How emerging viruses jump from species to species

雷竞技官网 reporting from the Royal Society, January 2004

The list of emergent viruses continues to grow. In the early 1990s, there was HIV, ebola, lassa, and others, almost all having jumped from their natural host species to humans. More recently, hepatitis C, Sin Nombre, West Nile, and of course SARS emerged. The common factor, said Dr Eddie Holmes of the University of Oxford, is that they use RNA rather than DNA to carry their genetic code.

Holmes believes that the genetics of our immune systems and viral genetics should be an equally important research focus. To infect a new species, an emerging virus has to overcome the new host’s immune system and to replicate in its cells, the success of which depends on both viral and host genetics and other factors.

But, Holmes asked, why do such pathogens emerge and what controls the emergence? Ecological change, as emphasized in Tony McMichael’s talk, is the governing factor – change in human proximity and change in host-species population density. The key to understanding lies in the fact that RNA viruses mutate a million times more rapidly than organisms with DNA. This endows them with great adaptability. On the other hand, a high mutation rate constrains viral evolution by capping the viral genome’s size, which limits adaptability. Higher mutation rates, after all, mean more chance of error in the viral genes. This “error-threshold”, explained Holmes, means that if a virus has to evolve a lot to jump between species then it is more likely to fail. We eat a multitude of plant viruses every day but no one has yet fallen prey to turnip mosaic virus.

The coronaviruses such as SARS, are different. They have a much bigger genome than other RNA viruses, which means that SARS and its relatives should evolve more slowly but their larger genome gives them greater adaptability. A better understanding of the constraints to RNA virus evolution will allow us to make better predictions about the emergence of new viruses and help us find improved therapeutic procedures. Rather than thinking about what RNA viruses can do, we should concentrate on their limitations.

Read on… Influenza and emerging viruses

Alchemist Checks Oxy Cholesterol Levels

copper-alchemistThe Alchemist this week learns how fluorine chemistry is blooming, how to melt proteins, and how cholesterol is all about the good, the bad, and the oxy. Also this week, a technique borrowed from organic LED fabrication could lead to a new way to manufacture tiny inorganic LEDs for next generation displays, while a conductive flip has been observed with clusters of atoms close to absolute zero. Finally, the American Chemical Society announces this years previously unsung chemical heroes from across the industry.

Previously on ChemWeb, we heard rumors of silicon neurons and the coming cyborg age, he discovers that a compound that leads to ovine Cyclops has now been synthesized for cancer drug research, and how chicken poop down on the shooting range could help solve the problem of lead in the soil. Also, in the news, a new type of fuel cell for truckers that reduces their emissions during rest periods and the increasing cost in water of producing bioethanol. Finally, a major award for a generic pharmacologist.

Swine Flu Update

swine-flu-leafletSwine flu (H1N1) information leaflets are being delivered to households across the UK today. I suspect they do nothing but increase fear and confuse people, especially as the WHO/UN are about to lower the swine flu alert level.

In the UK, 27 people now have the virus, with 23 in England and four in Scotland and the first P2P transmission in the UK has been reported. But, what happened to the thousands, if not millions, affected we were warned of by the media and government and WHO and UN over the last few weeks? It just hasn’t happened, thankfully.

The leaflets will, of course, explain exactly what is swine flu (I wonder whether they will explain why we now have to call it H1N1 though), who is most at risk, what are the symptoms, and what people can do to reduce their risk of catching the disease.

There was a panic on Monday when the WHO was set to raise the alert level, but it didn’t happen they are maintaining it at Phase V, one below the red alert Phase VI, and may lower the panic level in coming days.

I suspect that the average person reading the government leaflet will disregard it as contradictory with what they are now hearing in the news. They may also see it as simply yet another kneejerk reaction from politicians who always to pander to the media biases rather than making their own scientifically informed decisions.

In my original swine flu article, I rather flippantly advised readers to forget avian influenza and to switch their worries to pigs. But, there was a serious thought behind my silliness because a single disease should not be the focus of fear. Emergent diseases could appear in almost any host animal at any time and cross the species barrier through random mutation.

Indeed, it’s certainly not only pigs, birds, and humans, that catch flu. Horses, and even whales and seals, get a form of the disease. But influenza is not the only virus.

If a second wave of swine flu does not evolve in the Northern autumn this year, there’s no reason to assume that some other respiratory virus, perhaps akin to SARS, perhaps avian, or something entirely different will appear. Will we be prepared for the onset of a previously unknown respiratory, or other, infection spreading from some obscure mammal in central Asia or elsewhere? Or, will the media incite mass hysteria through scaremongering once again?

How will a swine flu pamphlet look in six months time? Confusing and useless, that’s how. The scaremongering that has gone way beyond any seen at the time of SARS and certainly way beyond the avian influenza concerns, will ultimately look like a story of “cry wolf” when the next virus emerges.

The WHO told us a week or two ago that we could no longer contain swine flu, but as it turns out there really was no need to contain it in the first place. It appears (in this wave) not to be as virulent as first feared, mortality rates even in Mexico City are far lower than one would have expected of a serious illness with the number of dead from H1N1 being revised downwards several times already.

Flu experts from Cambridge, the National Institutes of Health, and The Cleveland Clinic will be talking about the science behind the news of the swine flu outbreak at a free webinar on Friday.

All that said, the UK’s chief medic Liam Donaldson, has warned against complacency because flu viruses can change character “very rapidly”. It is too early to assume the swine flu outbreak is a mild infection just because no-one in the UK has died, he says.

For years we have been warned that a lethal flu pandemic to match the Spanish Flu of 1918 was long overdue. Birds, and now pigs, have so far failed to deliver, but what’s that unidentified, flea-bitten rodent running around the market square? Is the tiny creature the harbinger of doom? Will we ever conquer infectious disease?

Research Blogging IconO’Dowd, A. (2009). Confirmation of first person to person transmission of swine flu in UK expected soon BMJ, 338 (may01 1) DOI: 10.1136/bmj.b1838

Raspberry Ripple Galaxy

galactic-rasberry-flavorRecently, an innocuous-seeming press release was released by German astronomers announcing that they had found two of the most complex molecules ever in space – n-propyl cyanide, more commonly known to chemists as butyronitrile, and ethyl formate. Now, butyronitrile is a nasty poison with a characteristic odour and I’m sure you’d get a whiff of bitter almonds as you lay dying should you breathe it in too deep or get a mouthful of the stuff. Ethyl formate is altogether different.

Ethyl formate, The Guardian’s science correspondent Ian Sample found out (I think already knew) is the fragrant ester molecule that gives raspberries their distinct flavour. It also smells vaguely of rum. Having latched on to this fact, Sample went to town on his galactic press release suggesting, in a Pythonesque manner, that your galaxy smells of raspberries.

It was a great hook for his popular science article in the paper, of course, and the idea was subsequently picked up by other outlets that had initially missed the raspberry flavour additive. With my SpectroscopyNOW deadline looming, I reasoned that the research was valid enough, ignoring the raspberries, for the news channel and set about explaining the ins and outs of the discovery and its relevance.

If complex molecules such as ethyl formate and butyronitrile can be found in space then perhaps the building blocks of proteins, amino acids, might also be present, which could lend evidence to space as being the seeding ground for the precursors to life on earth and perhaps extraterrestrial life too.

I contacted the leader of the astronomical team that had made this startling discovery to find out more details about the research. Arnaud Belloche of the Max Planck Institute for Radio Astronomy (MPIfR) in Bonn, Germany, was unsurprisingly quick to point out that the raspberry connection was essentially a journalistic invention of The Guardian and has no bearing on the research at all.

“We did not report on the flavour of raspberry or the smell of rum,” he told me, “For us, astronomers, it is unimportant. What is important is that these two molecules are quite complex compared to the other molecules discovered in space, and that their discovery suggests that even more complex molecules are likely present in the interstellar medium.”

He did, however, concede that the reference to raspberries and rum makes the story more interesting for the lay public. “It is fine to mention it, but it should be made clear that it is astronomically irrelevant.” Of course, that much should be immediately obvious to most readers of SpectroscopyNOW.

It does raise an interesting point about science journalism. Is it stretching the truth, or dumbing down, too much to mention that the molecules found in outer space have a link with the flavour of raspberries? How far should we go to make rather technical and esoteric science appeal to a lay audience? Surely, it would have been enough that these complex molecules were found in space and may have a bearing on the origins of life on earth.

Perhaps not. A press release blankly referring to two chemicals with names obscure to non-chemists would usually have little impact. It was picked up by some outlets. However, it was only once Ian Sample had made the raspberry connection and used the Monty Python Holy Grail insult allusion (if your galaxy doesn’t smell of raspberries then your mother certainly still smells of elderberries) that more of the wider media jumped on to the idea of a galaxy smelling faintly of raspberries and rum and took it mainstream.

Indeed, we have a control to test this, because the same team use the same data lasts year to reveal that the same galactic gas cloud also contains aminoacetonitrile. This molecule is a
likely chemical precursor of the amino acid glycine, which has perhaps a much greater bearing on the origins of life than the raspberry flavouring, but unfortunately has none of the fruity allusions.

Which headline would grab you?

Scientists Spot Amino Acetonitrile in the Middle of Milky Way

or

Make That A Raspberry Pan Galactic Gargle Blaster

You can read my full write-up complete with overblown flavouring-enriched title in the May 1 issue of SpectroscopyNOW.

Finally, I asked Belloche for his predictions of when we might discover amino acids in space and get a true feeling for the notion of cosmic dust seeding the primordial earth.

“I guess we’ll have to wait many years…” he told me, “A simple estimate we did in
our publication on aminoacetonitrile (Belloche et al. 2008, A&A, 482, 179)
suggests that the abundance of glycine, if present in the interstellar
medium, is well below the best upper limits derived so far, by maybe one
or two orders of magnitude, so it will be hard (but not impossible!) to
find it.”

His prediction doesn’t leave a bitter taste in the mouth, but nor does it come up tasting of raspberries.

Alchemy Under the Spotlight

atlantic-bathymetryThis week, The Alchemist is digging in the dirt to find out about the carbon cycle and climate change, taking his whisky (or is it whiskey) with or without water, and discovering how to juggle molecules, on the other hand. Also in biochemical news this week, the crystal structure of a plant hormone receptor is revealed while researchers in Israel focus on blocking the protein misfolding that occurs in Alzheimer’s disease.

And, under the December physical sciences Spotlight

It’s all in the marine mix – Mixing of surface waters in the Atlantic Ocean seems to have reverted in the winter of 2007/2008 to “normal” levels for the first time in almost a decade…

Well, wooden you know? – New materials that look and behave like plastics can be produced from a renewable raw material known as liquid wood. The bioplastics promise to displace petroleum as a feedstock for certain applications…

Running with knives – Stabbing is the most common form of murder in the UK and Ireland. However, while forensic scientists understand the basics of the process…

Top Ten Mutants

dna-testIf you ever thought genetics was only about disease, then check out the popular SNPs list on SNPedia. A SNP (pronounced “snip”) is a single nucleotide polymorphism, which in BradSpeak(TM) is basically a difference in a bit of your DNA that makes you different from the rest.

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

  • rs1815739 sprinters vs endurance athletes (I reckon I lack both)
  • rs7495174 green eye color and rs12913832 for blue eye color
  • rs6152 can prevent baldness (this was discovered far too late for me)
  • rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
  • rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

  • rs9939609 triggers obesity (not a genetic excuse for eating too much)
  • rs662799 prevents weight gain from high fat diets (ditto)
  • rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
  • rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
  • rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Shedding Light on Neon Signs

neon-signAs regular readers know, I like to keep a fairly close eye on what Sciencebase visitors are searching for so that I can put together new posts that provide answers to the questions readers want answering. Recently, there has been a spate of search queries related to neon signs. Perhaps not the most exciting of subjects, but there is some nice chemistry to be learned from all the different colours available, so I thought I’d shed some light on the subject of noble gas illumination.

Incidentally, for those unaware of the history of noble gases, they were at one time known as inert gases because chemists thought their full outer shell of electrons made them unreactive. As more and more reactions for these so-called inert gases were discovered, it became necessary to abandon the “inert” label and focus on their nobility.

A neon light is not really much more than a fluorescent tube (actually, it’s less as it needs no phosphor coating on the inside), neon tubes contain the noble gas neon, surprise, surprise. Pass an electric discharge through a tube containing low pressure neon and it will glow with that familiar orange-red glow, so evocative of late-night bars and sleazy movies.

A neon light uses a very high voltage to propel an electric current through a low-density gas of neon atoms held in a glass tube. Charges from the electrode at each end of the tube fly through the gas colliding frequently with neon atoms and transferring some of their energy to the neon atoms. This kicks the neon atoms into a higher energy, excited state, with an electron in a higher orbital than normal. This excited state does not last and as the electron loses energy the atom drops back to a lower energy state and releases a photon of light. The energy of this photon is equivalent to the energy fall and for neon atoms that coincides with an energy that produces a reddish glow.

Many people, unfamiliar with the noble gas group of the periodic table – the p-block, assume that all coloured fluorescent tubes used in signage are neon signs. However, there are two ways to produce other colours – paint a standard mercury tube with the colour you want or far more effectively use a different noble gas in the tube instead of neon, perhaps together with mercury vapour to give a stronger glow. Here’s a break down of the discharge colours for each noble gas.

Helium (He) – Orangey white, usually
Neon (Ne) – Orange-red glow
Argon (Ar) – Violet, pale lavender blue
Krypton (Kr) – Grayish dim off-white
Xenon (Xe) – Blue-grey
Radon (Rn) – radioactive, not used in lighting

Of course, it is not only the noble gases and mercury vapour that can be added to lighting tubes. Nitrogen produces a slightly pinker glow than argon, oxygen glows violet-lavender but dimly. Hydrogen glows lavender at low currents, but pinkish magenta above 10 milliAmps, while carbon dioxide produces a slight bluish-white. Mercury can be made to glow in the ultraviolet, and is used in so-called black lights. Sodium vapour at low pressure glows the bright yellow of street lighting, particularly in England. And, even water vapour produces a glow similar to hydrogen, only dimmer .

Open Access in Africa

development-heatmap-africaThere is much talk about Open Access. There are those in academia who argue the pros extensively in all fields, biology, chemistry, computing. Protagonists are making massive efforts to convert users to this essentially non-commercial form of information and knowledge.

Conversely, there are those in the commercial world who ask, who will pay for OA endeavours and how can growth (current recession and credit crunch aside) continue in a capitalist, democratic society, without the opportunity to profit from one’s intellectual property.

Those for and against weigh up both sides of the argument repeatedly. However, they often neglect one aspect of the concept of Open Access: how they might extend it to the developing nations, to what ends, and with what benefits.

Writing in a forthcoming paper in the International Journal of Technology Management, Williams Nwagwu of the Africa Regional Center for Information Science (ARCIS) at the University of Ibadan, Nigeria and Allam Ahmed of the Science and Technology Policy Research (SPRU) at the University of Sussex, UK, suggest that developing countries, particularly those in Sub-Saharan Africa (SSA), are suffering from a scientific information famine. They say that beginning at the local level and networking nationally could help us realise the potential for two-way information traffic.

The expectation that the internet would facilitate scientific information flow does not seem to be realisable, owing to the restrictive subscription fees of the high quality sources and the beleaguering inequity in the access and use of the internet and other Information and Communication Technology (ICT) resources.

Nwagwu and Ahmed have assessed the possible impact the Open Access movement may have on addressing this inequity in SSA by removing the restrictions on accessing scientific knowledge. They highlight the opportunities and challenges but also demonstrate that there are often mismatches between what the “donor” countries and organisations might reasonably offer and what the SSA countries can actually implement. Moreover, they explain the slow uptake of Open Access in SSA as being related to the perception of the African scientists towards the movement and a lack of concern by policymakers.

The researchers suggest that the creation of a digital democracy could prevent the widening information gap between the developed and the developing world. Without the free flow of information between nations, particularly in and out of Africa and other developing regions, there may be no true global economy.

“Whatever might emerge as a global economy will be skewed in favour of the information-haves, leaving behind the rich resources of Africa and other regions, which are often regarded as information have-nots,” the researchers say. It is this notion that means that it is not only SSA that will lose out on the lack of information channels between the SSA and the developed world, but also those in the developed world.

“The current pattern of the globalisation process is leaving something very crucial behind, namely the multifaceted intellectual ‘wealth’ and ‘natural resources’ of Africa,” they add. “The beauty of a truly globalised world would lie in the diversity of the content contributed by all countries.

From this perspective, they say, the free flow of scientific articles must be pursued by developing countries, particularly SSA, with vigour. “African countries should as a matter of priority adopt collaborative strategies with agencies and institutions in the developed countries where research infrastructures are better developed, and where the quest for access to scientific publication is on the increase.”

They suggest that efforts could begin locally having found that even within single institutions in most African countries, access to scientific articles is very scant. “Local institutions should initiate local literature control services with the sole aim of making the content available to scientists,” they suggest.

Proper networking of institutions across a country could then ease access to scientific publications. One such initiative in Nigeria has started under the National University Commission’s NUNet Project but wider support from governments is necessary to build the infrastructure. Research oriented institutions could use their funds to grant free access to their readers, especially given that many already pay subscription fees for their readers in large amounts.

Meanwhile, can music bring open relief to Africa?

Williams E. Nwagwu, Allam Ahmed (2009). Building open access in Africa International Journal of Technology Management, 45 (1/2), 82-101 I put in a request with the publishers for this paper to be made freely available, it is now so. You can download the PDF here.

Bird Flu Flap

Bird flu duckI’m not entirely convinced that bird flu (avian influenza) is going to be the next big emergent disease that will wipe out thousands, if not millions, of people across the globe. SARS, after all, had nothing to do with avians, nor does HIV, and certainly not malaria, tuberculosis, MRSA, Escherichia coli O157, or any of dozens of virulent strains of disease that have and are killing millions of people.

There are just so many different types of host within which novel microbial organisms and parasites might be lurking, just waiting for humans to impinge on their marginal domains, to chop down that last tree, to hunt their predators to extinction, and to wreak all-round environmental habitat on their ecosystems, that it is actually only a matter of time before something far worse than avian influenza crawls out from under the metaphorical rock.

In the meantime, there is plenty to worry about on the bird flu front, but perhaps nothing for us to get into too much of a flap over, just yet.

According to a report on Australia’s ABC news, researchers have found that the infamous H5N1 strain of bird flu (which is deadly to birds) can mix with the common-or-garden human influenza virus. The news report tells us worryingly that, “A mutated virus combining human flu and bird flu is the nightmare strain which scientists fear could create a worldwide pandemic.”

Of course, the scientists have not discovered this mutant strain in the wild, they have simply demonstrated that it can happen in the proverbial Petri dish.

Meanwhile, bootiful UK turkey company – Bernard Matthews Foods – has called for an early warning system for impending invasions of avian influenza. A feature in Farmers Weekly Interactive says the company is urging the government and poultry industry to work together to establish an early warning system for migratory birds that may carry H5N1 avian flu. “Armed with this knowledge, free range turkey producers would be able to take measures to avoid contact between wild birds and poultry.” That’s all well and good, but what if a mutant strain really does emerge that also happens to be carried by wild (and domesticated birds) or, more scarily by another species altogether? Then, no amount of H5N1 monitoring is going to protect those roaming turkeys.

While all this is going on, the Washington Post reports that the Hong Kong authorities announced Wednesday (June 10) that they are going to cull poultry in the territory’s retail markets because of fears of a dangerous bird flu outbreak. H5N1 virus was detected in chickens being sold from a stall in the Kowloon area and 2700 birds were slaughtered there to prevent its spread. In closely related news, the International Herald Tribune has reported that there has been an outbreak of bird flu in North Korea. “Bird flu has broken out near a North Korean military base in the first reported case of the disease in the country since 2005, a South Korean aid group said Wednesday.” But, note, “since 2005”, which means it happened before, and we didn’t then see the rapid emergence of the killer strain the media scaremongers are almost choking to see.

Finally, the ever-intriguing Arkansas Democrat Gazette reported, with the rather uninspiring headline: Test shows bird flu in hens. Apparently, a sample from a hen flock destroyed near West Fork, Arkansas, tested positive for avian influenza. A little lower down the page we learn that the strain involved is the far less worrisome H7N3. So, avian influenza is yet to crack the US big time. Thankfully.

Flu Clinic Widget

Flu shot

Is flu vaccination a shot in the dark? Regular readers will recall the recent debate on multiple vaccines, statistics, and risk we had here in September. I also have rather close personal experience of one of the risks associated with having the annual flu vaccine – Guillain-Barré Syndrome (GBS). This autoimmune disorder is purportedly associated with a respiratory or gastrointestinal tract infection although there is a statistical risk that connects it to the flu vaccine. A close relative of mine developed GBS symptoms about six weeks after having the flu jab last December and has not yet fully recovered. GBS support groups recommend she not have the vaccine again.

So, it is with mixed feelings that I read an email from Charles Forsyth (a public relations professional at www.btstrategies.com apparently working for the American Lung Association). Charles is helping the ALA raise awareness of the importance of getting an influenza vaccination at this time of year. He explains that part of the campaign involves persuading bloggers and other website owners to add a widget to their site. The widget helps readers find a local flu clinic quickly and easily where they can be vaccinated.

You can try the widget here http://www.flucliniclocator.org and download it to add to your site. Just enter your zip code to find clinics in your area and make an appointment. You could use it to find a clinic for elderly or infirm friends or relatives too or others in high-risk categories, such as asthma sufferers, and those on immunosuppressant drugs.

Tragically, influenza kills about 36,000 people each year in the US, Charles tells me, and requires another 200,000 to be hospitalized. Most of these deaths are preventable by getting a simple flu shot each fall.

The following groups are considered at higher risk than the general population

  • People who are 50 years of age and older
  • Women who will be pregnant during influenza season
  • Young children 6 to 59 months of age [Not sure what changes at 59 months, presumably they just mean under fives]
  • People with chronic medical conditions such as asthma, emphysema, chronic bronchitis, TB, CF, heart disease, kidney problems, diabetes, and severe anaemia
  • People who have diseases or having treatments that depress immunity
  • Caregivers of those at risk

Charles suggested I add the widget to the Sciencebase bird flu symptoms page, but I think that would be a little irresponsible, given that a vaccine against human influenza will most likely provide absolutely no protection against an impending bird flu epidemic. Instead, I’ve added it to my seasonal page on how to avoid colds and flu in the first place. This page rears its ugly head at this time of year on an annual basis, so it’s as good a place to slot the widget as any. I should emphasize though, that if you have any concerns about the protective efficacy of vaccination or the risks associated with the flu jab you should discuss them with your GP.

Oh, and if you think you have flu or a bad cold, don’t spread it around, stay at home.