Avian influenza, bird flu, H5N1

TL:DR – Scientists are worried that we might soon see the emergence of another pandemic, this one originating in avian influenza.


A bird flu pandemic has killed thousands of wild birds over the last couple of years. Scientists have now seen infection in mammals, and very recently a person died from avian influenza and several close contacts show signs of  infection. The concern is that we might be headed for another H5N1 pandemic. Previous strains of H5N1 that infected people had a mortality rate of 60 percent.

Avian influenza, bird flu, H5N1

There are fifteen known variants of avian influenza. The most virulent, and usually fatal in birds, are the H5 and H7 strains. There are then nine variants of the H5 strain and the type of most concern because of the risk to human health is H5N1.

Up to May 2020, the World Health Organisation had reported a total of 861 human cases of bird flu, which killed 455 people since 2003. However, in February 2003, an 11-year-old Cambodian girl died of H5N1, her father tested positive and several close contacts had symptoms. At the time of writing, the WHO believes this strain of H5N1 is spreading among people and is pushing for a new human vaccine against the disease to be produced urgently.

How emerging viruses jump from species to species

David Bradley 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

H7N9 bird flu

Is another bird flu on the rise? Report from Nature on H7N9 type A influenza virus and reported outbreak in China.

Scientists and public health officials worldwide are on alert after China announced on 31 March that two people had died and a third had been seriously sickened from infections with a new avian flu virus, H7N9, that has never been seen before in humans.

via Novel bird flu kills two in China : Nature News & Comment.

There are numerous subtypes of flu, labelled with an H number, referring to the specific type of protein hemagglutinin and an N number, neuraminidase enzyme type. There are 17 H antigens (H1 to H17) and nine different N antigens (N1 to N9) and any combination might be possible. The newest H antigen type, identified as H17 by researchers, was isolated from fruit bats in 2012.

Bird flu, swine flu, now seal flu H3N8

US scientists have identified a new strain of influenza in New England harbor seals – H3N8. They say the strain, presumably made the species leap from birds, might now be a reservoir for an emergent human flu virus.

H3N8 is an influenza type A virus (Orthomyxoviridae) endemic in birds, equines and dogs and although highly contagious was not as such considered a risk to people. A flu outbreak in people in 1889 or 1900 was blamed on this strain but evidence suggests that it was due to H2N2. If H3N8 has mutated and evolved from an avian form into one that infects harbor seals (Phoca vitulina), there is a chance that it could now infect people. Indeed, the virus already has the relevant structure to attack a protein in the human respiratory tract.

Experts have for some time recognised that emergent flu viruses need not only come from East Asia, swine flu, H1N1, being a case in point, the pandemic of 2009 emerging from South America. So, the emergence of a putative pandemic strain in the waters off New England, USA, is worrying, but perhaps not surprising.

It is worth noting that a paper in the same group of journals from 1984 reports on the emergence of an avian influenza virus (H4N5) in harbor seals in the early 1980s. There are presumably other instances so this would suggest that transfer to harbor seals from birds is not an uncommon leap.

BBC News – New flu virus found in seals concerns scientists.

Moscona et al, 2012, mBio; DOI: 10.1128/mBio.00166-12

Influenza A viruses are classified into subtypes based on the antibody response to the viral proteins hemagglutinin (HA), neuraminidase (NA). This distinction gives us the different names, e.g. H5N1, H1N1, H3N8 etc. There are 16 H and 9 N subtypes known, but only H 1, 2 and 3, and N 1 and 2 are usually found in people.

Bird flu research halted

The UK’s Guardian newspaper is reporting that researchers working to prevent the spread of bird flu and the possible millions of deaths it could cause should a pandemic occur, have suspended their research for 60 days amid fears that they might accidentally trigger the very  epidemic they hope to stop. A letter published on Friday in the scientific journals Nature and Science and signed by scientists from around the world appeals for public debate about the security of the work.

Bird flu scientists suspend work amid epidemic fears.

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.