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Ever since H7N9 was thrown at the world by the Chinese the night of March 31st, everyone familiar with events in China has wondered if there was truly any correlation between the sudden/whiplash emergence of this new flu substrain and the equally sudden and gut-wrenching sight of thousands of dead pigs floating down the Huangpu River. 

The Huangpu is the principal water supply for Shanaghai, as well as other areas.  From Wikipedia:

Shanghai gets most of its drinking water from the Huangpu, and dumps most of its sewage into it (4 mln tonnes in 1990., only 4% of it treated in any way). As a result of pollution, the tap water must be heavily chlorinated.^[2]

In February and March 2013, thousands of pig carcasses were found floating in the Huangpu River in Shanghai. Some of the pigs carried ear tags saying they were from Jiaxing, so that city in Zhejiang may be the source; however local farmers deny that.

Let us look at Apple Maps.  Apple Maps has the Huangpu running through Cleveland.  No!  Dang that Apple Maps! 

Let's look at a different source. The Huangpu is, by all accounts, a beautiful river.   Regrettably, these days it has looked like this:

The latest count has more than 20,000 dead pigs having been recovered from the Huangpu, many/most of them in and immediately around Shanghai. 

It would be natural to speculate whether or not the pigs are the vector causing H7N9 to appear in humans.  However, testing of roughly 34 carcasses has not revealed the presence of the virus.

Admittedly, a sample of 34 pig carcasses in a twenty-thousand carcass deluge is a small sample.  However, it does appear that the two events are just coincidental.

From the British newspaper The Guardian:

This area of Zhejiang province, 60 miles from Shanghai, has become the subject of public and media scrutiny after more than 16,000 dead pigs were found in tributaries of the city's river, the Huangpu, a source of tapwater. As clean-up efforts wind down, mystery surrounds the cause of the pigs' demise and their appearance in the river.

As public concerns about water safety grow, what has emerged is a picture of a rural region marred by catastrophic environmental damage, inherent malpractice and a black market meat trade.

The first pigs were spotted on 7 March and were soon traced to Jiaxing through tags in their ears. Early tests show they carry porcine circovirus, a common disease among hogs not known to be infectious to humans. Shanghai's municipal water department maintains that the water meets the national standard, but hasn't said much more.

Again, the two events appear unrelated.  However, the dates intersect with such similarity, and the provinces and cities are the same ones that are impacted by H7N9, that it is easily understood why the linkage would be there. 

However, had the pigs been the vector, I have to think the Chinese Army would have exterminated and either buried or burned the pigs, and loudly proclaimed that the source of the infection was found and eradicated. they also would have found the presence of H7N9 in pigs upstream of Shanghai.  In the Internet age,

The simple fact is that these events, however crazily coincidental, appear to be unrelated. However, I offer the possibly opposite view, by none other than Laurie Garrett.  Laurie is well-known to infectious disease experts and readers of blogs.  Her works have garnered her much distinction, and she is a Fellow at the Council on Foreign Relations (CFR).  She was a consultant for the film COntagion and is highly-respected. 

In Laurie's view, there is a possible connection between H7N9, the pig die-off (and she makes a very persuasive case for this), and the mass die-off of swans and ducks near Qinghai Lake.  Qinghai is well-known to veteran flu followers:  It is the origin of Clade 2.3 of H5N1 bird flu.  It would not be a stretch to imagine Qinghai spawning yet another mutated bird flu.  Laurie's excellent article can be found here.

In this fog of flu reporting, we will hear many things.  Like most pandemics, and if H7N9 indeed becomes pandemic, the view will be in hindsight, via historians and researchers.  But Laurie brings an interesting perspective to this puzzle.

Indeed, perhaps there are no coincidences here.  Let's just hope that's all they are.

Hat-tip to Valerie Mansuy of France for posting this link on Facebook. Mike is a great guy and one of the world's top infectious disease experts.  You may recall his hour-long interview with Oprah in 2006 on H5N1 bird flu.

The Chinese are reacting to both the introduction of H7N9 into humans, and the fact that birds are not showing symptoms as they usually do. 

The Chinese have ordered the culling of poultry in the city of Shanghai.  A live bird market has been ordered culled of anything with feathers.  Specifically, according to the Chinese news service Xinhua, it was the Huhuai wholesale agricultural products market in the Songjiang district of Shanghai.

The article can be found here. And a huge hat-tip to my friend and birthday boy Mike Coston.

In the meantime, it appears a contact of one of the H7N9 confirmed fatalities has gotten sick. The entire world press corps will be camped at that hospital while we openly wonder if H2H has begun.

The news today brings two more cases of human infection with H7N9 avian flu, and the confirmation of the fourth death I mentioned in yesterday's blog. 

WAIT!  NEWS FLASH!  Now, according to Treyfish, veteran Flutrackers poster, China has reported 14 cases of human H7N9 infection. And one pigeon.  Five humans are dead.  The pigeon's status is uncertain.

I am only half-joking when I mention the pigeon.  As I blogged yesterday, birds appear to be unaffected by this bird flu.  Ordinarily, when a bird has bird flu, it gets very sick and then dies. 

As ESPN celebrity and former FSU player Lee Corso would say, not so fast, my friend. This bird flu is not making birds sick.  If it were, we would have seen H7N9 coming.

Now, Corso did not say that about bird flu.  I said that.

At least one of the two newly-reported cases is in Zhejiang Province.  This province has previously reported cases of H7N9 recently.  Please refer to the map of Chinese provinces I posted in a previous H7N9 blog. The location of the second new case today is not confirmed.

There is feverish (so to speak) activity taking place among those who know the genetics of influenza. These intrepid individuals have been studying the anatomy of H7N9 and sharing that data via the Internet.  The crowdsourcing of H7N9 data is most helpful and extremely important, for it allows a much greater number of qualified researchers to begin the process of dissecting this troubling new virus.

As one can imagine, samples of this new strain of H7N9 are rare.  I can only imagine the frantic process of obtaining these samples and sending them via fighter jet halfway around the world to ground transports, those transports, in turn, racing these samples to facilities such as St. Jude and Drs. Webster and Webby.  Well, that's how it would work in the movies. The reality is probably based around Fed Ex and UPS.  "Sign here for your lethal bird flu virus, Doctor Webster."

Anyway, you have eleven positive victims, and four deaths, and only so much tissue to go around.  So those lucky enough to have actually processed the samples themselves are able to post their research online.

We are a long, long way from being able to replicate things in a laboratory.  We are a long, long way from growing H7N9 in quantities sufficient to conduct any real experiments, with ferrets, birds, or any other creatures. So all we have right now are the phylogenetic charts showing the antecedents of H7N9, and where we have seen their individual component parts before. 

For example, GeneWurx, which posts to Flutrackers, says this about what they have seen:

Though H9N2 is regaled as the nearest relative on file for these internal gene segments of the H7N9 emerging zoonosis, note the highlighted areas including a fatal H5N1 human, pH1N1 in swine (with human homology) and sH3N2. These H7N9 sequences have developed from pedigrees not entirely disjunctive from human infection.

You will recall the (not so) little problem America had with its rural county fairs the past two summers.  People were petting farm animals and then winding up with swine H3N2. I really meant to blog about those cases.  Anyway, an excellent CIDRAP article from last October showed now closely related the swine H3N2 and the longtime seasonal human H3N2 were related.

The press has been running excerpts of an interview with Dr. Richard Webby, of St. Jude.  For new readers:  St. Jude has arguably the top influenza research facility in the world.  Its director, Dr. Robert Webster, is nicknamed the "Pope of Influenza."  Dr. Richard Webby works with Dr. Webster and he is also an email buddy of mine.  Dr. Webby said this to the press about H7N9:

"I think that's what's concerning about this ...This thing doesn't any longer look like a poultry virus," Webby, a swine flu expert, said in an interview.

"It really looks to me like it's adapted in a mammalian host somewhere."

If the virus is spreading in mammals, finding that source is critical to try to reduce human exposure and prevent additional cases, he said.

Also weighing in is Dr. Henry Niman.  Dr. Niman has composed an excellent map of the human cases so far, cases known and suspected.  He also is seeing the progression that Dr. Webby has seen, but he does have a rather flamboyant writing style:

The latest cases increase concerns that the presence of D225G and Q226L represents human adaption of a lethal bird flu virus that has a greater pandemic potential than H5N1.  This potention is enhanced by the presence of PB2 E627K.

Veteran readers of this Blog know that the presence of PB2 E627K signals a move away from avian proclivities and toward mammals.  These are the changes that worry researchers so much.  Also knowing that the birds are not dying means surveillance using conventional (and cheaper) methodology is out the window.  We need a better way to detect the presence of this new flu, and we need it quickly.

There is no question that, somewhere along the line, a pig -- or a human -- was the Mixing vessel that produced this new, novel and immensely troubling virus. 

Fasten your seat belt.

The H7N9 outbreak continues to grow.  This morning, both Flutrackers and Avian Flu Diary are reporting multiple Chinese stories that two new and previously unreported human H7N9 cases have been found in Hangzhou, Zhejiang Province.  Both cases have died.

The machine translation from Chinese to English can be problematic where date (well, pretty much anything else) is concerned, so it takes skill to parse correct dates from the rest of the dialogue.  Regrettably, that is a skill I lack.  But many others do, and these talented people are all located on Flutrackers.com.

There appear to be two separate dates of infection.  One apparently is the 7th of March, and the other is the 25th of March. But what is plain is that this brings a fourth province -- and third coastal province -- into the picture. By any yardstick, we have not yet defined the scope of this outbreak.  Although it appears human-to-human transmission may or may not yet be possible, and as we covered at length yesterday, H7 can and does infect humans, the cat appears to be out of the bag.

The biggest impediment to getting our arms around the scope of the crisis (yes, I consider this to be a crisis, because we have a novel strain of influenza that no one, outside a random poultry worker or hunter is immune to, and it is killing people):  It is not killing poultry.  Sentinel chickens (the proverbial canary in a coal mine), used to help detect the presence of avian influenza, may be asymptomatic carriers of the disease.  At least that is one oprevailing theory, which would also explain why and how this virus escaped surveillance and, thus, early detection. 

You always knew when H5N1 bird flu was close by:  You could follow the trail of dead and soon-to-be-dead chickens.  H7N9 is not killing chickens.  Nor, contrary to what our deepest nightmares and feelings might tell us, is it killing pigs. 

My blog of yesterday mentioned a Dr. Yin of the Bill and Melinda Gates Foundation.  Apparently Dr. Yin is the Foundation's leader in China.  And it was quite satisfying, knowing Bill and Melinda are spending funds in China, including, but not limited to, surveillance.  Dr. Yin's statement is worth paraphrasing.  He said, basically, if you don't test for H7N9, you won't find it.  But if you do test for it, you'll find it.  The inference is that there have been numerous unexplained and undiagnosed severe respiratory ailments there this season.  Retroactive testing of samples, based on Dr. Yin's inference, will yield a significant increase in the number of H7N9 human cases. 

I am hopeful that the CDC here will start looking at the number of "A (subtyping not performed)" samples still lingering around.