Scott McPherson's Web Presence

Dorset, England, is a busy place today.  Several mute swans were found dead in a nature preserve there, and they have tested positive for highly pathogenic H5N1.

Dorset is in southern England, specifically located adjacent to the English Channel and across from continental Europe.  The swans in question are indeed wild (they keep the neighbours up all night, apparently, and have wild parties).  But they are NOT migratory, which means someone -- a party crashing duck or other migratory bird, apparently -- brought the virus into the preserve and the "swannery."

Authorities will not attempt to cull the wild birds, fearing they will fly away and deposit high-path H5N1 elsewhere.  So they will test, place a cordon along the preserve, and try to contain.

The story and photo are from Guardian Unlimited.  Here goes:

http://www.guardian.co.uk/birdflu/story/0,,2238598,00.html

I have just finished reading the MIT study on the relationship between different-shaped receptors in human respiratory cells and H5N1, and all I can offer is the Monty Python rejoinder:

"My brain hurts!  My brain hurts......"

But here we go, anyway.  I will put this as simply as I can.  First, some background: We take as gospel the prevailing theory that all influenza A viruses originated within the intestinal tracts of wild birds, and are carried by migratory wildfowl.  It is theorized that influenza A started attacking humans back when the Chinese domesticated ducks a few thousand years ago.  You know, the old "Poultry, pigs and people" mantra.  We also know for certain that the cell receptor of wild bird intestines is of the type scientists call alpha 2-3.  The shape is somewhat elongated, like a cone. A cell receptor is a kind of landing strip for viruses.  The conventional description used in most media reports is a lock.  Whatever the metaphor, it involves joining the host cell with the invading cell. 

By the way, the same basic alpha 2-3 receptor is also found in the lungs of humans.  Most cases of H5N1 infection were attributed (very accurately, as it turns out) that the virus had a love-in with those alpha 2-3 receptors and the virus settled deep in the lungs of people, which also explains why the antiviral inhalant Relenza is basically worthless against the current strains of H5N1, except possibly as a precautionary measure.  The medicine cannot penetrate the crap in victims' lungs to get the antiviral medicine down there.  So swallowing Tamiflu is better than trying to inhale Relenza.

Somewhere along the way, influenza A viruses of the subtype H1, H2 and H3 grew away from this alpha 2-3 receptor and their hemagglutinin began to favor the alpha 2-6 receptors of human nasal passages and throats.  The theory was that as the virus mutated to infect people more easily, this had to do with a simple change that would make the 2-3 receptor less appealing and the 2-6 receptor more enticing, especially since it was so much easier to transmit via the nose and throat than the lungs. 

But as Lee Corso would say, "Not so fast, my friend!"  An intrepid bunch of researchers at MIT have found something a little more sophisticated than all that.  You see, the conventional theory has failed a few times in previous years.  We all know that ferrets mimic the nasal and throat capabilities of humans, so ferrets are used routinely in experiments.  We also have read about tests where high-path flu has killed humans, but ferrets keep plugging along.  Indeed, the study references this in the first page, talking about the maddening experiments where some highly pathogenic influenza A viruses -- including derivatives of the 1918 pandemic strain -- would infect some ferrets, while other subtypes known to be deadly to humans would do nothing to the fuzzy little creatures.

May I also remind everyone that the CDC's own attempts to create a pandemic H5N1 virus failed to produce infection in ferrets.  Therefore, the CDC proclaimed, it was going to be much, much harder to produce a reassortant H5N1.  As a reminder, here is the link to the CDC report (which the new report also references):  http://www.pnas.org/cgi/content/abstract/0605134103v1 .

Now, MIT has given us an important road map to analyze the pandemic potential of any avian flu.  It is not as cut-and-dried to say the virus needs to adapt to alpha 2-6 receptors.  You see, H5N1 has apparently always had the ability to infect those upper tract tissues!  That, according to the MIT study, has more to do with the viral load than any other single factor.  MIT says that there are actually two different types of alpha 2-6 receptors in humans: those little cone-shaped doobers, plus some that are umbrella-shaped ( I think they look more like a mushroom cap, but what do I know?). 

The key to human-to-human sustained transmissibility is therefore NOT a simple matter of moving from alpha 2-3 to alpha 2-6.  It is the move from cone-shaped 2-6 to umbrella-shaped 2-6 receptors.  So if the virus can, indeed, infect humans via the nose and throat cone-shaped alpha 2-6 receptors, we can attribute that to an overwhelmingly devastating whiff of the virus.  A huge viral load. 

But if H5N1 is to really, really cause a mess, it has to change its affinity from cones to umbrellas/mushrooms.  And that, says MIT, is what people need to look for now:  A change in geometry, not simply an amino acid change.  So we need to think in three dimensions, not two. 

To paraphrase my buddy Shakespeare (why I return to Hamlet is unknown to me): Aye, there's the rub: The samples the scientists used were from 1997 and 2004, respectively.  They then data-mined the results against other H5N1 substrains.  Nowhere in the report does it indicate they matched this against data on Qinghai or Fujian strains of H5N1, nor Clade 2.1 Indonesian H5N1.  maybe they did and maybe they didn't.  That, apparently, is for the world's scientists to get busy with.

A good place to start looking for that new alpha 2-6 umbrella affinity would be China.  The WHO has admitted that human-to-human transmission was probably responsible for the hospitalization of a father, whose son died of confirmed H5N1 last month. 

Man in China got bird flu from contact with infected son: officials

BEIJING (AFP) — A man in China contracted bird flu because he was in close contact with his infected son, although the virus had not mutated into a form that is highly contagious among humans, authorities said Thursday.

A 52-year-old man, identified only by his surname Lu, was hospitalised with the potentially deadly H5N1 strain of the virus soon after his son died from it on December 2. Lu has since recovered.

Chinese health ministry spokesman Mao Qunan said Lu's infection was due to close contact with his son, but that the transmission was not technically "human-to-human".

"It has no biological features for human-to-human transmission," he told journalists.

Like many human cases of bird flu in China, authorities have not been able to identify the source as neither Lu nor his son had close contact with sick or dead poultry prior to infection, he said.

He refused to elaborate on the findings, which was reached by the ministry's expert group on bird flu.

Human-to-human transmission of bird flu remains rare, but experts fear such routes of infection could cause a global pandemic if the virus mutates with each person it infects and becomes more adaptable to humans.

The World Health Organisation (WHO) said Thursday that human-to-human transmission of bird flu in the case of Lu was possible but said it had not mutated into a highly contagious form.

"A human-to-human transmission through close contact between the son and the father cannot be ruled out in this family cluster," Hans Troedsson, the WHO representative in China, told AFP. (bold mine)

"However, the biological findings at this stage show that the virus has not mutated to a form that can be transmitted from human to human efficiently."

Bird flu has so far infected at least 27 people in China, 17 of whom have died.

http://afp.google.com/article/ALeqM5gTYR7isTn-MX_ok9VfTkZ_TVOm_Q: 

Maybe, in light of this discovery, CDC should reassess the success or failure of its own experiments.  And authorities need to be very careful about making proclamations that the virus has not yet mutated, unless the samples meet this new "umbrella" test.  Now how easy or hard is it to conduct this test?  I leave that for others to answer.  My brain hurts too much for me to start looking again.

(Map from Laidback Al above).

It is extremely difficult to try and nail down what is happening in Egypt right now.  But from all accounts, and from reading a multitude of postings on flu sites, the best description I can come up with is:  Sheer bedlam.

The last time I looked into the ongoing and escalating situation in the upper Nile delta, the number of suspected cases was at 102, with 5 confirmed human H5N1 infections and four deaths (see earlier blog).Now, it is believed that at least 25 people per day are being admitted with bird flu symptoms, and the Egyptian government has begun exterminating tens of thousands of birds, banned the sale of live poultry, and are at least debating the mass slaughter of pigs.  This would seem to underscore a growing concern in Egypt that pigs have become a reservoir of H5N1, or could become the fabled "mixing vessel" that produces the reassortant Pandemic Strain of H5N1.  Or it could be that the Egyptian government is considering the adoption of a South Korean-esque methodology toward H5N1 eradication.  The South Korean protocol is now to kill every single non human living creature within a 1-3 kilometer radius of an H5N1 source infection.  Every dog, cat, horse, goat, bird, pig, you name it, it's dead -- except for homo sapiens.

All this activity would be cause enough for concern, with one important new development:  The evidence of numerous suspected H5N1 family clusters emerging in familiar locations throughout the nation. We also know that seasonal flu is raging across Egypt.  That should scare us almost as much as if all these current suspected H5N1 cases tested positive (they won't all test positive).  That is because every single case of human H5N1 is now, especially, a potential case of reassortment and the instantaneous production of H5N1 that is adapted to humans.

One look at the lastest Google map, maintained by Dr. Henry Niman, underscores that concern. Go ahead and open a new browser window and follow along.  The map can be found by clicking here: http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=106484775090296685271.000442accf347f22ad5d4&t=h&om=0&ll=30.145127,31.398926&spn=3.932693,6.130371&z=7

While there are still only 5 confirmed cases of human H5N1 infection (color blue), look at how close those cases are to other suspected H5N1 cases.  Now even if those suspected cases test negative for bird flu, their close physical proximity to actual confirmed H5N1 flu cases is unsettling.  And the disclosure that some people who are testing negative for H5N1 are still being held for observation shows that there are some who may not completely trust the accuracy of the tests, and may elect to place caution at the front of the queue.  Good for them!

The fact that pigs are showing up as an area of concern in a multitude of machine-translated missives from the Egyptian government and media should warn us that they are genuinely concerned about the potential for a reassortant H5N1 to emerge from swine.  As we all know, human and avian flus can reassort, or exchange their genes, via pigs.  Pigs acting as the "mixing vessel" is a theory that has been proven as close to cold hard fact as one can get in the year 2008.  The latest St. Jude/Iowa State/U. of Minnesota study should do away with any lingering misgivings about the theory of reassortment.

An interesting post from new Egyptian blogger Zeinobia and her Egyptian Chronicles, located at: http://egyptianchronicles.blogspot.com/2008/01/forget-about-bird-flu-now-it-is-pig-flu.html, also talks about the pig industry in Egypt and how local government decisions to exterminate pigs have been overruled by the farm lobby.  By the way, any independent-thinking Egyptian blogger/ette is a wonderful thing.  Freedom of speech (at least for the moment) over there is good.

This emerging situation in Egypt deserves close scrutiny. 

The post-mortem (forgive the expression) for H5N1 around the world in 2007 shows, by any yardstick, an improved situation.  There were fewer reported human cases; fewer nations experienced the disease; and fewer human deaths.

Poultry, however, did not fare so well.  The numbers of poultry culled were in the tens of millions of birds.  There may be no real way to measure how many ducks, geese, swans, turkeys and chickens gave their lives for the eradication of H5N1.  Well, most of them were going to give their lives sooner or later, anyway.  Some 600,000 birds were culled in Russia in one week in late 2007. 

It reminds me of the 1976 swine flu scare, when it was revealed to President Ford how many eggs were going to have to be laid in order to produce enough vaccine for every American.  Ford called in the ever-jovial Earl Butz, whose joviality eventually cost him his job as Secretary of Agriculture.  When Ford queried him about the sheer volume of eggs required for 200 million-plus doses of vaccine, Butz replied in deadpan:

"Mr. President, the roosters of America are prepared to do their duty!"

The economic impact of H5N1 was especially felt hard in Britain this year.  Roughly two hundred thousand British turkeys, geese and chickens in total were culled in February, November and December of 2007.  Holiday fowl had to be imported from as far away as Brazil.  And Britons were shelling out as much as $200 for a holiday bird! 

Britons Buy $200 Turkeys as Bird Flu Shrinks Christmas Supplies
By Brian Lysaght

Dec. 19 (Bloomberg) -- The 1,800 turkeys on Sheepdrove Farm in Britain's Berkshire Downs spent the summer and autumn feasting on grubs and wheat and roaming through meadows.

This month, these Norfolk Bronze birds with dark plumes and scarlet beaks were being slaughtered, hand-plucked and hung for 14 days on the 2,500-acre organic farm 60 miles west of London. It's the end of their rural idyll and the first step toward a hallowed British holiday tradition -- Christmas Day lunch.

Organic farms such as Sheepdrove are flourishing after one of the toughest-ever years for Britain's poultry industry. Nearly 200,000 birds were culled after outbreaks of a deadly form of bird flu and feed prices surged on higher wheat costs. That's pushed up holiday bird prices by as much as 38 percent and increased demand for organic turkeys, which cost as much as 100 pounds ($205).

Although Sheepdrove Farm stopped taking orders on Dec. 10, ``we've had about 100 calls since we sold out,'' said Michael Benson, the farm sales manager. He plans to raise 2,500 turkeys next year.

Sales of organic turkeys, which must be free ranging and raised on additive-free feed, will jump 46 percent this year, the British Retail Consortium predicts. That compares with a 7 percent increase the industry group forecasts for total turkey sales.

Consumers say the organic birds are safer and tastier.

Helen Day, a 36-year-old administrative assistant in London, said she'll splash out on a free-range turkey for Christmas. ``The flavor's better, and it's worth the money,'' she said.

A Better Bird

Richard Corrigan, chef at the Michelin-starred Lindsay House restaurant in central London, isn't balking at paying 15 percent more this year for organic birds to be served in his festive turkey salads as part of the restaurant's 55 pound tasting menu.

``The food I put in my mouth has to have lived a certain life,'' Corrigan said. ``Who wants to have hundreds and hundreds of birds in a shed?''

England had its first outbreak of the deadly H5N1 strain of bird flu last February at a turkey farm operated by Bernard Matthews Holdings Ltd., Europe's largest factory poultry producer. More than 150,000 turkeys were killed to control the virus.

In November, another outbreak forced the slaughter of 15,500 turkeys, ducks and geese on two farms in Suffolk, eastern England. That may have been caused by wild birds mixing with free-range farm poultry, the U.K. government said in a report on Nov. 29.

Waitrose Ban

Premium supermarket chain Waitrose said Dec. 7 it won't stock organic Christmas turkeys this year because the farms where the disease was found, Redgrave Park Farm and Hill Meadow Farm in Suffolk, were suppliers.

The cancellation will probably further boost independent organic farmers, according to Anna Bassett, a poultry specialist with Britain's Soil Association. The group advises farmers about organic methods, which include rules about crop rotation, natural fertilizer and additive-free animal feeds.

In addition to the aftermath of the bird-flu outbreaks, farmers also face higher feed prices because of rising commodity costs. Wheat traded in Chicago rose above $10 a bushel for the first time on Dec. 17. The grain's price has more than doubled in the last year as drought reduced output from Canada to Australia.

Tom Copas, who raised 50,000 free-range and organic birds at his farm in Cookham, England, boosted his prices by 10 percent.  A medium-size organic Copas turkey is 13 pounds a kilo (2.2 pounds) with free-range, non-organic birds costing 9 pounds a kilo.

American Import

``Orders are coming in very well,'' said Copas, whose family has raised turkeys for 50 years and said most of the birds have been sold.

Turkeys first arrived in Britain in 1526, brought by Yorkshireman William Strickland, who acquired six birds from American Indian traders, according to the British Turkey Association. The tradition of eating turkey at Christmas dates from the 19th century, when it began to replace goose and more exotic fare such as swan and peacock. Last year, Britons bought 10 million Christmas turkeys.

Wholesale prices for turkeys have risen as much as 38 percent, according to a Nov. 30 survey by the U.K. government. Birds of up to 9 kilos are selling for 2.60 pounds a kilo compared with 1.88 pounds a year earlier, the survey said.

Last year, retail sales of organic products in the U.K. rose 22 percent to 1.94 billion pounds, the Soil Association said. The country's market for organic goods has grown 27 percent annually on average over the last decade. It's still a relatively small market, with organic making up 3 percent of all meat, poultry and fish sales, the group estimates.

Farmers say they believe the crisis will continue to drive sales.

``Our customers have the money to spend, they want the best for their families and are willing to pay the price,'' said Sheepdrove's Benson.

http://www.bloomberg.com/apps/news?pid=20601085&sid=aohK8JhZoZLo&refer=europe with a hat-tip to Shannon of FluTrackers.

So why was 2007 more moderate for H5N1 than 2006?  I would give the following reasons:

Climate.  The year 2007 was, on balance, a much milder year than 2006. http://www.hprcc.unl.edu/nebraska/winter-2007-global.html  The effects of climate on Influenza A are still not clearly understood, but the rule of thumb has been the milder the winter, the milder the virus.

Surveillance.  Surveillance has dramatically improved since 2003.  The world is, for the most part, operating solidly when it comes to surveillance.  There are far too many surveillance holes for us to become even remotely comfortable, but it is a much more favorable situation than in 2003.

Education.  People in remote areas have learned to better handle sick, dying and dead wildfowl, and to practice better hygiene.  People are also learning how to fully cook the virus out of their food. Word travels fast, even in remote areas of the planet, when death and disease are concerned.

Payments.  Compensation to farmers is becoming more equitable, and farmers are thus more apt to report when their flocks are infected.  This is not the rule everywhere, sadly.  It needs to become more prevalent.

Culling.  While difficult to track all culling operations, indications are that more poultry were culled in 2007 than in 2006.  This equates to fewer opportunities for the virus to mutate.  Also, culling technology and science is improving, as information and knowledge passes in ones and zeros, in real-time over the Internet.

Fewer nations reported the virus.  The FAO reports that 2007 saw initial emergence of H5N1 in five new nations, which is bad.  But the number of nations reporting H5N1 in poultry and in humans declined over the same period in 2006. http://www.fao.org/docs/eims/upload//237149/ah693e.pdf

While we all can light cigars and celebrate this collective series of improvements, we also must recognize the flip side: 

Indonesia continues to worry us.  Sub-Saharan Africa is a powderkeg when it comes to -- well, when it comes to everything, including H5N1.  The new cluster cases in Pakistan and Egypt show us the virus is continuing to confound the experts. 

And finally, the sobering conclusion from the FAO:

Happy New Year.  Keep watching.

Welcome back, everyone. 

Apparently H5N1 decided to stage an unsettling comeback in the final month of 2007 -- and nowhere is that news more disconcerting than in Egypt.  In no less than six days' time, five Egyptians were reported to have officially contracted the H5N1 virus -- and four of those cases were dead.

All the latest fatalities have been women.

I am just back at the keyboard from a few days of downtime, so I am still sorting through all the various media and blog/posting reports.  The number of confirmed human cases stands at five, but the number of suspected human cases currently rests at 27 or 28.  There may be one or more family clusters.  But from what I can gather, these human infections are not in an isolated location -- that are coming from all over the upper Nile Delta.  Furthermore, the numbers of dead relative to the number of cases is especially troublesome.  A Google Earth map, found on the FluTrackers Website and maintained by Dr. Henry Niman,  shows us the confirmed and suspected human cases.  It is at this link:

http://maps.google.com/maps/ms?ie=UTF8&hl=en&msa=0&msid=106484775090296685271.000442accf347f22ad5d4&ll=30.575268,31.117401&spn=4.123611,7.976074&t=h&z=7&om=0

If all these cases had come from one geographic area, that might be considered (in some perverse way) good news.  But the fact the confirmed cases are in such a widespread area could (and I cautiously use the word "could") potentially signify the emergence of a more easily transmitted bird-to-human (B2H) strain of H5N1.  It would be otherwise difficult to explain this sudden explosion of H5N1 all over the region simultaneously.

In all of 2006, Egypt reported 18 cases, with 10 deaths. This year, prior to Christmas, Egypt confirmed a total of 21 human cases of H5N1, and 6 deaths.  But in just one week in late 2007/early 2008, Egypt has reported reported 5 additional cases and 4 additional deaths. 

And if we look at a chart prepared by fluposter Laidback Al, we can expect to see the situation worsen in the coming months.  Laidback Al took all the suspected cases and overlaid the actual cases.  What he found was a peaking of the 2007 H5N1 cases in April of 2007.  So we can assume (though the data is admittedly sketchy, for Egypt didn't even have a human H5N1 case until 2006), that the 2007/08 holiday sledgehammer return of H5N1 to the Upper Nile, coupled with a particularly nasty proclivity of the current virus to infect -- and  kill -- younger women, distributed over such a wide geographic area, means trouble for 2008.