Archive for July, 2012

Ebola reaches Uganda’s capital

31 July, 2012

See on Scoop.itVirology News

Uganda’s president has warned against shaking hands and other physical contact after the first death from the deadly Ebola virus in the capital.

The latest outbreak started in Uganda’s western Kibale district, about 200km from Kampala, and around 50km from the border with Democratic Republic of Congo.

The fatal case in Kampala was a health worker who “had attended to the dead at Kagadi hospital” in Kibale, Health Minister Christine Ondoa told reporters.

 

And it’s deja vu all over again…this is how I started reporting virology on the Web, back in 1995 – with the Kikwit Ebola outbreak.  It’s possibly the first time Ebola has hit a major centre, so it could be interesting to see what develops.  Let’s hope nothing…!

 

I thank Russell Kightley Media for the Ebola virus graphic

See on news.ninemsn.com.au

‘SA safe from Ebola’ – Times LIVE

31 July, 2012

See on Scoop.itVirology News

South Africans need not be worried about contracting the Ebola virus after a new outbreak of the disease in Uganda.

The SA National Institute for Communicable Diseases said the risk of South Africans being infected was “extremely low”.

Ugandan President Yoweri Museveni has placed a ban on physical contact in the country after the virus was reported in the capital, Kampala, for the first time.

The institute’s spokesman, Professor Lucile Blumberg, said yesterday: “There is no travel restriction. It is unlikely that patients from the Kibaale district, Uganda, who are very sick, will find their way here. One does need direct contact with infected patients to become ill.”

 

As with ANY Ebola outbreak in fact, the peril for any but the immediately exposed is more imgained than real.  What Ed Regis once termed “Ebola Preston”, or a virus that is spread by print and electronic media, rather than by droplets.

See on www.timeslive.co.za

A bit of viral archeology

20 July, 2012

We were sifting through stuff found in a service room the other day, when I found a box of glass slides – undisturbed since about 1979 or so.  A very interesting box: double- and triple-width microscope slides, coated with dried agarose gel, and stained with Coomassie Brilliant Blue.  With my handwriting on them.  With whole virus electropherograms on them….

Backing up a bit: back in a previous research career, I was a plant virologist who had become an expert, during my MSc project, on physical and serological techniques to do with plant viruses, and the multicomponent isometric bromoviruses in particular.  This included differential, density gradient and analytical centrifugation; methods for purification of virus, capsid protein and genomic nucleic acid (all ssRNA); double-diffusion gel precipitin (=Ouchterlony’s technique) assays; the then new-fangled enzyme-linked immunosorbent assays (ELISA) – and whole-virus agarose gel electrophoresis, and immunoelectrophoresis.

This is mostly published – in my first-ever paper published in 1981, that I was too naive to know I shouldn’t submit to a good journal, so got it into Virology.

However, there were some bits that only ever made it into my Masters write-up – and then only in monochrome.  Here, then, is a little piece of virological and personal history: electropherograms of Brome mosaic bromovirus strains, electrophoresed in 1% agarose on glass slides, then dried down and stained with CBB.  Left all alone, in a drawer, undisturbed from then till now.

It is very easy to see how the three strains on the right have a pI between pH 6.0 and pH 7.5, and that the two on the left and the one on the furthest right seem to be mixtures of differently-charged variants.

Interesting technique, this: it’s a very nice way of characterising and in fact separating virus strains that differ only in a couple of charges in their capsid proteins – for future infectivity assays, if need be, or for preparative purposes by sucrose gradient “zone” electrophoresis, as done here.  The thing about the slide gels, though, is that it is very cheap, very easy, and very quick – ideal for practicals and demonstrations.

I’m going to make my current MSc student characterise his plant-made virus-like particles this way…B-)

Oh, and while we’re archeologising: here is a 30+ year experiment in sedimentation at one gravity, of Tobacco mosaic virus.  Shows why one should stay in one place for a while.  Or not…B-)

Evidence for Antigenic Seniority in Influenza A (H3N2) Antibody Responses in Southern China

20 July, 2012

See on Scoop.itVirology and Bioinformatics from Virology.ca

“A key observation about the human immune response to repeated exposure to influenza A is that the first strain infecting an individual apparently produces the strongest adaptive immune response. Although antibody titers measure that response, the interpretation of titers to multiple strains – from the same sera – in terms of infection history is clouded by age effects, cross reactivity and immune waning. From July to September 2009, we collected serum samples from 151 residents of Guangdong Province, China, 7 to 81 years of age. Neutralization tests were performed against strains representing six antigenic clusters of H3N2 influenza circulating between 1968 and 2008, and three recent locally circulating strains. Patterns of neutralization titers were compared based on age at time of testing and age at time of the first isolation of each virus. Neutralization titers were highest for H3N2 strains that circulated in an individual’s first decade of life (peaking at 7 years). Further, across strains and ages at testing, statistical models strongly supported a pattern of titers declining smoothly with age at the time a strain was first isolated. Those born 10 or more years after a strain emerged generally had undetectable neutralization titers to that strain (<1:10). Among those over 60 at time of testing, titers tended to increase with age. The observed pattern in H3N2 neutralization titers can be characterized as one of antigenic seniority: repeated exposure and the immune response combine to produce antibody titers that are higher to more ‘senior’ strains encountered earlier in life.”

 

An interesting paper, which helps explain several observations made over the years with pandemic flu: for example, in the 2009 H1N1 pandemic, older people seemed to be more protected – and rhe same was probably true of the 1918 pandemic.

See on www.plospathogens.org

The man with the golden banana

18 July, 2012

See on Scoop.itVirology News

“In Uganda, where food insecurity has been the order of the day, enterprising scientists have taken biotechnology a step further by producing bananas that are rich in vitamin A and iron and that have the colour of carrots once peeled.

During a media tour at the National Agricultural Research Laboratories in Kampala this week, scientists said they aimed to ensure that bananas, a staple food in Uganda, were rich in vitamin A and iron and resistant to nematodes.”

 

And behind that effort were two things: the Bill and Melinda Gates Foundation, and an Australian scientist named James L Dale.  I photographed him in his office at the Queensland University of Technology in 2010, when he had literally just opened the picture file associated with latest results being reported from his research crew – the banana picture in the background, with the golden vitamin A-containing version on top.

See on www.iol.co.za

Bird flu vaccine now? More than a shot in the dark | Reuters

11 July, 2012

See on Scoop.itVirology News

“LONDON (Reuters) – Culls of hundreds of thousands of chickens, turkeys and ducks to stem bird flu outbreaks rarely make international headlines these days, but they are a worryingly common event as the deadly virus continues its march across the globe.

As scientists delve deeper into H5N1 avian influenza, they have discovered it is only three steps way from mutating into a potentially lethal human pandemic form, adding new urgency to a debate over how to protect humans.

In 2009, during the H1N1 swine flu pandemic, vaccines only became available months after the virus had spread around the world – and even then there was only enough for one in five of the world’s 7 billion people.

Next time, experts say, we need another approach.

Talk is centred on “pre-pandemic vaccination” – immunising people years in advance against a flu pandemic that has yet to happen, and may never come, rather than rushing to create vaccines once a new pandemic starts.”

 

Yes, well: regulars of this blog will recognise that I have been rattling on about this topic for some time now; nice to see serious heavyweights are starting to do the same thing.

 

Seriously, pre-emptive vaccination could almost certainly not hurt, would probably help a LOT – and would amp up production capacity for H5 and other potential pandemic influenza viruses [see Mexico H7N3 outbreak] as well, for pandemic vaccine production readiness.

 

And of course, you could do it all in plants.  Just saying.

 

See on in.reuters.com

A feeling for the Molechism* – revisited

10 July, 2012

This is an update of a post I did on Alan Cann’s MicrobiologyBytes back in 2007, before i started ViroBlogy: I am doing this because (a) it’s mine, (b) I want to update it – and the MB version is archived, so I can’t.  So here we are again:

I think it’s permissible, after working on your favourite virus for over 20 years, to develop some sort of feeling for it: you know, the kind of insight that isn’t directly backed up by experiment, but that may very well be right. Or not – but in either case, it would take a deal of time and a fair bit of cash to prove or disprove, and would have sparked some useful discussion in the meantime. And then, of course, the insights you have into (insert favourite virus name here) – if correct – can usually be extended into the more general case, and if you are sufficiently distinguished, people may actually take them on board, and you will have contributed to Accepted Wisdom.

I can’t pretend – at least, outside of my office – to any such Barbara McClintock-like distinction; however, I have done a fair bit of musing on my little sphere of interest as it relates (or not) to the State of the Viral Universe, and I will share some of these rambles now with whomever is interested.

I have been in the same office now, and teaching the same course, more or less, for 32-odd years. In that time I have worked on the serology and epidemiology of the bromoviruses, cucumovirus detection, potyvirus phylogeny, geminivirus diversity and molecular biology, HIV and papillomavirus genetic diversity, and expressing various bits of viruses and other proteins in plants and in insect cells. However, much of my interest (if not my effort) in that time has been directed towards understanding how grass-infecting mastreviruses in particular interact with their environment and with each other, in the course of their natural transmission cycle.

Maize streak virus

Maxwell’s Demon (left, lower) and Martian Face (right, upper) visible on a MSV virion

Fascinating little things, mastreviruses: unique geminate capsid architecture, and at around a maximum of 2.8 kb of single-strand circular DNA, we thought they were the smallest DNA genomes known until the circoviruses and then the zoo of anello- and anello-like viruses were discovered. Their genomes code for only 4 proteins – two replication-associated, one movement and one capsid – yet we have managed to work on just one subgroup of mastrevirus species for 27 years, without exhausting its interest – at least, to us… (see PubMed list here). We also showed that one could see Martian faces quite distinctly on virions – and possibly even Maxwell’s Demon. But I digress….

Maize streak

Severe symptoms of MSV on sweetcorn

We have concentrated on the “African streak viruses” – related species Maize streak virus, Panicum streak virus, Digitaria streak virus, Sugarcane streak virus and friends – for two very simple reasons:
1. They occur in Africa, near us, and nowhere else;
2. Maize streak virus is the worst viral pathogen affecting maize in Africa.

So we get situational or niche advantage, and we get to work on an economically-important pathogen. One that was described – albeit as “…not of…contagious nature” – as early as 1901, no less.

Maize streak virus

Maize streak virus or MSV, like its relatives, is obligately transmitted by a leafhopper (generally Cicadulina mbila Naudé): this means we have a three-party interaction – of virus-host-vector – to consider when trying to understand the dynamics of its transmission. Actually, it’s more complicated than that: we have also increasingly to consider the human angle, given that the virus disease affects mainly the subsistence farming community in Africa, and that human activity has a large influence on the spread of the disease. So while considering just the virus – as complicated as that is – we have to remember that it is only part of the whole picture.

So how complicated is the virus? At first sight, not very: all isolates made from severe maize infections share around 97% of their genome sequence. However, however…that 3% of sequence variation hides a multitude of biological differences, and there is a range of relatives infecting grasses of all kinds, some of which differ by up to 35% in genome sequence. Moreover, maize is a crop plant first introduced to Africa a maximum of 500 years ago, so it is hardly a “natural” host – yet, all over Africa, it is infected by only a very narrow range of virus genotypes, from a background of very wide sequence diversity available.

So here’s an insight:

the host selects the virus that replicates best in it.

And lo, we found that in the Vaalharts irrigation area in the north of South Africa that the dominant virus genotype in winter wheat was a different strain – >10% sequence difference – to the one in the same field, in summer maize. Different grass species also have quite different strains or even species of streak viruses best adapted to them.

DendrogramNot all that profound a set of observations, perhaps, but they lead on to another insight:

streak viruses travel around as a cloud of variants or virus complex.

Not intuitively obvious, perhaps…but testable, and when we did, we found we were right: cloning virus genomes back out of maize or from a grass infected via leafhoppers gave a single predominant genotype in each case, with a number of other variants present as well. Looking further, we discovered that even quite different viruses could in fact trans-replicate each other: that is, the Rep/RepA complex of one virus could facilitate the replication of the genome of a virus differing by up to 35% in DNA sequence. We have also – we think – made nonsense of the old fancy that you could observe “host adaptation” of field isolates of MSV: we believe this was due to repeated selection by a single host genotype from the “cloud” of viruses transmitted during the natural infection cycle.

So, insight number three:

there is a survival benefit for the viruses in this strategy.

This is simple to understand, really, and relates to leafhopper biology as well as to host: the insects move around a lot, chasing juicy grasses, and it would be an obvious advantage to the streak virus complex to be able to replicate as a complex in each different host type – given that different virus genotypes have differential replication potential in the various backgrounds. This is quite significantly different, incidentally, to what happens with the very distantly-related (in terms of geological time) begomoviruses, or whitefly-transmitted geminiviruses: these typically do not trans-replicate each other across a gap of more than 10% of sequence difference.

Boring, I hear you say, but wait…. Add another factoid in, and profound insights start to emerge. In recent years, the cloud of protégés or virologist complex around me has accumulated to critical mass, and one of the most important things to emerge – apart from some frighteningly effective software for assessing recombination in viral genomes, which I wish he’d charge for – was Darren Martin’s finding that genome recombination is rife among African streak viruses. This was unexpected, given the expectation that DNA viruses simply don’t do that sort of thing; that promiscuous reassortment of components between genomes is a hallmark of RNA viruses. Makes sense in retrospect (an exact science), however, because of the constraints on DNA genomes: how else to explore sequence space, if the proof-reading is too good? And if you travel in a complex anyway…why not swap bits for biological advantage?

MSV web

Linkage map of the MSV genome, showing what interacts with what

So Darren swapped a whole lot of bits, in a tour-de-force of molecular virology, to create some 54 infectious chimaeric MSV genomes – and determined that

The pathogenicity of chimeras was strongly influenced by the relatedness of their parental viruses and evidence was found of nucleotide sequence-dependent interactions between both coding and intergenic regions“.

In other words –new insight:

the whole genome is a pathogenicity determinant, and bits of it interact with other bits in unexpected ways.

At this point you could say “Hey, all his insights are in fact hypotheses!” – and you would be partially correct, except for

Profound Insight No. 1hypotheses are the refuge of the linear-thinking.

Or its variant, found on my office wall:

“**c* the hypotheses, let’s just discover something”. I also have

“If at first you don’t succeed, destroy all evidence that you tried” and a number of exotic beer bottle labels on my wall – but I digress….

As an aside here, I am quite serious in disliking hypothesis-driven science: I think it is a irredeemably reductionist approach, which does not easily allow for Big Picture overviews, and which closes out many promising avenues of investigation or even of thought. And I teach people how to formulate them so they can get grants and publications in later life, but I still think HDS is a tyranny that should be actively subverted wherever possible.

Be all this as it may, now follows

Profound Insight No. 2genome components may still be individually mobile even when covalently linked.

Now take a moment to think on this: recombination allows genes to swap around inside genetic backgrounds so as to constitute novel entities – and the “evolutionary value of exchanging a genome fragment is constrained by the number of ways in which the fragment interacts with the rest of the genome*“. Whether or not the genome is RNA, DNA, in one piece or divided. All of a sudden, the concept of a “virus genome” as a gene pool rather than a unitary thing becomes obvious – and so does the reductionism inherent in saying “this single DNA/RNA sequence is a virus”.

So try this on for size for a brand-new working definition of a virus – and

Profound Insight No. 3a virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements.

Sufficiently paradigm-shifting for you? Compare it to more classical definitions – yes, including one by AJ Cann, Esq. – and see how much simpler it is. It also opens up the possibility that ANY virus as currently recognised is simply an operational assembly of components, and not necessarily the final article at all.

Again, my favourite organisms supply good object examples: the begomoviruses – whitefly-transmitted geminiviruses -

  • may have one- or two-component genomes;
  • some of the singleton A-type components may pick up a B-type in certain circumstances;
  • some doubletons may lose their B without apparent effect in model hosts;
  • some A components may apparently share B components in natural infections;
  • the A and B components recombine like rabbits with cognate molecules (or Bs can pick up the intergenic region from As);
  • in many cases have one or more satellite ssDNAs (β DNA, or nanovirus-related components) associated with disease causation;

…and so on, and on…. An important thing to note here is the lab-rat viruses – those isolated early on, and kept in model plant species in greenhouses – often don’t exhibit any of these strangenesses, whereas field-isolated viruses often do.

Which tells you quite a lot about model systems, doesn’t it?

But this is not only true of plant viruses: the zoo of ssDNA anello-like viruses found in humans and in animals – with several very distantly-related viruses to be found in any individual, and up to 80% of humans infected – just keeps on getting bigger and weirder. Added to the original TT virus – named originally for the initials of the Japanese patient from whom it was isolated, and in a post hoc exercise of convoluted logic, named Torque teno virus (TTV) [why don't people who work with human or animal viruses obey ICTV rules??] – are now Torque teno minivirus (TTMV) and “small anellovirus” SAV) – all of which have generic status. And all of which may be the same thing – as in, TTVs at a genome size of 3.6–3.8 kb may give rise to TTMVs (2.8-29 kb) and SAVs (2.4-2.6 kb) as deletion mutants as part of a population cloud, where the smaller variants are trans-replicated by the larger. Thus, a whole lot of what are being described as viruses – without fulfilling Koch’s Postulates, I might point out – are probably only “hopeful monsters” existing only as part of a population. Funnily enough, this sort of thing is much better explored in the ssDNA plant virus community, given that working with plant hosts is so much easier than with human or animal.

And now we can go really wide, and attempt to be profound on a global scale: it should not have escaped your notice that the greatest degree of diversity among organisms on this planet is that of viruses, and viruses that are found in seawater in particular. There is a truly mind-boggling number of different viruses in just one ml of seawater taken from anywhere on Earth, which leads respectable authors such as Curtis Suttle to speculate that viruses almost certainly have a significant influence on not only populations of all other marine organisms, but even on the carbon balance of the world’s oceans – and therefore of the planet itself.

Which leads to the final, and most obvious,

Profound Insight (No. 4)in order to understand viruses, we should all be working on seawater…. 

That is where the diversity is, after all; that is where the gene pool that gave rise to all viruses came from originally – and who knows what else is being

Hypolith – cyanobacteria-derived, probably – under a piece of Namib quartzite from near Gobabeb Research Station

cooked up down there?

And this is the major update: not only have I managed to get funded for a project on “Marine Viromics” from our local National Research Foundation - a process akin to winning the lottery, and about as likely to succeed - I am also collaborating with friends and colleagues from the Institute for Microbial Biotechnology and Metagenomics at the University of the Western Cape on viruses in desert soils, and associated with hypoliths- or algal growths found under quartzite rocks in extreme environments.

Thus, I shall soon be frantically learning how to deal with colossal amounts of sequence data, and worse, learning how to make sense of it.  We should have fun!

——————————————————————————————————————–

* And as a final curiosity, I find that while I – in common with the World Book Encyclop[a]edia and Learning Resources – take:mol|e|chism or mol|e|cism «MOL uh KIHZ uhm», noun. to mean any virus, viewed as an infective agent possessing the characteristics of both a living microorganism and a nonliving molecule; organule.
[molechism < mole(cule) + ch(emical) + (organ)ism; molecism < molec(ule) + (organ)ism] –
There is another meaning… something to do with sacrifice of children and burning in hellfire eternally. This is just to reassure you that this is not that.

Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

10 July, 2012

See on Scoop.itVirology News

“The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species.”

 

This is a fascinating study of host-pathogen interaction and disease emergence for gemini- and cucumoviruses in wild pepper in Mexico.  This is a great example of what one can do with modern technology coupled with good basic plant pathology / virology.

See on www.plospathogens.org

Polydnaviruses as Symbionts and Gene Delivery Systems

10 July, 2012

See on Scoop.itVirology News

“Textbooks define viruses as infectious agents with nucleic acid genomes (RNA or DNA), which replicate inside living host cells to produce particles (virions) that can transfer the genome to other cells [1], [2]. The Polydnaviridae was recognized as a family of viruses in 1995, and is currently divided into two genera named the Bracovirus and Ichnovirus [3]. Polydnavirus (PDV) virions consist of enveloped nucleocapsids and package multiple circular, double-stranded (ds) DNAs with aggregate sizes that range from 190 to more than 500 kbp [4]. PDVs are also strictly associated with insects called parasitoid wasps (Hymenoptera), which are free living nectar feeders as adults but which develop during their immature stages by feeding inside the body of another insect (the host) [3], [4]. Recent studies, however, indicate that PDVs differ from all other known viruses in ways that challenge traditional views of what viruses are and how they function.”

 

Great review on a group of viruses that has fascinated me since I first heard of them – mainly because there seemed to be no end to the discovery of new bits of genome, and no-one could ever seem to clone a whole one.  

 

I especially like this quote:

“The novelty is that BVs today are obligate beneficial symbionts, which persist entirely from a proviral genome yet produce virions that efficiently deliver genes to other organisms wasps depend upon for survival. Are PDVs still viruses? If we can accept that viruses are not always obligate intracellular parasites, we would suggest the answer is yes.”

See on www.plospathogens.org


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