H7N9 discussion thread: January 24, 2014 to Feb 5 2014 (closed)

[gsgs]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

I remember at least one study last year that tried to estimate the
prevalence of H7N9 in the Chinese population

http://wwwnc.cdc.gov/eid/article/19/8/13-0662_article.htm

-----------------------------
11 more cases, total 238 cases, 57 deaths
Hangzhou, Shanghai to halt live poultry trading

 

[Emily]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Good questions. I am not convinced pigeons are the carriers. As far as I know from postings here, pigeons are not high on the suspect list of probable reservoirs. If pigeons were the reservoir it would answer one burning question in my mind, why has the H7N9 virus never left the east coast region of China. Pigeons are not big on heading south for the winter. however, as a skilled doctor I am skeptical the doctor wouldn't have avoided the pigeons.

I doubt it's pigeons, too. If any sort of pet bird were the reservoir, I'd imagine that would be pretty easy to trace. I admit I'd hate to see that connection because of the emotional fallout if that were so.

 

[NS1]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

I doubt it's pigeons, too. If any sort of pet bird were the reservoir, I'd imagine that would be pretty easy to trace. I admit I'd hate to see that connection because of the emotional fallout if that were so.

Emotions have played a role in preventing discovery of an origin point and a reservoir for Emergent H7N9.

That trace is more difficult than we see on the surface. Methodologies remain rigid even when proven valueless. The passerines in China were not tested comprehensively during 2013.

More information is on hand now.

Jones, Webster, Yi Guan, Malik Peiris and colleagues demonstrated that intestinal shedding is not likely a primary means of pathogen spread from songbirds, but that that they contaminated water from their drinking with transmissible loads of H7N9 viral material.

--

Jones JC, Sonnberg S, Ko?er ZA, Shanmuganatham K, Seiler P, Shu Y, et al.
Possible role of songbirds and parakeets in transmission of influenza A(H7N9) virus to humans.
Emerg Infect Dis [Internet]. 2014 Mar [date cited].
http://dx.doi.org/10.3201/eid2003.131271
DOI: 10.3201/eid2003.131271
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<tr style="float: center;"><td style="font-size: 140%; font-weight: bold;">Possible Role of Songbirds and Parakeets in Transmission of Influenza A(H7N9) Virus to Humans
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<tr style="float: center;"><td style="font-size: 90%;">Songbirds are common household pets and are in close contact with humans and domesticated animals. Their wild counterparts also are likely to interact with poultry in backyard farms and in many farming sectors (14,15).
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<tr style="float: center; font-size: 60%;"><td>By Jeremy C. Jones, Stephanie Sonnberg, Zeynep A. Ko?er, Karthik Shanmuganatham, Patrick Seiler, Yuelong Shu, Huachen Zhu, Yi Guan, Malik Peiris, Richard J. Webby, and Robert G. Webster</td></tr>
<tr style="float: center; font-size: 60%;"><td><a href="http://wwwnc.cdc.gov/eid/" target="_blank">EID Journal</a>
Volume 20, Number 3?March 2014
Ahead of Print
January 24, 2014</td></tr>
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<span style="font-family: Georgia, Times New Roman, serif; font-size: 100%;">'Discussion Extract:

Shedding was limited to the oropharynx, which may have reduced contact transmission; however, at most times sampled, the water troughs contained large amounts of virus. Furthermore, low-pathogenicity influenza viruses (those lacking a multibasic cleavage site in the hemagglutinin protein), such as the A(H7N9) isolate used here, remain stable in water longer than their highly pathogenic counterparts (22) and could therefore serve as an inoculum for cage mates.

. . .

Preliminary data suggest that chickens and quail are highly susceptible to infection with this human A(H7N9) isolate and that the virus is readily transmitted by direct contact (9,10). The high titers recovered from the shared water troughs of all species tested in our study suggest that the virus could be transmitted to poultry and other birds through this route.

. . .

In caring for such pets, their owners could become infected by virus contaminated drinking water or from fomites on the feathers (deposited while bathing in water troughs or from saliva while preening) (30).'

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Related
Open-Access, Full-Text
H7N9 Publications
on
Passerine Involvement​

• 2013-04-03 [FT#490356] Cross SeroType Homology HA 118A Originated in Passerines
• 2013-04-09 [FT#491682] HA 541V H5N1 Avian 50 Species
• 2013-04-11 [FT#492191] HA 202V H5N1 China Pigeon 2010
• 2013-04-14 [FT#492898] Potential Passerine Involvement as Emergent H7N9 Reservoir
• 2013-04-17 [FT#493607] A Tale of Two Sequences
• 2013-04-29 [FT#495364] Passerines Fly Higher than Poultry
• 2013-04-30 [FT#495496] Unlocking a 3 Piece 4D Puzzle
• 2013-05-01 [FT#495674] Memorable Magpies & Martins, Probable Pets & Pigeons, Tasty Swallows & Swiftlets
• 2013-05-01 [FT#495839] RFI from Veterinary Pathogen Storage Facilities
• 2013-07-12 [FT#503849] Ignition v. Spread
• 2013-12-08 [eH7N9 Shaoxing] Shaoxing, Zhejiang Fall 2013 Human H7N9 Displays Varied Genetics from Two Laboratories

 

[morningperson]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Did you see that Dr. Zhang lived next door to someone who kept pigeons?

http://www.flutrackers.com/forum/showpost.php?p=521653&postcount=10

Another article in that thread indicates he was a very dedicated trauma surgeon, and worked for about a week with a fever. He passed away on the 18th, so if this were H2H, why no cases in his family, friends, co-workers or patients yet?

If he did indeed catch this from an undiagnosed patient, (whose illness perhaps was the cause of cognitive malfunctioning that caused some sort of accident that ended up being the patient's cause of death), why are no other HCW's infected yet?

Was the doctor the only HCW to be splashed with blood while desperately trying to save the life of a patient?

I wonder if the person next door kept only pigeons or other types of birds too. Not that we will ever know.

 

[Vibrant62]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Whilst we are not seeing the spread of H7N9 across the entire of china, nor its spread to adjacent countries, we are seeing a proponderance of cases in urban areas. That suggests a widespread dispersal of the virus, at quite high levels - possibly airbourne.

There are more cases amongst farmers than previously (spring outbreak in 2013, but we dont know what livestock they farmed. This would be helpful to know. So what animals live in high density in inner cities as well as farms? I think the obsession with chickens could be making us miss the problem vector.

Possibilities:-

Urban birds including pidgeons (that dont migrate)
Vermin
?? Backyard swine??? / Goats - but are these prevalent in urban centers?
Poultry - including quail, ducks, geese, as well as chickens

any other ideas?

 

[gsgs]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

remember H5N1 in Indonesia, 2006 . The chicken sequences were different from the human sequences
and we were searching for a "vector". Turned out it was still chickens.
Remember the picas,sparrows in China, they caught it from other birds.
Remember the recent domestic duck sequences from that lake in central/South China,
seemed to the origin of chicken sequences.
We have these domestic/wild ducks only in Asia

 

[Shannon Bennett]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Still doubtful. If it were prevalent in wild birds we would have found it somewhere besides Eastern China. Not that it doesn't infect birds but, I find it hard to believe the reservoir is some as yet undiscovered sparrow or nuthatch. In one years time this virus has moved less than 800 miles from Shanghai in any direction. That does not suggest to me any creature that migrates. Nor, does it make an obvious connection with the movement of domestic poultry. If that were the case, we would see pockets of cases in most major Chinese cities. Not only China but trading partners as well. I have chicken potstickers in my freezer that came from China right now.

The problem is not only avoiding sacred cows like caged birds, it is the unwavering belief that influenza only moves through bird populations before morphing into a human virus. We know flu virus infects everything from dolphins to cats. If you aren't going to look for it you aren't going to find it. We can state categorically that all flus do start out in the bird population. The problem is where do they go from there? Well pigs are one place but so far we haven't found any evidence to support that as a reservoir. What do we find in wet markets. Off the top of my head besides the vermin that are attracted to the offal are, chickens, ducks, pigeons, pigs, sheep, dogs, cats, people and evidently virtually every form of edible protein available. Why do we keep believing that birds are the key? When researchers go in to investigate possible contacts they only look for poultry or sometimes pigeon contacts. Sometimes they come up empty handed no matter how hard they try to come up with a link to fowl. No known contacts with birds. If you only look for bird contacts then no matter how remote or unlikely that contact may be it is still looked on as the probable cause.

Since people who look at reassortments never look for mammalian markers (except human), how would we know if the real villain wasn't a house cat? A mouse? If you are only going to expect a certain result in your research and you don't find it, it doesn't mean the testing was flawed it might mean your preconceived ideas are flawed.

 

[Vibrant62]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

It would be an easy argument to settle.

All that would be required is for China to conduct widespread screening e.g. to set vermin traps in an outbreak area with high activity and screen cats, dogs, pigs etc - all animal types that are for sale in wet markets or consumed as food. If that comes up 'empty handed' for H7N9 it would dismiss the argument, and send us back to chickens/ poultry.

As Shannon says, if they dont look, they wont find. And given the scale of the threat, it would not take much effort to determine.

 

[JJackson]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

We went through this with H5N1. The only question anyone seems to ask patients was about poultry contact in the last week. Given that over half of Indonesian house holds kept a chicken or duck and in China consumers traditionally eat a lot of ducks & chickens and prefer to buy them live the fact most patients have been in the proximity of a live bird in the last week is not surprising, or likely to be any different, were you asking the healthy. I always thought this was akin to asking a Western teenager if they had been in contact with a mobile phone within the last week. High positive response but not much useful data.

The Chinese authorities seem to be doing a lot of testing but does anyone have a comprehensive list of what and where. What I can tell you is that the GISAID sequence database is growing but mainly with human samples (100ish HAs) and some chickens (50ish). If you take these out and search for H7N9 in China with submission dates post 1/1/2013 (excludes environmental samples of which there are about 20) you get no mammals (pigs have been lab infected and can get it but do not seem to shed virus or infect other pigs), 2 Ducks (Anhui & Zhejiang) and 5 Pigeons (Shanghai 3, Zhejiang 1, Jiangsu 1, no Quail although these, when lab infected, did cause spread) . Not a lot to draw any conclusions on. What I can not tell you is if this is due to lack of virus or lack of testing. They may have tested 1000s of Quail but not found anything or may not have tested any/many.

As a general note when looking at sampling of wild birds and animals you have to exercise extreme caution in that many of the samples may all be from the same population on the same day - just because they happened to be out on that lake that day. Going back to the 7 ducks & pigeons in our sample a closer look at the meta-data (which is often left blank) reveals all of these were collected on either 2nd & 3rd or 16th & 17th of April last year and submitted by Harbin Vet. Research Inst. (the 3 Shanghai pigeons were all from the 2nd or 3rd)
Most of the environmental samples were also from Harbin in Apr. 2013.
P.S. While in the database looking for the data to write this I checked submissions for Korea H5N8 and there are non at the time of writing.

 

[NS1]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Jones JC, Sonnberg S, Koçer ZA, Shanmuganatham K, Seiler P, Shu Y, et al.
Possible role of songbirds and parakeets in transmission of influenza A(H7N9) virus to humans.
Emerg Infect Dis [Internet]. 2014 Mar [date cited].
http://dx.doi.org/10.3201/eid2003.131271
DOI: 10.3201/eid2003.131271

. . .

If you are only going to expect a certain result in your research and you don't find it, it doesn't mean the testing was flawed it might mean your preconceived ideas are flawed.

Absolutely, Shannon! Well said.

Absence of Evidence is not Evidence of Absence.

Not infrequently, however, public health-funded studies are designed to investigate a collection source that is known to produce negative results . . . from the onset. Those studies, repeated seemingly ad infinitum, then promote the fallacy of Evidence of Absence and are used to reinforce a literature bias.

For those who fund the studies, the judicious usage of these fallacies can be very profitable in maintaining the status quo. These designs are easy to undertake for the tenured and incurious researcher because nothing more than a rehash is required of them, little more than a headline update from their previous paper.

Using the same highways driving the same 4 door sedans, riding down the same rails in the same scheduled train passenger cars, researchers certainly don't surprisingly find themselves at the same destinations at necropsy time. Research reinforcement has displaced the basic discovery process. Managed messaging is a win / win scenario for the medical industry and the academic research industry.

Only the citizen suffers.

Because economic and logistical constraints limit all fields of scientific enquiry, the thoughtful and detailed annotation of all data collection points is essential to develop understanding of any dynamic system.

. . .

What I can not tell you is if this is due to lack of virus or lack of testing. They may have tested 1000s of Quail but not found anything or may not have tested any/many.

As a general note when looking at sampling of wild birds and animals you have to exercise extreme caution in that many of the samples may all be from the same population on the same day - just because they happened to be out on that lake that day.
. . .

Jones, Webster, Guan, Peiris, et al have demonstrated that a higher flexibility of experimental design and thought leadership will produce higher quality causal information that leads to actual understanding.

The previous testing for H7N9 and other influenza serotypes in these birds has principally focused on cloacal swabs. Many flu serotypes, those that generate intestinal viral load, are reliably detectable at that location; others aren't. Those serotypes that primarily generate a clinical upper respiratory finding, eH7N9 in songbirds, should be retrospectively expected to show an overall false negative if tested at the cloaca only.

Even a True Negative at a known non-detection area should not preclude the potential for a Positive test at the proper location and timing. A bird / mammal may be transmitting virus directly or indirectly, yet show a True Negative at these known non-detection areas.

Although the Influenza sequence database passed 100,000 sequence entries during late 2013, less than 1% of 1% of the important locations, species and relevant natural conditions are being sampled. Interpreting the Emergent H7N9 sequences that are on file, with all of their unknown unknowns (some intentionally left blank), is a work that requires the development of new insight, both technical and political.

 

[Vibrant62]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

This report released today suggests that either a) they are still swabbing cloacas and coming up negative, OR we are looking for a non-chicken vector.

China says H7N9 virus not detected in poultry farms
BEIJING, Jan. 27 (Xinhua) -- China's Ministry of Agriculture (MOA) said on Monday that the H7N9 bird flu virus has not been found in the country's poultry farms, but it has been detected in live poultry markets in some provinces.

Of the 33,400 samples from 2,402 sites tested since the beginning of 2014, eight samples tested positive for H7N9, said the ministry. The eight positive samples came from five live poultry markets in Guangdong, Fujian, and Zhejiang provinces and Guangxi Zhuang Autonomous Region, according to the MOA.

In 2013, 88 of a total of 1.63 million samples tested positive for H7N9. They came from 26 live poultry markets in 10 provinces, including Shanghai, Jiangsu, Anhui and Zhejiang.

The MOA urged local authorities to strengthen monitoring of live poultry, continue vaccine research and development, tighten cooperation in epidemic prevention and control, and prevent the virus from spreading to poultry farms.

On Sunday, three new human H7N9 cases were reported in east China's Zhejiang Province and south China's Guangdong Province.

More: http://www.shanghaidaily.com/article/article_xinhua.aspx?id=196526

 

[NS1]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

This report released today suggests that either a) they are still swabbing cloacas and coming up negative, OR we are looking for a non-chicken vector.

China says H7N9 virus not detected in poultry farms
BEIJING, Jan. 27 (Xinhua) -- China's Ministry of Agriculture (MOA) said on Monday that the H7N9 bird flu virus has not been found in the country's poultry farms, but it has been detected in live poultry markets in some provinces.

Of the 33,400 samples from 2,402 sites tested since the beginning of 2014, eight samples tested positive for H7N9, said the ministry. The eight positive samples came from five live poultry markets in Guangdong, Fujian, and Zhejiang provinces and Guangxi Zhuang Autonomous Region, according to the MOA.

In 2013, 88 of a total of 1.63 million samples tested positive for H7N9. They came from 26 live poultry markets in 10 provinces, including Shanghai, Jiangsu, Anhui and Zhejiang.

The MOA urged local authorities to strengthen monitoring of live poultry, continue vaccine research and development, tighten cooperation in epidemic prevention and control, and prevent the virus from spreading to poultry farms.

On Sunday, three new human H7N9 cases were reported in east China's Zhejiang Province and south China's Guangdong Province.

More: http://www.shanghaidaily.com/article/article_xinhua.aspx?id=196526

The non-detection at cloaca concern being discussed recently was demonstrated in songbirds.

Given the alleged millions of chickens tested with so few positives shows that either the sample location should be revised, the test should be revised or that gallinaceous avian species are not the reservoir.

 

[sharon sanders]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

If farm poultry have all tested negative then why the numerous government warnings against live poultry contact, the mention of poultry contact in patients' profiles, and the crash of the poultry industry?

It is possible to have H7N9 infections in both wild birds and domestic birds. In fact, they can re-infect each other - cycle after cycle.

 

[Vibrant62]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

What do we know?

1. That they are not finding H7N9 in poultry on farms, despite looking quite extensively. Now, in my thinking, poultry includes not just chickens but by definition is all farmed birds.

2. They are finding virus at wet markets, and some 'environmental' samples in and around wet markets.

So - what is at wet markets that isn't farmed poultry?

If its pidgeons that are the problem, could this account for environmental samples?

 

[sharon sanders]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

I do not believe the official central government announcements that H7N9 has not been found on poultry farms. I think it is a matter of food supply and the government not wanting to cut that important source of protein due to social unrest fears. Their actions indicate that their position is to warn people about poultry contact by advising them to thoroughly cook poultry and wash eggs before eating/handling.

After all, if wild birds land in live bird markets - they land on farms too.

How dumb do we look?

 

[Treyfish]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Dumb enough to believe the Canadian case was H5N1 then a few days later H7N9 is coming to light in Beijing..

 

[sharon sanders]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Here is the info on the recent Beijing H7N9 case.

Apparently he became ill on January 12, hospitalized on January 16, and tested positive for H7N9 on January 23. The next day he was transferred to another hospital in critical condition and under quarantine.

Ditan hospital is an infectious disease hospital in Beijing. It seems this person was not diagnosed for a week while a patient at the first hospital. Why is he the singular case out of 21 million?

 

[Skeeter]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Um, remember the fake "Lamb" racket from last year. The crackdown on that trade coincided with the ending of the H7N9 outbreak. I don't remember the exact mix of animals sold but some were non-domestic and one was a Mustelid.

Someone else pointed this out last year.

 

[alert]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Dumb enough to believe the Canadian case was H5N1 then a few days later H7N9 is coming to light in Beijing..

We know the Canadian case was H5N1, not H7N9, since the NML actually released the sequence from it.

What that means is that something in Beijing is capable of infecting humans with both H5N1 and H7N9. Asymptomatic poultry? Wild birds? Asymptomatic humans? A laboratory accident?

 

[Treyfish]

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

Re: H7N9 Discussion thread : recent (2014/01/23) increase in cases

We know the Canadian case was H5N1, not H7N9, since the NML actually released the sequence from it.

What that means is that something in Beijing is capable of infecting humans with both H5N1 and H7N9. Asymptomatic poultry? Wild birds? Asymptomatic humans? A laboratory accident?

Maybe she ate a pidgin?

..China's quality watchdog urged intensified H7N9 bird flu virus monitoring at the country's customs on Monday in a bid to prevent trans-border transmission of the fatal disease.

The General Administration of Quality Supervision, Inspection and Quarantine (AQSIQ) asked quarantine staff at customs to measure body temperature, conduct medical inspections and report health conditions of passengers.


People with abnormal temperature, cough, or respiratory distress will receive immediate medical examination to confirm whether the symptoms are caused by the H7N9 virus...http://www.shanghaidaily.com/article/article_xinhua.aspx?id=196607




WHO ‏<s>@</s>WHO <small class="time"> 4m </small> WHO does not advise special screening at points of entry w/ regard to <s>#</s>H7N9, nor does it currently recommend any travel, trade restrictions
..and how much longer could this statement actually have any meaning whatsoever?