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

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Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

No message
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Quote:
<TABLE cellSpacing=0 cellPadding=6 width="100%" border=0><TBODY><TR><TD class=alt2 style="BORDER-TOP: 1px inset; BORDER-RIGHT: 1px inset; BORDER-BOTTOM: 1px inset; BORDER-LEFT: 1px inset">Originally Posted by Shannon
People in China do not interact with ducks, gulls and waders any more than other nationalities do. Especially if they are from an urban environment as many of the patients are. Well over 100 people have gotten sick in the last month.

What did they come into contact with that they all had in common????



</TD></TR></TBODY></TABLE>
Humans


Snort. roflmbo Yes, we cannot discount humans. If a poorly matched virus is only (seriously) infecting people with compromised immune systems, then the New Year celebrations should theoretically mean an explosion of cases throughout China in the days following ~ 10/14 days. It also means there has to be a substantial number of subclinical cases wandering around Eastern China. This is an experiment I am very uncomfortable with. In fact I just got goose bumps. I suspect the reason I was so obtuse was this is a conclusion I did not want to come too. I keep reading that the polymorphisms just aren't there yet. However, as you have so aptly pointed out, we don't know exactly what combinations of polymorphisms are needed to make pandemic more likely....I think I will go pour myself an adult beverage.....maybe make it a double.

The same emotions you are feeling, the disbelief that follows a disaster epiphany, that strong desire to fiddle while the Titanic sinks, is a natural human emotion in the face of tragedy. Those managing the message depend on our suspension of belief, our ignoring the very facts in front of our faces, as they draw us with their Sirens' call.

But we are all here with a stated mission of understanding and avoiding a 1918 cataclysm redux. We all know that many ravages have occurred throughout history.

And we all know that another one is scheduled.

The Chinese holiday may or may not arc into a worldwide pandemic. Too little data has been produced during the very important smoulder stage to make an exacting prediction.

We had our chance and that opportunity was spurned by research recapitulators. Now we are at the mercy of ignorance, the most impractical of masters.

Sadly, ignorance is not bliss today. Knowledge acquisition was guaranteed given proper resource allocation then. Resources were intentionally mis-allocated toward managed messaging and away from bench science.

Not infrequently, an unguided path, a blind wandering, leads to the cliff, a fall and an undesired, but undeniable, landing.

Then it's too late . . . just 1 second after a thoughtful compass bearing would have saved the day. The tenured guide that we have paid and trusted to halt us at dangers, to prevent these falls, has abandoned us, but not before stealing our last compass. I know that all sounds very philosophical. It does and it is.

Mankind isn't impacted today so much by the lack of "science". We have plenty of "science", perhaps too much.

Mankind is hampered by a failure of philosophy concerning science, the demise of morality. To state a Hippocratic oath, to give one's mind and mettle to the pursuit of knowledge, to serve a people is no longer respected. To compromise, to hide data, to carefully construct experiments toward profit-conceived ends, now that is revered.

And the people pay.

They pay for the research and then they pay in suffering . . . unless they take a seat behind the telescope that is offered to them and finally look.

A universe of knowledge waits; non si deve aspettare per la conoscenza.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

NS1 thank you for your response. I am still having problems with the scope of the infection.

I will clarify one thing I said that obviously went awry. I do not think Chinese New Year will erupt in a pandemic. My rational was that so many people coming together in family units will increase the caseload significantly. Significantly does not mean pandemic. Although obviously it could. Since it takes a huge viral lode to infect someone, that means family units are most likely to foster that outcome. New Year is all about family coming together. That , in addition to people seated for hours in close proximity on planes, busses and of course trains should lead to a spike in the caseload. If there is a large number of people who must be subclinical, then those people will be forced to fall well within the 6 foot range for long hours as people move en masse around China. If we don't see a spike then we will have to rethink our hypothesis.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

mathematician, I think there was (almost) no H7N9 as we know it
at this time last year. It emerged later or had just emerged but
not spread much yet.
The decisive reassortment.
That's why there were no cases in Jan.2013 (IMO)
It's because all the H7N9 sequences showed little diversity,
there was no time for previous evolution.
It all started from one virus that emerged in Jan.2013
or Dec.2012
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

NS1 thank you for your response. I am still having problems with the scope of the infection.

I will clarify one thing I said that obviously went awry. I do not think Chinese New Year will erupt in a pandemic. My rational was that so many people coming together in family units will increase the caseload significantly. Significantly does not mean pandemic. Although obviously it could. Since it takes a huge viral lode to infect someone, that means family units are most likely to foster that outcome. New Year is all about family coming together. That , in addition to people seated for hours in close proximity on planes, busses and of course trains should lead to a spike in the caseload. If there is a large number of people who must be subclinical, then those people will be forced to fall well within the 6 foot range for long hours as people move en masse around China. If we don't see a spike then we will have to rethink our hypothesis.

Would we need to state a specific hypothesis first before rethinking it? We haven't configure a hypothesis yet for this discussion beyond the ongoing detailed analytics in publication.

The data shows that H7N9 is influencing pH1N1 all around the world, not just China. Therefore, at a minimum host level, we see birds as spreaders. Surprise would not enter my mind if US officials opened the books and said we had 1,000 cases under review . . . today. I should say that we would be surprised that they offered the useful facts, but we would not be surprised at the case count.

Back to the holiday portfolio of outcomes. Ignition is a strange thing. Large caseloads are not required.

Additionally, asymptomatic spread of an asymptomatic version, by definition, should not result in a larger caseload. Variably, if a sparking genetic event occurs in a subject during any of those infection chains, then a new kind of case may arise and only then the possibility exists for transmission from that patient of the new variant and / or the asymptomatic variant.

So you see, we are looking at a possibility divided by a possibility for any single infection chain.

Masses of people can congregate without sparking an outbreak. Everything depends on the sigma of the viral reservoir in the congregated population and the effects of congregation on individual immune response.

If Multiplicity of Exposure is an essential factor, as we've been told, then caseloads may increase after the 'sardine' effect is at work for a few days.

Tracing and knowing the superset of genetics at play in any given population provides a base to evaluate these potentials. While at least 3 variants were circulating in humans this fall, the Chinese told us repeatedly that "no change" had occurred. Now that the caseload is uncontainable, they present unbacked press releases hinting at a change?

With at least 3 distinct lineages in known circulation in China from the genetics and at least one more from their continual press releases about genetic change, material is available for the virus to conduct its function.

Not enough genetic information has been made public to know how far that function will proceed unabated.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

mathematician, I think there was (almost) no H7N9 as we know it
at this time last year. It emerged later or had just emerged but
not spread much yet.
The decisive reassortment.
That's why there were no cases in Jan.2013 (IMO)
It's because all the H7N9 sequences showed little diversity,
there was no time for previous evolution.
It all started from one virus that emerged in Jan.2013
or Dec.2012

The current H7N9 Emergence has been in development since 2006 from a different H7 lineage in quails and other birds. That lineage has been influencing the human Pandemic Influenza reservoir since December 2012 and perhaps much earlier, perhaps even nearing the beginning of the pH1N1 emergence.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

. . . I will clarify one thing I said that obviously went awry. I do not think Chinese New Year will erupt in a pandemic. My rational was that so many people coming together in family units will increase the caseload significantly. Significantly does not mean pandemic. . .

Although the reported cases of H7N9 are very sick, there is little evidence of H2H transmission. Only a few small family cluster have been identified with another three-person cluster reported today in Xiaoshan District in Zhejiang Province. Also, there has been few reports of HCW workers becoming infected.

MERS-CoV provides a comparative yardstick for an H7N9 epidemic outbreak with large concentrations of people. We know that MERS-CoV can be easily transmitted between humans in a hospital setting creating large clusters. But we only need to look back to Hajj 2013 to see that even with millions of people pouring into Saudi Arabia, a MERS-CoV epidemic did not occur.

We simply do not have enough credible information to estimate the number of mild and asymptomatic H7N9 cases to suggest an epidemic outbreak will occur with the aggregation of people and families during the Chinese New Year.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

however, influenza tends to reassort, that's how usually pandemics start,
how new successful strains are created.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

however, influenza tends to reassort, that's how usually pandemics start,
how new successful strains are created.

Agreed. However, we will only recognize that after it is starting to transmit, many cases have been reported, and the novel reassortant identified.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

JJ - looking at your venn diagram it brings to mind my original question to NS1 (which has been answered) i.e given the quite avian nature of pH1N1, is there a chance that it has brought the mammal 'circle' into a greater degree of overlap with its adjacent (1 or more) avian venns, leading to a higher degree of genetic exchange with the human influenza gene pool than previously. As NS1 has pointed out, without a whole heap more genetic data, there is no way anyone could say 'yes' or 'no' definitively or to what degree, but pH1N1 does seem to be interacting and influenced by H7N9. Given the severity of pH1N1 in susceptible individuals, it could yet have a sting in its tail for us all if it undergoes an H7N9 reassortment and a substantial antigenic shift. i.e its not just H7N9 we have to worry about. Lets hope not.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

We simply do not have enough credible information to estimate the number of mild and asymptomatic H7N9 cases ....

For instance, the H7N9 infection in a 2 year old boy found by routine surveillance and announced today. His case is mild. All of the cases in children have been mild. We must ask the question - How widespread is this infection if children show very few symptoms and their cases are mild?


#14 - Child, 4, onset date March 31, mild case. Shanghai

#44 - Child, 7, hospitalized April 11 Shunyi District Beijing

#61 - Child, 4, PCR positive in routine screening of contacts/neighbors of case #44 - asymptomatic Beijing

#76 - Child, 2, Onset March 17 - recovered, Shanghai treated in Hunan Province Note.

#127 - Child, 4, onset date April 27, Zaozhuang City in Central City, Shandong Province

#131 - Child (male), 9, Onset on April 26. Currently recovered and discharged after mild illness. Cangshan District, Fuzhou. Fujian province

#266 - Child, 2, found through routine surveillance from Xiang'an district, mild case hospitalized in Xiamen - Fujian province
 
Last edited:
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Deleted original post - found article referred to. I have patched in the whole thing as there is some important data in here. The 11% was the lower level of mortality in Guangzhou region, and it also talks about mild cases found through screening/contact tracing. Could we usefully reverse extrapolate this data to the wider China region?

Zhong Nanshan: H7N9 bird flu need to guard against "limited human to human transmission"

At 09:31 on January 24 2014 Source: Dayang - Guangzhou Daily
http://translate.googleusercontent.com/translate_c?depth=1&hl=en&prev=/search?q=%E5%8C%97
%25E4%25BA%25AC%2Bh7n9%26client%3Dsafari%26rls%
3Den&rurl=translate.google.com&sl=zh-CN&u=http://health.sohu.com/20140124/n394103411.shtml&usg=
ALkJrhihWr8XV-NZsTDA5_6Zq62mmXe4HA

Limited cases of human to human transmission is the occasional occurrence of relatives

Zhong Nanshan also said two possibilities of interpersonal communication does not appear

2014 New Year's Day has been less than in January, H7N9 human infection in Guangdong new bird flu cases, 20 cases, 3 deaths occurred. Yesterday, the provincial people infected with H7N9 bird flu prevention and control team leader academician Zhong Nanshan, director of the provincial CDC Zhang Yonghui, chief expert of the provincial disease control and prevention and control of infectious diseases Jianfeng, director, Institute in Guangzhou call interview. They say, H7N9 controllable and curable in Guangdong can prevent, on the "person to person" issue, Zhong Nanshan said, according to the Guangdong cases, the virus strains showed genetic variation, group two cases of the phenomenon does not exist, and therefore does not appear human to human transmission, but be wary of limited human to human transmission.

Talk therapy: 7 to 10 days longer treatment stopped

The presence of the virus in critically ill patient than the general guidelines when it comes time to be long, the longest presence of the virus 30 days.

"We treated the four cases of severe patients, one patient died, and the rest are currently (condition) stable, one case has been extubated," Zhong Nanshan estimated that two cases are expected to discharge before the Spring Festival.

The sooner the better with the effects of Tamiflu

Admitted from the current clinical situation, Zhong Nanshan that treatment is still the right direction is to early intervention neuraminidase inhibitors, "such as Tamiflu use sooner the better, to develop into the more severe the less" . He suggested that, regardless of the city or the countryside, once the live bird markets or been associated with chickens, flu-like symptoms, medication right away, except for the more expensive drug with no apparent side effects, the treatment effect is very clear, positive obvious effect.
Longer on medication, medication should be extended Zhong Nanshan pointed out, do not be like the past seven to 10 days on the disabled.
Because not only discovered the extent of critically ill patients have a great relationship with the viral load, the higher the viral copy number, the heavier the disease; and an important new finding is that the presence of the virus in critically ill patient than the general guidelines when it comes to the time of longer, the presence of the virus up to 30 days.

Drug peramivir treatment effect is not obvious

In addition to Duffy, the other a new drug peramivir effects are much outside attention. In this regard, Zhong Nanshan said that at present the drug has only been used in two critically ill patients, but did not see a significant effect, which may be related to disease progression in patients with fast, simple anti-virus does not work, oseltamivir , Zhalamiwei same everywhere. "Prepare to develop programs with the relevant departments, but how accurate comparison of other issues yet to answer," Zhong Nanshan considers it necessary to continue to observe from an academic perspective.
In addition, he reminded, H7N9 critically ill patients need to have the strength of the general hospital for emergency treatment, because more involved in multi-organ failure, such as heart, lung, liver, kidney and other organ systems circulation, even the blood system, and some also require comprehensive rescue with plasmapheresis to cross the border.

Tan epidemic: Guangdong H7N9 infection mortality by 11%

26 cases of close contacts of cases in 1076 in Guangdong, all their medical observation, now 780 people have been lifted medical isolation, more than 200 people are still observed, has not found someone occasion infection.

Jianfeng reminder, ended Jan. 22, 26 cases were reported in Guangdong, mild cases of five cases (discovered by the province's influenza surveillance system active monitoring), seven patients were cured, and death for the three cases, the overall mortality was 11% lower than the national (country overall mortality was approximately 30% of cases). "Guangdong is still in the local sporadic cases, and each case reported to the public."

Why are there before the Spring Festival peak of the epidemic? Jianfeng explained that the bird flu virus has obvious characteristics of cold-span, Guangdong is located in subtropical regions, humid climate, suitable for the survival and reproduction of the virus; addition, around the Spring Festival live poultry market trading is more active, increasing the exposure of live poultry market opportunities.

Chicken trading at vulnerable transit

Zhong Nanshan pointed out, more and more evidence that, where there are chickens trade, transit places most prone to cross-infection.

Monitor displays information from the agricultural sector, the province of all breeding farms are not detected H7N9 avian influenza virus, Jianfeng, due to the virus originated in East China, East China and supply of poultry farms, mainly in Guangdong, "so experts speculate, virus is mainly spread and diffusion through the market route. "

Be wary of limited human to human transmission

At present four cases of H7N9 infection were reported in Guangzhou, two cases of father and daughter, has the disease, whether the person signs successor exists?

In this regard, Jianfeng response, after the onset of detailed, close contact, such as epidemiology, there is currently no evidence of human to human transmission of the existence of these two cases, there is exposure to live poultry markets, "the father of the stalls in a dish market, but children and the grandmother went to another market to buy food every day, we can not distinguish between what is human to human transmission, or the role of the market. "

"We are also very concerned about the signs of human to human transmission, but to achieve interpersonal communication, it is necessary to have a gene mutation in interpersonal communication, and second, there will be groups of cases," Zhong Nanshan said that at present none of these two possibilities to achieve, including before the emergence Doctors in Shanghai died after infection, and later found that the hospital where he was surrounded by live bird markets, drove a motorcycle to work, there is a certain history of contact with live poultry markets, and people in close contact with patients are not infected.

Zhong Nanshan reminded to be very wary of limited human to human transmission. For example, Jiangsu daughter's case, her personal care after his father got sick, was not to emphasize her daughter live poultry market, but clothes, **** urinated all her care; Guangzhou father and daughter cases also diagnosed six days after his father, daughter mild infection. Therefore, he suggested: "Patients not diagnosed before, but there is history of exposure to poultry and flu-like symptoms, were not in close contact with their families too."

"Limited human to human transmission, is the occasional, relatives, kinship which occurred a few." Jianfeng explained.

Most people infected with H7N9 is not easy

"Guangdong isolated 15 people infected with H7N9 avian influenza virus strains, the provincial disease control do sequencing, sequencing also sent to Beijing Influenza Center, are not mutation." Zhang Yonghui introduction.
Jianfeng said that epidemiological studies recognized, H7N9 is not susceptible to most people, "nearly a year, the number of cases nationwide just over 200 cases"; from virological analysis also found no public health significance of mutations, including the ability to communicate, virulence, drug resistance, there is no resistance found.

Tan Prevention: centralized slaughtering of live poultry chilled listed

It is understood that the Guangdong annual capacity of 1.1 billion poultry slaughter, meat consumption habits to use of live poultry, hence the chance of exposure in live bird markets.

Spring Festival is approaching, how do H7N9 prevention and control? Zhong Nanshan said it is still an urgent need to change eating habits, to strengthen the government's industrial upgrading of the live bird markets, standardized management. In the reported cases, more than 80% of patients had a clear history of contact with live poultry markets, and from the current monitoring perspective, focus on keeping the virus has not been found, the problem still lies in the backyard and markets do best centralized slaughter, slaughter-place, chilled market.

Be sure to wash your hands after touching buy chicken chicken

Similarly shopped in live bird markets, why some people infected with the disease, but some people right? Zhong Nanshan, explained that this is a lot of misunderstanding and questions of human existence, or not infected with the human body may also be susceptible genes, "in my opinion, is not one to be infected by the market, but we must have been to this place after advocate, Be sure to wash your hands. " He explained that in addition to hand washing, once the symptoms should seek immediate medical attention and inform if there is live bird markets exposure history.

Jianfeng said, you can buy chicken chicken, as long as the masses of the people to eat cooked cooked birds, chickens and ducks are no problem, but be sure to wash your hands immediately after contact with live birds.
Chopping raw and cooked separately recommended home
Jianfeng strongly recommend chopping separate raw and cooked at home, cut off the fresh chickens and ducks, not to chop cooked poached; cut off the meat, the best scalded with boiling water, may very well prevent transmission of the virus or infection.

In addition, experts reminded the public, but also to differentiate better between colds and coughs and flu-like symptoms, the flu in addition to colds and coughs, but also fever, body pain and other symptoms, if there would be further vigilant.

Bulletin: Shenzhen, Guangzhou, Foshan, add one case each one cases were cured

Another hearing yesterday informed the Guangdong Provincial Health and Family Planning Commission of Shenzhen 1 new confirmed cases of human infection with H7N9 avian influenza, there are two cases cured.

Patients Zhang, female, 34 years old, currently residing in Baoan, Shenzhen, January 23 confirmed cases of human infection of H7N9 avian influenza, the patient is currently in critical condition in Shenzhen designated hospital admission. In addition, Guangzhou City on January 18 confirmed cases Panmou, Foshan City, January 10, Liu confirmed cases were cured and discharged on January 22. So far, the province's total of seven cases of human infection with H7N9 avian flu cured.

Since August 2013 the first reported case in Huizhou since, as of January 23, 2014, the province reported a total of 27 cases of patients have been cured in 7 cases, 3 deaths (residence were in Dongguan, Yangjiang, Guangzhou), there are still 17 patients admitted to hospital in point. By patient place of residence, Guangzhou four cases, 8 cases in Shenzhen, Foshan eight cases, one case of Huizhou, Dongguan three cases, Yangjiang 3 cases.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

NS1 I know you will correct me if I make a blunder.

  1. You stated what these cases all have in common are other humans.
  2. Fact: The only people who are becoming severely ill are those who have compromised immune systems.
  3. Fact: The only people who are severely ill are on average older than 54.
  4. Fact: We have discovered a small number of sick children.
  5. Fact: The flu exhibits mild flu symptoms in all the children thus far.
  6. Fact: The virus is as yet difficult to pass h2h.
  7. Fact: The virus in its present form requires a high viral lode to make a person sick.
  8. Fact: Chinese New Year is the largest annual human migration on earth.
  9. Fact: People are traveling in close proximity to multiple strangers for several hours. i.e. planes, trains, busses... They also will be spending time in close quarters with multiple family members of all ages from all over China.
  10. Fact: If humans are the vector then what is needed to pass the virus to another is close proximity for a period of time exceeding a casual encounter.
Hypothesis: If we put a large number of people in close proximity for a lengthy period of time, some of which are older than 54 and have compromised immune systems, and within this group are children (or others with strong immune systems) who are subclinical or only exhibiting mild flu symptoms, then those who are traveling or staying at their final destinations who meet the criteria for compromised immune systems and are older than 54 should then have a much greater likelihood of becoming ill. The number of sick older adults will depend on how many people are sub clinically sick and have spent hours in their company at close range.

If the number of sick following the New Year celebrations does not increase given the already on-going experiment, then I am going to suggest that the number of those who show no or little symptoms but are actually sick is a very small number. If however, the number of sick increases significantly then the number of subclinical cases is high.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

JJ - looking at your venn diagram it brings to mind my original question to NS1 (which has been answered) i.e given the quite avian nature of pH1N1, is there a chance that it has brought the mammal 'circle' into a greater degree of overlap with its adjacent (1 or more) avian venns, leading to a higher degree of genetic exchange with the human influenza gene pool than previously.
While I may have apologised for the length of the the first of the two part post - in which the venn bit was an attempt at clarification - I obvious had to leave out a vast amount in trying to express my, possibly erroneous, overview of the AIV Type A genetic pool in a few paragraphs. One thing I glossed over is the prevalence of different HAs and their position(s) in the venn. Also bear in mind that the HA numbers were assigned as new sero-types were found so the common HAs were found first like H1 while H16 was not allocated until 2004 when it was first identified in a wader. While our H1N1(2009) is an H1 it is one of many and all the venn groups include H1s which are fairly specific to there respective host. In the 'H5N1 and H1N1(2009) reassortment – are we quacking up the wrong tree?' thread I was looking at the same questions but with H5N1<=>H1N1(2009) in mind and could only find one Turkey which had a high homology with H1N1(2009) everything else aligned with avian index H1s.

I have created a spread sheet today which I will try and post a table from below. It also has quite a lot of explanatory text which would not be paste-able. Also I can not think of a way of fully explaining what it means without writing a book length post, so what I suggest is if anyone is interested PM me and I will send you a copy and, if there is interest, I will try and set up a Skype call or conference to discuss what it means.
Anyway here is the core table. I queered the GISAID database for samples from 1/1/2000 to present for each HA(1 to 16) for each of the columns and just counted the hits. The sheet also has info like which NAs were associated with given HAs for each column and the A/anuhi/1/2013(H7N9) type numbers for 'Zoonotic edge' events etc.
HA table.webp
The area highlighted in red are the endemic mammalian flus in pigs and humans. The blue bit are 'zoonotic edge' incidents. Some of the other main points are
The collection bias towards humans and commercially important species.
The fact that the ducks catch everything (on the sheet, but not shown, each H also has multiple Ns).
H13 and H16 very much Gull viruses but the Duck/Gull interface is porous.
The chickens - while better than the mammals - are still lot a more isolated from the primary (Duck) and secondary (Gull/wader) groups also where there is exchange it is with Duck group.
The numbers in the table don't add up as the Total include everything including the third venn bird group, Horse, Dogs, environmental samples etc
I have not add a non-Duck/Gull avian group because there is no easy search that would cover them.

Based on the table I would speculate that flu developed in the primary group (sometime after birds split form reptiles), found the Gull group easy to get into, the AIV 'improved' its efficiency producing H13 & 16 which, when fully wader optimised, were then too different to go back, same for mammals.
If I try and incorporate these finding into my venn 2.0 it might look something like this.
Venn2.webp
The red line is the zoonotic edge, The Hs are forms that have now wandered too far from the pack to join the orgy going on in the middle.
Without a 3rd dimension it is not easy to draw but humans have another 'Zoonotic edge' with the pigs which both have edges with the Ducks group and 3rd bird group (which inc. poultry).
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Fact: The only people who are becoming severely ill are those who have compromised immune systems.
I am not sure about that. I have noticed 'hypertension' popping up fairly regularly in the meta-data may this be a 'risk factor'? (not a quantitative finding I was just surprised to see it coming up).
It is not obvious to me why it might be - more an MD question.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Did a google scholar search and came up with several papers saying hypertension does lead to a poorly functioning immune system. I imported one of the studies.

http://www.karger.com/Article/FullText/216188

http://ajpregu.physiology.org/content/260/3/R459.short

Cytokinic dysregulation is a factor in mis-firing variant vascular pressuring. Though poorly understood, the hormones used in biological dialogue are involved in intricate feedback loops. Systems cross more frequently than medicine, at present, has cared to examine.

An individual already suffering from something beyond vascular suppleness failure, such as a signalling flaw, also is probable to have a compromised immune signalling system.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

You stated what these cases all have in common are other humans.












Amended Hypohesis
  1. Fact: People who are becoming severely ill are those who have compromised immune systems.
  2. Fact: People who are severely ill are typically older than 54.
  3. Fact: We have discovered a small number of sick children.
  4. Fact: The flu exhibits mild flu symptoms in all the children thus far.
  5. Fact: The virus is as yet difficult to pass h2h.
  6. Fact: The virus in its present form requires a high viral lode to cause infection.
  7. Fact: Chinese New Year is the largest annual human migration on earth.
  8. Fact: People are traveling in close proximity to multiple strangers for several hours. i.e. planes, trains, busses... They also will be spending time in close quarters with multiple family members of all ages from all over China.
  9. Fact: If humans are the vector then what is needed to pass the virus to another is close proximity for a period of time exceeding a casual encounter.
Hypothesis: If we put a large number of people in close proximity for a lengthy period of time, some of whom are older than 54 and have compromised immune systems, and within this group are children (or others with strong immune systems) who are subclinical or only exhibiting mild flu symptoms, then those who are traveling or staying at their final destinations who meet the criteria for compromised immune systems and are older than 54 should then have a much greater likelihood of becoming ill. The number of sick older adults will depend on how many people are sub- clinically sick and have spent hours in their company at close range.

If the number of sick increases 10/14 days following the New Year celebrations, and is statistically significant as compared to the graph LaidbackAl has posted, we may assume some factor has influenced that rise. I postulate that rise may be due to an extant number of sub-clinical patients infecting those who are susceptible due to age and health. While this experiment does not prove sub-clinical cases, it does suggest the possibility of sub-clinical cases.



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Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

JJ - got your point on the Haemaglutinin component of flu genetics, which ultimiately is the key dividing line between species susceptibility. However, the thing I was wondering about is if the other internal flu genes play a greater part in host adaptation than we have previously supposed and that these genes might have a greater degree of overlap between avain and mammalian species than current thinking allows for.

We have seen some evidence of this in the M gene from pH1N1.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

Given the seemingly growing number of conditions that quality as underlying health issues that may compromise immune response, it seems that the majority of the population would fit into this category.

I'm sure obesity isn't nearly as much of a factor in China as it is in the US. I found it odd when one report on hospitalization pH1N1 cases in the US stated that 50% of the cases were considered obese. When you look at the criteria describing obesity, it's not what first comes to mind. Many reasonably healthy looking individuals meet the medical criteria for obesity. I'd be willing to bet that the percentage of hospitalized patients with flu in the US that are obese is similar to the percentage in the population at large.

Similarly, given the living conditions in many parts of China (air pollution, unsanitary or crowded conditions, etc.), it seems possible that a majority of people would have one or more underlying health conditions such that the government could claim that those who have died had compromised immune systems.
 
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