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

[Shannon Bennett]

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

Now I have a few questions. If the virus is now mainly in two bird types Anseriformes (fresh water birds - Ducks) and Charadriiformes (shore birds - Gulls & waders), then why aren't we seeing more human cases outside of China? What is the intermediary in China? If it is the song birds that old men keep as pets, then why hasn't it been found in samples taken from the homes of sick patients? Why don't all victims have a pet song bird? And the question that is truly baffling me is why no human cases farther than 800 miles from the first case after one years time? Shanghai to Hong Kong 765 miles. Shanghai to Beijing 769.5 miles? Most of the birds cited migrate. Is it possible there is some unknown reservoir that is neither song birds, Charadriiformes nor Anseriformes? NS1 you stated earlier that the virus should be looked at as multi host. I certainly intuitively must agree. 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 cone into contact with that they all had in common????

[NS1]

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

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????

Humans

[Shannon Bennett]

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

Quote:
<TABLE cellSpacing=0 cellPadding=6 width="100&#37;" 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.

Added: Stream of consciousness thinking here.
Frankly given that scenario, I am hugely surprised the disease has not left the country. But then, how many business people are immune compromised. I wonder what the number is for subclinical infected? How close to the victims would you have to be to deliver a high enough viral lode to infect given the poor match? I assume family close. Should we be seeing more family clusters? No, that would mean a closer match. My glass of wine awaits. Cabernet anyone?

[JJackson]

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

Now I have a few questions. If the virus is now mainly in two bird types Anseriformes (fresh water birds - Ducks) and Charadriiformes (shore birds - Gulls & waders)

I may not have been totally clear. What I am talking about here are two overlapping genetic pools or constellations of viruses. A search for Gull HA sequences in the database is going to throw up a number of HA which we don't often discuss like H4 & H16 plus some we do like H1. For a Duck you will get a wider range with lots of familiar numbers H1, 3, 5, 7 etc. All the other Aves Orders which include the Pigeon, Sparrows and Poultry etc I do not see as being as central to the flu story. They draw from one or both of these pools - and pass material back - but I suspect they are not where flu started and are less central to flu genetics. Although I have no data to back it up I also think they probably commonly host less sero-types than you would get in a Mallard which could be expected to host every subtype in the primary pool.
NS1's last post talks about my 'Zoonotic edge' in terms of set theory, if I were to draw my pools in terms of Venn diagrams then they might be something like this.
NS1 talks about the Zoonotic edge "very slightly touching" the primary pool which I would say was about right. Any virus that makes the jump into our pool is likely to rapidly mutate into a mammalian form which then can not easily go back. Cross infections between these two pools are rare as the host are just too different. Now the primary pool and the Gulls & Other Birds pools overlap sufficiently for regular two way traffic of genetic material.

, then why aren't we seeing more human cases outside of China? What is the intermediary in China? If it is the song birds that old men keep as pets, then why hasn't it been found in samples taken from the homes of sick patients? Why don't all victims have a pet song bird? And the question that is truly baffling me is why no human cases farther than 800 miles from the first case after one years time? Shanghai to Hong Kong 765 miles. Shanghai to Beijing 769.5 miles? Most of the birds cited migrate. Is it possible there is some unknown reservoir that is neither song birds, Charadriiformes nor Anseriformes? NS1 you stated earlier that the virus should be looked at as multi host. I certainly intuitively must agree. 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 cone into contact with that they all had in common????

To this part I just do not know where we are getting infected from.

I also do not understand spread. H5N1 broke out of Qinhai and went west. We tracked it here at FT along the migratory flyways with cases popping up as it went across Asia, into Europe causing the Turkish cluster and then to Egypt and on to W Europe inc. France, Germany and the UK.
At this point I really was not expecting it to just stop and reverse. All that ground was covered in less than a year but its range has retracted out of NW Europe and it has settled for being endemic in the ME and points East. Eight years of stasis - geographically - why?
People in China do interact with Ducks as they eat them in vast numbers bought from wet markets just like the chickens.
I have a question about poultry contact in wet markets. When I was younger I lived in Saigon for a while and used to shop in the massive 'Marche Noir' covered market. Our practice was to first go to the 'pets section' (we had to call it that as my younger sister had not twigged that all the song birds in cages. snakes etc. were sold for food). You would then select some healthy looking chickens or ducks and pay for them. Then you do the rest of your shopping and come back to pick up the meat which has been killed, plucked and gutted and is in a plastic bag to take home. Given this MO yes we are buying live chickens but unless I want to pick them and feel the breasts for plumpness I need never touch the bird anymore than a supermarket chicken here. My question is - is this normal for China or do they really take the bird home live and then kill it? There is a big difference in terms of exposure.

[Shannon Bennett]

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

Your Venn diagram was inspirational. What I was foggy about is now clear.

[morningperson]

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

No message

[NS1]

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.

[Shannon Bennett]

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.

[gsgs]

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

[NS1]

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.

[NS1]

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.

[Laidback Al]

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.

[gsgs]

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.

[Laidback Al]

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.

[Vibrant62]

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.