been induced by expressing hairpin RNAs delivered through plasmids, sequences integrated in fungal or plant genomes, or by RNAi generated in planta by a plant virus infection. All these approaches have some drawbacks ranging from instability of hairpin constructs in fungal cells to difficulties in preparing and handling transgenic plants to silence homologous sequences in fungi grown on these plants.

Here we show that RNAi can be expressed in the phytopathogenic fungus Colletotrichum acutatum (strain C71) by virus-induced gene silencing (VIGS) without a plant intermediate, but by using the direct infection of a recombinant virus vector based on the plant virus, tobacco mosaic virus (TMV). We provide evidence that a wild-type isolate of TMV is able to enter C71 cells grown in liquid medium, replicate, and persist therein. With a similar approach, a recombinant TMV vector carrying a gene for the ectopic expression of the green fluorescent protein (GFP) induced the stable silencing of the GFP in the C. acutatumtransformant line 10 expressing GFP derived from C71.

The TMV-based vector also enabled C. acutatum to transiently express exogenous GFP up to six subcultures and for at least 2 mo after infection, without the need to develop transformation technology. With these characteristics, we anticipate this approach will find wider application as a tool in functional genomics of filamentous fungi.

TMV graphic from Russell Kightley Media

Ed Rybicki‘s insight:

This is a nice paper for two main reasons: one, they were able to get VIGS – virus-induced gene silencing – working in a non-model fungus; two, they did it with TMV.

TMV! A plant virus in good standing, not previously shown to infect fungi productively, even if it has been studied in yeast as far as replication requirements go.

This is very interesting, not the least because it opens up the possibility that TMV NATURALLY infects some soil / leaf surface fungi.

Which could open up some investigation of just how the virus gets around, because it has always been touted as being only “mechanically” transmissible – even though we and others have shown it CAN be transmitted by aphids (reasonably inefficiently).

Mind you, Barbara von Wechmar and others in our lab showed in the 1980s that wheat stem and leaf rust fungi could transmit Brome mosaic virus and that Puccinia sorghi could transmit a potyvirus; they just did not have the techniques to look at whether or not it replicated too.

As far as my last post here is concerned, I think there is going to be a LOT of stuff coming out in the next few years on how “plant” and “insect” and “fungal” viruses are in fact considerably more promiscuous in choice of host(s) than we have hitherto been aware.

Now, just to prove what Barbara always said, that Tobacco necrosis virus is also a bacteriophage….

Thanks to Gary Foster (@Prof_GD_Foster) for pointing this out!

See on

TRSV or not TRSV, that is the question. In bees, obviously.

25 February, 2014

I promised some time ago now to blog on the exciting topic of whether or not a plant virus is infecting honeybees – and here it is!  I was also contacted by the legendary Dr Adrian Gibbs about this paper, because he has read this blog, so I am including a commentary from him as well.

A little while ago, Ji Lian Li and co-workers published a paper entitled “Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera” in ASM’s Open Access journal mBio.  They stated that:

“Pathogen host shifts represent a major source of new infectious diseases. Here we provide evidence that a pollen-borne plant virus, tobacco ringspot virus (TRSV), also replicates in honeybees and that the virus systemically invades and replicates in different body parts. In addition, the virus was detected inside the body of parasitic Varroa mites, which consume bee hemolymph, suggesting that Varroa mites may play a role in facilitating the spread of the virus in bee colonies. This study represents the first evidence that honeybees exposed to virus-contaminated pollen could also be infected and raises awareness of potential risks of new viral disease emergence due to host shift events. About 5% of known plant viruses are pollen transmitted, and these are potential sources of future host-jumping viruses. The findings from this study showcase the need for increased surveillance for potential host-jumping events as an integrated part of insect pollinator management programs”.

This paper has caused all sorts of excitement, as well as coming to some possibly misleading conclusions, and leading to quite a lot of uninformed speculation – so I think it is as well to explore quite carefully what they did.

Adrian first:

“This paper reports that tobacco ringspot nepovirus, a well-known virus of plants, replicates in honeybees.  TRSV, first identified nearly a century ago in the USA, has a wide range of plant hosts, and is spread in pollen and seed, and also by many unrelated vectors, not only root-feeding nematodes, like other nepoviruses, but also insects and mites.

This report tells us that TRSV virions have been isolated from bees, and that their gene sequences are closely similar to those of TRSV.  Convincingly, biochemical tests showed that there were replication intermediates of the TRSV genome in the bees, so the virus had not merely contaminated the bees when they fed on the honey and pollen of infected plants, but had seemingly multiplied in them.

However, there are several gaps in this story.  Surprisingly, it seems that no tests were done to show whether the virus isolated from bees infected known plant hosts of TRSV; perhaps this crucial evidence will be in the sequel.  Furthermore, the reported sequences of the virus represented only around 20% of the RNA1 of typical nepoviruses, and around 50% of their RNA2, so there is still the possibility of further genetic surprises when the genome sequence is completed.

Although TRSV is a well-known and long studied virus with many distinct symptom variants, there are relatively few of its gene sequences in Genbank.  When these are compared with those of the ‘bee TRSV’ it is obvious that more sequences will be required to sort out exactly where this virus clusters; differences in the homology patterns of the RNAs 1 and 2 suggest that recombination or reassortment is active among nepoviruses.

The gene sequencing revolution is, to paraphrase Pliny the Elder, revealing that in virology the only certainty is that nothing is certain.”

Me next:

I have the same reservations as Adrian: the TRSV sequence isolated from bees and from Varroa mites is only partial (~30%); thus, it is by no means certain that the whole genome is colinear with genomes of established TRSVs or of other nepoviruses, although they assume that it is – with some justification, possibly, as sequence identities of up to 96% were found in Genbank for the putative CP fragment sequence.  They could isolate particles: why, then, in this metagenomic and NGS age, could they not sequence the whole thing??

nepo fig1

Another reservation I have concerns their methodology.  First, while I was impressed that they did strand-specific PCR to show  both the presence of viral (+ strand) and of replicative form (- strand) RNA in bee and mite tissue (see their Figure above), and did in situ hybridisation to show (-) strand presence in mites, they did not do something very simple that could have shown the same thing, AND given them genome-length +/- strand RNA to play with.

I refer, of course, to dsRNA isolation, which is a very easy and extremely clean technique that can be used to get full-length dsRNAs for many (+) strand RNA viruses from plant or insect tissues.  Moreover, the simple fact of isolating dsRNA forms for a single-strand RNA virus is indicative that replication is occurring – and was used by our group as long ago as 1988 (C Williamson, PhD Thesis, UCT) to isolate full-length ~10 kb dsRNA for two aphid picorna-like viruses.

Scan 04 Jan 2014, 16.31-page8

This means they could have had clear and simple evidence via dsRNA extraction of ALL of the coinfecting viruses present – without all of the expense of total cDNA sequencing.  And sampled more hives….

Second, I have to echo Adrian: “…no tests were done to show whether the virus isolated from bees infected known plant hosts of TRSV”.  Why ever not?  I am afraid that if I were a referee, I would have insisted on this: they did enough other work, after all, that this would not exactly have been an onerous requirement!

And here’s another thing: the authors say, in their Discussion,

“The finding from this study illustrates the complexity of relationships between plant pathogens and the pollinating insects and emphasizes the need for surveillance for potential host-jumping events as an integrated part of insect pollinator conservation.”

Ummmm…no, it doesn’t.  This is overstating the significance of their results by an order of magnitude at least.  They have simply illustrated that ONE species of honeybee may be infectable by ONE species of plant virus, and that this is ASSOCIATED with “weak” colonies.  Moreover, while the presence of TRSV was apparently associated with four weak colonies (out of only ten surveyed), it is quite possible that this is simply the emergence of a commensal-type infection against a background of known bee viruses, and in particular Israeli acute paralysis virus which was found in the same colonies (and blogged on here).  The authors also seem to take it as a given that the “emergence” of TRSV into bees is a recent jump – when it may not be recent at all.  Their statement in the abstract that

“The tree topology indicated that the TRSVs from arthropod hosts shared a common ancestor with those from plant hosts and subsequently evolved as a distinct lineage after transkingdom host alteration”

is pretty much unsubstantiated, in the absence of any investigation of the lineage in plants or in other bee colonies.  Further, they say that

“This study represents a unique example of viruses with host ranges spanning both the plant and animal kingdoms. “

Ummmmm….it doesn’t really do that, either: there are a LOT of arboviruses, with quite a few of them infecting insects and plants.  Here, for example, is an illustration from my teaching material of why it is that I think that viruses of insects and plants are an underappreciated evolutionary link for later evolution of viruses that got into mammals.

Transkingdom viruses

I note that bunyaviruses, rhabdoviruses, reoviruses and (not shown) picorna-like viruses appear linked by the fact that insects have possibly the most diverse representatives of these families, which may indicate that these originated in insects.  Which were the first complex animals to crawl out of the oceans, to join…plants on dry land?  Which explains how plants link up with the far more closely related (in evolutionary terms) insects and vertebrates: plants and insects were alone together for a long, long time before things with spines lurched up out of the water to join them.  So were their viruses.

I also said the following in the material there:

“A complicating factor in the picture of viruses co-evolving with their hosts over millennia is the fact that viruses apparently can – and obviously do – make big jumps in hosts every now and then.  It seems obvious, for example, that arthropods are almost certainly the original source for a number of virus families infecting insects and mammals - such as the Flaviviridae - and probably also of viruses infecting insects and other animals and plants - such as the Rhabdoviridae and Reoviridae - as well (see also here).  For example, picornaviruses of mammals are very similar structurally and genetically to a large number of small RNA viruses of insects and to at least two plant viruses, and – as the insect viruses are more diverse than the mammalian viruses - probably had their origin in some insect that adapted to feed on mammals (or plants) at some distant point in evolutionary time.”

Now quite a lot of interest has been shown in this paper in the blogosphere, and there have been quite a few conclusions drawn from the results that I think are largely unsubstantiated.  For example, this Sci Am blog claims

“When HIV jumped from chimpanzees to humans sometime in the early 1900s, it crossed a gulf spanning several million years of evolution. But tobacco ringspot virus, scientists announced last week, has made a jump that defies credulity. It has crossed a yawning chasm ~1.6 billion years wide.”

Again, ummmm…in light of the discussion above, not necessarily!  I am of the opinion that picorna-like viruses were shared between insects and plants, and then between insects and animals, hundreds of millions of years ago.  And TRSV is a nepovirus – and nepoviruses look like nothing more or less than a picornavirus with a divided genome.

I think TRSV represents something coming back into insects.  And I think we will probably find a lot more of them.

Maize streak virus revisited: 25 years on

20 March, 2013
Maize streak virus: photo from 1978

Maize streak virus: photo by Robert G Milne in Cape Town from 1978

Twenty-five years ago, I wrote a brash, naïve little piece entitled “Maize streak virus virus: an African pathogen come home?” for the South African Journal of Science, laying claim to a virus that we had just started working on – Maize streak virus (MSV) – on the basis that it had first been described from this country in 1901, that it was endemic here, and that it still caused major crop losses.  I did this because research on this and related viruses seemed to have moved almost completely offshore, to Europe and the USA, and

“…the most interesting of the viruses that grow all around us have already been whisked away to foreign laboratories; [that] there they have been cloned, sequenced, and had their most intimate details exposed, far from their native shores”. [Yes, I really did write like that back then].

I asked at that time, if we should

“…perhaps be content to supply foreigners with the (pathogenic) fruits of our fields, and to marvel when the answers come filtering back from abroad?”.

I answered myself by saying that

“…prospects for worthwhile research on African geminiviruses, and on any other indigenous pathogens, are at least as good here as anywhere else.  Our facilities are the equal of those abroad, the necessary expertise is certainly not lacking, and the viruses are on our doorstep.”

I’m a little shocked now that I could have said that then: the paper quotes only three pieces of work from our lab, one of them a Masters dissertation and two papers done by my erstwhile supervisors; we had not yet sequenced any virus, let alone a geminivirus, and all we had was brashness and hope.  Indeed, I went on to say the following:

“We are, incidentally, the only research group with access to molecular biological techniques which is actually working on the virus in its natural environment: this is very useful, as with the virus in all its forms and its vector(s) literally on our doorstep, we can rapidly accumulate, identify and characterize distinct isolates for study here or elsewhere.  We hope there will be a little more of the ‘here’, and a little less of the ‘elsewhere’, from now on”.

I outlined what it was that we ambitiously wanted to do – seeing as we had no money, and only one PhD student at the time – as follows:

“…we now have distinctly different genomic maps of three isolates [!] which differ in serology and symptom expression; we have cloned genomic DNA of several more isolates, and can potentially clone and [restriction] map many more.  With this type of work now solidly established, we intend to investigate other biological variants of MSV – and other native cereal geminiviruses – in maize, cereal grains and other members of the Gramineae.  The aim is to explore the genetic diversity of naturally occurring types of MSV and related viruses, and to identify any isolates that appear unusual in terms of symptom expression, serology or transmission.  These would be interesting to map, and potentially useful in recombinational analyses for the fine mapping of determinants of pathogenicity and host range.” [see later]

The article obviously sank without trace: I can find only three citations to it; two of them mine, and the third from a South African maize breeder.  How the overseas labs that I compared us to must have sniggered…actually, I doubt that happened at all; I am sure none of them ever read it!  In retrospect, we really were regarded as a backwater, and as wannabe geminivirologists; I had at least one collaboration request rebuffed with “we don’t feel our work would be advanced by working with you”, and was told “we’re already working on that, so you shouldn’t bother” for a couple of other proposals.

My hubris was not entirely misplaced, however: we did in fact go on to develop into a world-leading MSV and geminivirus molecular virology laboratory; it just took another fifteen years or so!

So where are we, twenty-five years on from my cheeky article?  Much water has flowed under several bridges; I expanded from molecular virology in the 1990s into plant and vaccine biotechnology in the 2000s, while keeping a geminivirus research group going – and we have published and co-published something like 55 peer-reviewed journal articles and several encyclopaedia and book chapters on MSV and other “African streak viruses” alone, let alone another 14 or so articles on other geminiviruses, with some 1200 citations.  We have papers on geminivirus mapping and sequencing, virus diversity, biogeographical variation, quantitation of symptoms, molecular determinants of pathogenicity, recombination, engineering maize for resistance, the use of two of the viruses as gene expression vectors – and cover pictures for Plant Biotechnology Journal and Journal of Virology.

Cover Illustration: J Virol, October 2011, volume 85, issue 20

Cover Illustration: J Virol, October 2011, volume 85, issue 20

I started with one Honours student in 1986, who went on to do a Masters in 1988; we moved on to having one PhD student in the late 1980s to up four PhD students simultaneously in the mid- to late 1990s, and a postdoc at the same time.  The projects went from simple diversity studies of a few viruses using restriction mapping, through the application of PCR, to partial genome sequencing and studying the molecular biology of infectious clones of the viruses, with a very profitable sideline in phylogenetic analyses; we also moved – with Professor Jennifer Thomson – into a parallel track of plant biotechnology, aimed at engineering resistance to MSV in maize.  We added another track early this century, working on similar ssDNA circoviruses of parrots, using all of the expertise we had accumulated on geminiviruses.  We truly work on “circomics” now – the study of small circular genomes – with its subsets “geminiviromics” and “circoviromics”, with a library of literally hundreds of sequenced MSVs and distinct grass mastreviruses and BFDVs.

Geminivirus particle: characteristic doubled icosahedron containing a single ssDNA

Geminivirus particle: courtesy of Russell Kightley Media

The geminiviromics group has pretty much got away from me now; the folk I trained as PhD students in the late 1990s and early 2000s were enthused enough with the field that they have gradually usurped my leadership and supervisory role, and made the field their own.  I still maintain an interest in using Bean yellow dwarf mastrevirus (BeYDV) as an expression vector for “biofarming” purposes; I am also maintaining a project on Beak and feather disease circovirus (BFDV) diversity and plant-made vaccines.  I think we pretty much did what we set out to do – including the brave prediction I made about host range and pathogenicity, which led to some very interesting work on recombination and genome modularity, and the successful engineering of pathogen-derived resistance to MSV.

So I owe some thanks, in retrospect: first, to Barbara von Wechmar, who sparked the interest – and provided isolates, leafhoppers, and expertise.  Second, to Bev Clarke and Fiona Tanzer (aka Hughes), who were brave enough to blaze the trail, and clone our first MSVs – and make one infectious, in the case of Fiona.  Thanks to Wendelin “Popeye” Schnippenkoetter, for your single-minded perseverance in mixing and matching genomes; thanks Kenneth Palmer, for showing the way for transient expression assays in maize cells and engineering MSV as a vector.  Thanks Janet Willment, for mapping replication origins in MSV and expanding us into wheat viruses; thanks Jennifer Thomson for the collaboration, and Fiona and Tichaona Mangwende and Dionne Shepherd for breaking us into maize resistance engineering.  Thanks Christine Rey for the collaboration, and Leigh Berrie for your quiet competence in our detour into South African cassava mosaic virus.  Thanks Darrin (aka Darren) Martin and Eric van der Walt, for so brilliantly exploring MSV diversity, evolution and recombination – and Darrin for endless amusement in the lab, as well as for two completely distinct and invaluable software packages, for symptom quantitation and recombination analysis.  In the present generation, thanks to Suhail Rafudeen and our student Rizwan Syed (and Dionne and Darrin as supernumerary supervisors); thanks Aderito Monjane for doing such a ridiculous amount of work for a superlative PhD; thanks Dionne and Marian, for keeping the maize engineering afloat – and thanks also to Arvind Varsani, for retraining himself from a papillomavaccinologist to a circomicist, and for popping up everywhere.

ViroBlogy: 2012 in review

1 February, 2013

So: thank you, anyone who clicked in, and regular visitors.  You make it worthwhile!!

The stats helper monkeys prepared a 2012 annual report for this blog.

Here’s an excerpt:

4,329 films were submitted to the 2012 Cannes Film Festival. This blog had 33,000 views in 2012. If each view were a film, this blog would power 8 Film Festivals

Click here to see the complete report.

Help! We’re all going to die! Or – are we??

5 December, 2011

My son has just alerted me to a news item from the Russia Today site, which reports the following dry little item:

“A virus with the potential to kill up to half the world’s population has been made in a lab. Now academics and bioterrorism experts are arguing over whether to publish the recipe, and whether the research should have been done in the first place.

The virus is an H5N1 bird flu strain which was genetically altered to become much more contagious. It was created by Ron Fouchier of the Erasmus Medical Centre in Rotterdam, the Netherlands, who first presented his work to the public at an influenza conference in Malta in September.”

Right – nothing to get upset about, then?  Or….

Some background: what researchers did was to passage – that is, repeatedly infect new animals with virus from another animal – H5N1 influenza virus from birds, in ferrets.

Why ferrets?  Well, it was discovered by accident some 70+ years ago, that human flu viruses are very infectious in ferrets, and the reaction of ferrets to some extent predicts what will happen in humans – although they tend to die rather often from lab infections.

The result of the passaging was that the H5N1 became aerosol-transmissible – in other words, via droplets produced by sneezing – which was a new property.  From the article:

“After 10 generations, the virus had mutated to become airborne, which means ferrets became ill from merely being near other diseased animals.

A genetic study showed that the new, dangerous strain had only five mutations compared to the original one, and all of them were earlier seen in the natural environment – just not all at once. Fouchier’s strain is as contagious as the human seasonal flu, which kills tens of thousands of people each year, but is likely to cause many more fatalities if released.

“I can’t think of another pathogenic organism that is as scary as this one,”
Paul Keim, a microbial geneticist who has worked on anthrax for many years, told Science Insider. “I don’t think anthrax is scary at all compared to this.””

Hence the rather alarming headline on RT – which was

“Man-made super flu could kill half humanity”

Nothing scare-mongering there, then!

Let us dissect this so called apocalypse bug, though.

“Fouchier’s strain is as contagious as the human seasonal flu, which kills tens of thousands of people each year, but is likely to cause many more fatalities if released.”

In ferrets.  No-one has shown that it causes disease in humans at all.  And there’s another problem: the article reports that:

“…the US National Science Advisory Board for Biosecurity (NSABB)…[has] a very difficult decision to make. Fouchier wants his study to be published. So does virologist Yoshihiro Kawaoka, who led similar research in collaboration with the University of Wisconsin, Madison, and the University of Tokyo, and reached comparable results. And it is up to NSABB to give them the green light.”

Pardon me for being confused, but…the NSABB is a US body, right?  And Ron Fouchier and Yoshihiro Kawaoka are Dutch and Japanese, respectively?

And pardon me again, but isn’t it a good idea to know which mutations would turn H5N1 into a ravening, destructive supervirus?  So we can look for it??  I would also think the cat is at least half out of the bag, because didn’t Ron Fouchier report the thing at a large conference already?

Letting paranoid folk in one country decide what is in the best interests of world science is NOT a good idea, in my opinion – but as has already been made abundantly clear, the developed world does not much care about our opinion.

So it goes.

Goodbye, Mimi – we got Mega!

11 October, 2011

Through the unlikely medium of a local online version of a local daily paper, comes the following:

“A virus found in the sea off Chile is the biggest in the world, harbouring more than 1,000 genes, surprised scientists reported on Monday. The genome of Megavirus chilensis is 6.5 percent bigger than the DNA code of the previous virus record-holder, Mimivirus, isolated in 2003. “

The relevant article is from the group led by Jean-Michel Claverie, of the Institut de Microbiologie de la Méditerranée, in Marseilles, and appears in the October 10th online issue of PNAS.

From the abstract:

An electron micrograph of Megavirus: thanks to Jean-Michel Claverie

Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the

genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).

I could argue with the choice of name as it does not conform to ICTV rules, as far as I can see – but then, neither did Mimivirus.  The important fact about the discovery – apart from the fact that it is a discovery, and therefore not amenable to hypothesising, which I rather like – is that it shows how very diverse these viruses are, and how long they must have been evolving.  For example, despite their morphological similarity, Mimi- and Megavirus genomes do not share nearly 25% of their ORFs – and sequence identities of  predicted homologous proteins are as low as 50%.

I have blogged earlier on Mimivirus structure and evolution – see “Mimivirus unveiled” – and it is nice to see that an important speculation from those earlier papers appears to be borne out here.  Namely, and quite important when considering both viral and cellular origins, is further evidence that very large viral genomes do not seem to have evolved by extensive horizontal gene transfer from cells, and in fact, the reverse may be true.  The authors state in their conclusion, in discussion of opposing views of the origin of these viruses:

“The potential origin of giant mimivirus-like genomes has been hotly debated, basically opposing two views. One is depicting Mimivirus as an extremely efficient gene “pickpocket,” explain- ing its large genome as the result of considerable HGTs from its host, bacteria, or other viruses. This scenario has been criticized in detail elsewhere [see paper for refs]. The opposite view claims that the level of HGT remained marginal (10%) and that most of the Mimivirus genes originated from an even more complex viral ancestor, itself eventually derived from an ancestral cellular genome.”

I have fond memories of an essay I won a school prize with, in about 1970, entitled “The Sea, and All that Therein Is”.  I should update it to “The Sea, and All the Viruses that Therein Are”…B-)

Virus Origins II

28 September, 2011

I have updated the blog on virus origins quite considerably – new pictures, more detail, more speculation!

Pathways on information flow for RNA viruses

Virus structure visualisation – from here at home!

23 June, 2011

I was most pleased to discover via their blog that two of my colleagues here at UCT – Andrew Lewis and Timothy Carr, who do High Performance Computing support – have (a) been taking a more than passing interest in implementing some quite serious bioinformatics support (see Mr Bayes as well), and (b) doing visualisations of nasty virus proteins, just because they could!

Here is one for an Ebola virus protein, and here is another for Lujo virus, also covered quite extensively here.

And I liked it enough I stole it…B-)

Worm specificity: transmission of a plant virus

20 May, 2011

I have taught – when I did teach that is, two years ago now – for years that most plant viruses are transmitted by one or other form of vector, and that this transmission is very often relatively specific, even though it usually does not involve multiplication of the virus in the vector.  Unfortunately, this is an under-studied area (like most of plant virology), and even more so now in this era of folding plant virology into “biotic stress” and other concocted disciplinary areas.

However: amid the gloom is a bright light (or two – see here as well for some local SA news), and it comes from a PLoS Pathogens paper entitled “Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission” [need to leave out the italics there, guys; only a species name as an abstract concept gets italicised, and this is an entity you're talking about!].

Schellenberger P, Sauter C, Lorber B, Bron P, Trapani S, et al. (2011). PLoS Pathog 7(5): e1002034. doi:10.1371/journal.ppat.1002034

Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV), a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP), carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD) poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp) in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by X. index. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode’s feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.

And yes, they do – and illuminate very nicely the concept of structural complementarity as a means of ensuring specific transmission by any vector of a plant virus.  That this can happen in the absence of any replication of the virus in the vector, as is the case here and in fact for most plant virus / vector associations, indicates that an evolutionary process that probably started with fortuitous low-efficiency transmission by pure random chance of an ancestor GFLV  by the nematode, resulted in selection of increasingly more efficiently transmitted viral variants.

The same sort of thing has undoubtedly happened for specific aphid transmission of viruses like Cucumber mosaic virus and other cucumoviruses [note to virologists: correct usage!] and Potato virus Y and other potyviruses, and my favourite geminiviruses.

I look forward to an explosion of research in this area, not the least because it may lead to simple agents that specifically block the transmission.  One can hope…B-)

…and again, XMRV. Or absence thereof.

14 May, 2011

So it is, again, we are driven to report evidence-based absence of evidence for a very contentious virus: the murine retrovirus known as XMRV.  From a preprint online publication in Journal of Virology:

Absence of XMRV and other MLV-related viruses in patients with Chronic Fatigue Syndrome
J. Virol., published ahead of print on 4 May 2011 doi: doi:10.1128/JVI.00693-11

Clifford H. Shin, Lucinda Bateman, Robert Schlaberg, Ashley M. Bunker, Christopher J. Leonard, Ronald W. Hughen, Alan R. Light, Kathleen C. Light, and Ila R. Singh

“Chronic fatigue syndrome (CFS) is a multi-system disorder characterized by prolonged and severe fatigue that is not relieved by rest. Attempts to treat CFS have been largely ineffective primarily because the etiology of the disorder is unknown. Recently CFS has been associated with xenotropic murine leukemia virus-related virus (XMRV) as well as other murine leukemia virus (MLV)-related viruses, though not all studies have found these associations. We collected blood samples from 100 CFS patients and 200 self-reported healthy volunteers from the same geographical area. We analyzed these in a blinded manner using molecular, serological and viral replication assays. We also analyzed samples from patients in the original study that reported XMRV in CFS. We did not find XMRV or related MLVs, either as viral sequences or infectious virus, nor did we find antibodies to these viruses in any of the patient samples, including those from the original study. We show that at least some of the discrepancy with previous studies is due to the presence of trace amounts of mouse DNA in the Taq polymerase enzymes used in these previous studies. Our findings do not support an association between CFS and MLV- related viruses including XMRV and off-label use of antiretrovirals for the treatment of CFS does not seem justified at present.”

I would have said “enough said, then!”  Except that this will not be the end.  Oh, no….


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