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H7N9 – Discussion, April 1, 2013 to June 3, 2013 (Closed)

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Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

the G at position 237 codes as GGA
G237S is a concern-mutation

but it's nor so easy, 2 nucleotide-changes are required

if GGA mutates to GGC (still G, synonymous)
then G237S suddenly becomes much more likely ...


NSABB please censor this post before the evil
Kawaoka and Fouchier see it
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

suppose researcher YK puts A711C(4) into a ferret and it escapes.
Then ferretcatcher OL catches it and sells it on the wet ferret market in Shanghai.
Suppose that during the years 711C replaces 711A in H7N2 poultry.
Then researcher RF , buys a flu sample with 711C and finds
mutation G709A through passage in ferrets, which he had missed before
since he previously had started with 711A.
Then he publishes his result and the world panics.
Could we hold YK responsible ?
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I'm calling for transmission certificates for confirmed cases as we have death certificates
or birth certificates.
They should have the history of animal contacts, locations, travel history, and human contacts
that had animal contacts, medical conditions, treatment, swabs, sequences.
They should be public to researchers in anonymized form.

There is so much speculation about the contacting chain but rarely is this backed
with statistical data from the actual cases.


----------------------------
pets,jobs,tasks in household,grandchildren,walks in the park, own conjecture, where they got it from
(10 most likely)
--------------------------------
same for seasonal flu (sample of some thousand statistically random certificates)
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I'm calling for transmission certificates for confirmed cases as we have death certificates
or birth certificates.
They should have the history of animal contacts, locations, travel history, and human contacts
that had animal contacts, medical conditions, treatment, swabs, sequences.
They should be public to researchers in anonymized form
. . . . .
A review of the article in the NEJM entitled Preliminary Report: Epidemiology of the Influenza A (H7N9) Outbreak in China shows that the Chinese doctors and public health officials who authored the article have access to the specific details of each of the first 82 cases of A(H7N9). Those details have not been made public and we have no way of verifying the conclusions and interpretations of the authors of the article.

These data should be publicly released.

FluTrackers has continually campaigned over the years for open access to data on novel influenza infections. see: Call for Open Data on All Influenza, Human & Animal, from Around the World
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Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

There has also been reference to a duck sequence which was said to be highly homologous with the others sequences but no duck sequences have been released.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

weren't all tested ducks negative ?

check the geese, especially when they are bar-headed

http://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H7N9

-------------------edit-------------------
http://www.cidrap.umn.edu/cidrap/content/influenza/avianflu/news/apr1213china.html
Apr.12,2013 - H7N9 detected in ducks
In other developments, China's National Avian Flu Reference Laboratory said today
that the H7N9 virus has been detected in samples of ducks from the city of Huzhou
in Zhejiang province, the Global Times, an English-language newspaper based in Beijing,
reported. Two of 10 samples were positive. The findings prompted the culling of 7,000 birds
in one of the city's major trading markets, and sales at 15 other live-bird markets have
been suspended
-----------------------------------------------
http://www.promedmail.org/direct.php?id=20130426.1674487
Fri 26 Apr 2013
390628 samples from 13014 monitoring points
218897 tested :150837 serological and 68060 for antigen
46 out of 68060 were positive

wild pigeon in Nanjing,
pigeon farm in Nantong
all Ducks samples of thirty, failed to reveal the H7N9 virus
------------------------------------------------
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Malik Peiris told reporter about 'missing ''poultry'' link' in the H7N9 event.

Source: VOA, xhttp://www.voafanti.com/gate/big5/direct.voanews.com/audiovideo/cn-china-bird-flu

Credit:
VOA - Broadcasting Board of Governors

H7N9, the latest variant of the avian flu virus, has spread 700 kilometers across three Chinese provinces since it was identified last month. With researchers struggling to identify how the disease is transmitted, concern is mounting about its danger to humans. Ivan Broadhead has this report from Hong Kong.

Transcript

China Bird Flu (TV) Hopes and Fears in China Bird Flu Battle

DATE: 04/09/2013
PUBLISHED AT:
BYLINE: Ivan Broadhead
DATELINE: Hong Kong
CAMERA: VIDEO EDITOR:
VIDEO FROM:
NUMBER:
TYPE: VPKGN TRT: 2:53))
((INTRO ))

[[H7N9, the latest variant of the avian flu virus, has spread 700 kilometers across three Chinese provinces since it was identified last month. With researchers struggling to identify how the disease is transmitted, concern is mounting about its danger to humans. Ivan Broadhead has this report from Hong Kong. ]]

((AX-APTN-2030:SKoreaPoult 12-23 0662 AP-APTN-2030: SKorea Poultry Tuesday, 23 December 2003 5. Pan along racks holding chickens 2.Medium shot of dead chickens being dumped in truck 4. Various shots of people in protective clothing putting live chickens in bags))

((NARRATOR))

Authorities culled poultry in Shanghai markets after detecting H7N9 in local pigeons. Taiwan will make anti-viral drugs available for public purchase, at a subsidized price, through April.

((AP-APTN-0830: ++<< China Flu>> Wednesday, 13 May 2009 10. Medical staff inside patients' room 11. Doctors inspecting an X-ray film 12. Researcher inspecting tests under microscope ))

While China reported that a four-year-old boy made a full recovery from H7N9 flu, of 24 known cases, seven people have died.

((PEIRIS SET UP SHOT FROM BROLL))

Professor Malik Peiris is director of the Pasteur Research Centre at Hong Kong University.

((PEIRIS INTERVIEW CLIP 1 FROM IVAN?S FOOTAGE))
((PROF MALIK PEIRIS, HKU PASTEUR RESEARCH CENTRE))

?You have to be cautious about interpreting mortality rates because, usually, only the most severe cases are investigated. There could be milder cases that go unrecognized. So on the one hand this would make the mortality and the severity less. But on the other, it would mean there is more transmission occurring in humans too.?

((BC-APTN-0930:ChinaBirdFl 11-29 0619 AP-APTN-0930: China Bird Flu Tuesday, 29 November 2005 3. Various of agricultural workers spraying disinfectant on chicken cages 4. Close up chickens in cage 5. Wide of medical staff inspecting chicken house 6. Various of medical staff giving chicken vaccine shot))

((NARRATOR))

Beginning April 11, imported live poultry will only be sold in Hong Kong after a 3-percent sample is tested for H7N9. To develop vaccines and break the infection cycle, Peris says, the source of the outbreak must be identified.

((PEIRIS FOOTAGE FROM IVAN))
((PROF MALIK PEIRIS, HKU PASTEUR RESEARCH CENTRE))

?It is an unpredictable virus. There are hundreds of people working closely with poultry who do not seem to get infected. But there is the one person who may have quite a tenuous contact who ((does)). "

((B-ROLL OVER SOUND BITE)) AX-APTN-1000:++SKoreaBir 01-27 0530 AP-APTN-1000: ++SKorea << Bird Flu>> Tuesday, 27 January 2004 1. Pan of chicken farms in Cheonan where one farm had confirmed birdflu infection 2. Various dead chickens on the ground inside chicken farm 3. Officials in decontamination suits 4. Dead chicken on ground 7. Various shots of dead chickens))

((PEIRIS SOUND BITE CONTINUED))

?What is crucial is to go upstream, along the poultry marketing chain, ideally to the farms, and identify which species is the main source.?

((BROLL ABRAHAM FROM IVAN ))

((NARRATOR))

Thomas Abraham, who wrote a book about the 2003 SARS epidemic, says the Chinese government cover-up which contributed to the spread of SARS, is unlikely to be repeated with H7N9.

((ABRAHAM FOOTAGE FROM IVAN ))
((THOMAS ABRAHAM, PUBLIC HEALTH MEDIA PROGRAM))

?One of the early ((H7N9)) cases in Shanghai, even though the hospital said nothing, the patient?s admission slip was photographed and put on ((the Chinese website)) Weibo. This kind of information flow is a dam that is unstoppable."

((AX-APTN-2030:SKoreaPoult 12-23 0662 AP-APTN-2030: SKorea Poultry Tuesday, 23 December 2003 16. Wide shot of quarantine people kicking chickens 12. Pan of people dumping eggs 13. Close up of eggs culled 14. Zoom out quarantine people dumping dead chickens 15. Close up of chickens dumped))

((NARRATOR))

While World Health Organization officials say there is no need for panic, Laurie Garrett, an expert at the Council on Foreign Relations, is concerned that the H7N9 death toll will rise.

((GARRETT FOOTAGE IN DC FILE))
((LAURIE GARRETT, COUNCIL ON FOREIGN RELATIONS))

?What 2009 taught us with swine flu is that global solidarity can break down very fast. Countries start closing airports and quarantining travelers. They start hoarding drugs and vaccines. It is not a pretty picture.?

((ANY CHANCE OF FOOTAGE OF HONG KONG/CHINA PEOPLE IN MASKS LUIS/AMY?))

((NARRATOR))

With public fear an issue, researchers in Hong Kong have announced they will revisit a 2009 study to confirm that surgical masks - widely worn during flu season - are indeed 70 percent effective in preventing the spread of flu viruses.

(...)

-
------
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I have been having a look at the latest Chinese human H7N9 sequence release A/Zhejiang/DTID-ZJU01/2013 and there are a few points of interest.
Firstly it is very similar to the other released sequences generally where the Shanghai/1 sequence varied from the others this one is more like S2 and H1. The two strands of interest where it does vary are PB2 and NA.

Starting with PB2 it has K627 which puts it a odds with all the other mammal sequences (they have E627) but in-line with the birds. I don't find this odd as I have been arguing that the most likely scenario is that birds are the host reservoir with K627 and that the human infections from birds start with that but select for E627K mutations as they work better in mammals. The second change is more interesting it is D701N. This is also a mammalian trait and improves the viruses' RNP's ability to traverse a mammalian cell's nuclear membrane which it needs to do to get to where it becomes biologically active.
I do not know if the NA changes have any biological significance they are all close together (possibly a recombination event?) and as far as I know well away from the Oseltamivir binding pocket but I would like someone more knowledgeable to confirm that (a lack of numeric proximity need not imply proteins are not adjacent in the tertiary protein structure).
The NA changes are W434L, S437G & N438D.
One other change I noted was on NS T170I.
All the numbers are as per the alignments and may differ from other numberings.
Edit:
Does anyone know of a good numbering off sets table for all strands?

Numbering provided at detailed evaluation:

Human Emergent H7N9 from Zhejiang, Jiangsu and Shanghai
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

I am sorry NS1 but I did not understand what you were saying in your post. That certain species tend to use one triplet while another species uses an alternative. e.g. Glycine can be coded for GGx where x is any of the four alternatives and in birds x is usually different to mammals? If that is what you are saying then I have no problem with that and it is not at odds with what I wrote. If you are saying that the finished protein is in anyway different please post back because that would mean I have badly misunderstood something (by no means impossible) and I need to work out what lest I mislead anyone else.

We'd like to understand why multiple codings per amino occur if "no difference" exists in the resulting amino sequences?

Substantial room for doubt exists when some aminos code 6 ways and those codings readily correlate to host species. Form follows function in the viral world. Science may find that some currently unmeasured characteristic will account for the difference.

What is the functional difference? We don't know yet . . . but we've begun modifying our language so that we may investigate for causality.
 
Re: H7N9 ? Discussion

Re: H7N9 ? Discussion

Journal of the Formosan Medical Association
Available online 3 June 2013

Is avian influenza A (H7N9) virus staggering its way to humans?

Guang-Wu Chena, b, , , Michael M.C. Laic, d, Suh-Chin Wue, Shih-Cheng Changb, Li-Min Huangf, Shin-Ru Shihb, g, h,
...
Results
This report analyzed the genomic characteristics of this new H7N9 virus. Nucleotide sequence analysis clearly reveals its origin from avian viruses. In this article, we particularly focus on its internal genes that are found to derive from H9N2?another subtype of avian influenza A virus which has been circulating in birds for years. Amino acid sequences at species-specific genomic positions were examined. Although the new virus contains mostly avian-like residues at these signature positions, it does contain several human-like signatures. For instance, at the position 627 of PB2, the new virus has human-characteristic K instead of avian-characteristic E; in addition, PB2-627K, PA-100A, PA-356R, and PA-409N are also human-like signatures in the new H7N9 virus.

Conclusion
The new H7N9 is an avian influenza A virus; however, it does harbor several human virus-like signatures, which raises great concern that it may have a higher probability to cross species barriers and infect humans.

(need to purchase to read the full report)

http://www.sciencedirect.com/science/article/pii/S0929664613001654
 
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