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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+

WOW that was fast. Very impressive.

In a display of intellectual and logistical expertise, the Public Health Laboratory Services Branch, Centre for Health Protection in Kowloon, Hong Kong sampled material from a man on January 28, 2014, sequenced, annotated and published early on January 30, 2014, much less than 48 hours after the sample, autopsy to full genetic report in 2 days.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

Rapid Release
Emergent H7N9
Centre for Health Protection
Hong Kong

The sequences from Hong Kong in January demonstrate a virus on the move.

In a display of intellectual and logistical expertise, the Public Health Laboratory Services Branch, Centre for Health Protection in Kowloon, Hong Kong sampled material from a man on January 28, 2014, sequenced, annotated and published early on January 30, 2014, much less than 48 hours after the sample, autopsy to full genetic report in 2 days.

We are grateful for their demonstration of intellectual prowess because for this one, timeliness is extremely important.

Early January Hong Kong has homology at the HA to the circulating human strains with the gain of material from pH1N1. More recent Hong Kong data shows a variance at key aminos from the circulating human Emergent H7N9 Hemagglutinin segments. The reservoir in China is under revision and is quite potentially now attractant to pH1N1 sub-segment input.

We'd like to see the clinicals on the latest case and additional passage strategies when available.

If a dominant input reservoir switch is at work from sH3N2 to pH1N1 for new genetic material, potential risk increases due to the established "give / take" relationship of H7 to pH1N1.

From the press release today:

30 January 2014

Epidemiological investigation and follow-up actions by CHP on confirmed human case of avian influenza A(H7N9)

snip

"Upon genetic analysis by the PHLSB, genes of the virus from the patient's specimen were determined to be of avian origin. There were no significant differences from H7N9 viruses detected so far in the Mainland and Hong Kong, nor was there evidence of genetic reassortment with genes of human influenza origin or resistance to the antiviral Tamiflu," the spokesman remarked."

http://www.chp.gov.hk/en/view_content/33300.html
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

My thanks to HK CHP for being good at filling out the sequence meta-data as well.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

I know I stand on the outside of accepted thought here but, I too am doubtful that chickens are the vector. If they are, I don't think they are the only vector. When seeing a doctor for their allotted 6 minutes, one of the questions asked is if they have been in contact with chickens. If they don't answer in the affirmative they don't have H7N9. Therefore, they have H1N1. I cannot help but wonder how many cases are missed? My guess is a lot are slipping through the cracks. Roughly 30% say they have not been in contact with live chickens. If they say they haven't been in contact and either die or sicken, to the point they cannot answer questions, the doctors later try to reconstruct their lives through family. The assumption is if the family says they don't know of any contact with chickens then they must be ignorant or mistaken. The person really must have come into contact because that is how you get H7N9. Entrenched thinking.

I agree Shannon. Research suggest that mice, in particular, are a very possible vector. I posted a number of studies last year and just found the following:

ABSTRACT A novel avian-origin influenza A/H7N9 virus infecting humans was first identified in March 2013 and, as of 30 May
2013, has caused 132 human infections leading to 33 deaths. Phylogenetic studies suggest that this virus is a reassortant, with the
surface hemagglutinin (HA) and neuraminidase (NA) genes being derived from duck and wild-bird viruses, respectively, while
the six ?internal gene segments? were derived from poultry H9N2 viruses. Here we determine the pathogenicity of a human
A/Shanghai/2/2013 (Sh2/H7N9) virus in healthy adult mice in comparison with that of A/chicken/Hong Kong/HH8/2010 (ck/
H9N2) virus, highly pathogenic avian influenza (HPAI) A/Hong Kong/483/1997 (483/H5N1) virus, and a duck influenza A H7N9
virus of different genetic derivation, A/duck/Jiangxi/3286/2009 (dk/H7N9). Intranasal infection of mice with Sh2/H7N9 virus
doses of 103, 104, and 105 PFU led to significant weight loss without fatality.
This virus was more pathogenic than dk/H7N9 and
ck/H9N2 virus, which has six internal gene segments that are genetically similar to Sh2/H7N9. Sh2/H7N9 replicated well in the
nasal cavity and lung, but there was no evidence of virus dissemination beyond the respiratory tract. Mice infected with Sh2/
H7N9 produced higher levels of proinflammatory cytokines in the lung and serum than did ck/H9N2 and dk/H7N9 but lower
levels than 483/H5N1. Cytokine induction was positively correlated with virus load in the lung at early stages of infection. Our
results suggest that Sh2/H7N9 virus is able to replicate and cause disease in mice without prior adaptation but is less pathogenic
than 483/H5N1 virus.

http://mbio.asm.org/content/4/4/e00362-13.full.pdf
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

From the press release today:

30 January 2014

Epidemiological investigation and follow-up actions by CHP on confirmed human case of avian influenza A(H7N9)

snip

"Upon genetic analysis by the PHLSB, genes of the virus from the patient's specimen were determined to be of avian origin. There were no significant differences from H7N9 viruses detected so far in the Mainland and Hong Kong, nor was there evidence of genetic reassortment with genes of human influenza origin or resistance to the antiviral Tamiflu," the spokesman remarked."

http://www.chp.gov.hk/en/view_content/33300.html

The recent polymorphic additions to the human Emergent H7N9 reservoir that have been dropped from this latest sequence are quite significant, although the underlying framework of the HA is without ReAssortment (as expected).

Those significant drops on the current sequence considered next to the multiple pH1N1 adoptions on the HK sequence from earlier this month increase the HK reservoir risk potential due to present tense high plasticity on well-studied and on under-studied regions of the Emergent H7N9 H7 Hemagglutinin.

As previously noted, we'd appreciate seeing multiple passage strategies, especially LLC against Avian-inductive pathways, on all available Hong Kong human sequences.

We make this request understanding the cost and re-allocation of resources required. Defining the revision mechanism at this point in time in this particular disease pool is essential to mediating pandemic risk and, more importantly, in preventing a black swan event.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

snip

Editor?s note: Dr. Tom Frieden is the director for the Center for Disease Control. The views expressed are his own.
Today marks the Lunar New Year ? and the world?s largest annual migration. There will be more than 3.6 billion transit trips within China, in addition to countless international trips. Yet this celebration comes at a time of growing concern about the H7N9 avian influenza virus. And this concern is not unfounded ? should this virus change into a form that easily spreads between people, the world?s next pandemic could occur in the next three weeks.


http://www.flutrackers.com/forum/showthread.php?t=217856
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

temperature up in Shanghai
 

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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+

snip

Editor?s note: Dr. Tom Frieden is the director for the Center for Disease Control. The views expressed are his own.
Today marks the Lunar New Year ? and the world?s largest annual migration. There will be more than 3.6 billion transit trips within China, in addition to countless international trips. Yet this celebration comes at a time of growing concern about the H7N9 avian influenza virus. And this concern is not unfounded ? should this virus change into a form that easily spreads between people, the world?s next pandemic could occur in the next three weeks.


http://www.flutrackers.com/forum/showthread.php?t=217856

A change of strategy? A sincere warning? A probe? Now they are attempting to measure how the public will take the news, not the actual biological impact of the pathogenic event.

Predictions like that should be rather foregone for an organisation that is holding hundreds of relevant sequences from publication. The H7N9 reservoir has been actively influencing US pH1N1 for over a year, whether via avian transfer or human sub-clinical co-infection. The CDC has the information to provide a more adept guidance, but this Lunar proclamation is no more a sensible warning than it is a probe to determine net twitter traffic.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

..... The CDC has the information to provide a more adept guidance, but this Lunar proclamation is no more a sensible warning than it is a probe to determine net twitter traffic.
:applause:Not a word of this huge epidemic situation on any TV screens..but I did see it on a crwly one time..8 days ago..:rolleyes:
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

I think it does not matter if no one else has the opinion that genetic bits of H1N1pdm09 are potentially influencing H7N9. The fact is that the world is a huge mixing bowl of genetic material, of all sorts, that interact with no rules. We don't even know what we don't know.

H7N9 is an active avian flu outbreak in Eastern China with an approximate case fatality rate of 9% in the 2nd wave. H7N9 has the capability to develop into a more easily transmissible virus at any time.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

I think it does not matter if no one else has the opinion that genetic bits of H1N1pdm09 are potentially influencing H7N9. The fact is that the world is a huge mixing bowl of genetic material, of all sorts, that interact with no rules. We don't even know what we don't know.

H7N9 is an active avian flu outbreak in Eastern China with an approximate case fatality rate of 9% in the 2nd wave. H7N9 has the capability to develop into a more easily transmissible virus at any time.

No rules? Wrong!

The rules exist and are playing everytime everywhere: it is called evolution.

The apparent cfr of H7N9 is not well known but should be for hospitalized patient around 33%. Taking into account the tip-of-iceberg phenomenon, it is possible that a number of mild and undiagnosed cases may reduce the actual cfr below the 10% or less.

A pandemic species descending from H7N9 will have an unknown cfr.

The interference between subtypes is another unknown but the co-circulation of H1pdm09 and H7N9 should be investigated better.

H1pdm09 is a dominant strain in youngsters and this hardly would not play a role in current H7N9 epidemiology.

Other mechanism, for example the antigen dependent enhancement (A.D.E.) may also play a role.

Today Clinical Infectious Diseases journal published an open access report on the first wave H7N9 outbreak cases' characteristics. I recommend strongly a read.

Perhaps the most important thing in the paper is the conclusion that host factors may contribute to the epidemiology and pathology observed so far.

Host factors are overlooked regularly both by health agencies and flublogia and this is for me a mistake.

We could help people to reduce risk of fall ill and developing an adverse outcome disease if we attempt to search and disseminate information about the correlations between hosts factors and illness...

Or - as Sharon said - there is not further space for babbling and it is time to seek for a refuge.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

See Sci Library for Reference:

Comparison of patients hospitalized with influenza A H7N9, H5N1, and 2009 pandemic H1N1


(...)


Table 1. Characteristics of subjects hospitalized with H7N9, H5N1, and pH1N1.

[H7N9 (ref group) - H5N1 - P_value - pH1N1 - P-value]

  • Median age (range) - 63 (4, 91) - 26 (1, 75) - <0.001 - 25 (0, 100) - <0.001
  • Interval from onset ? admission days (IQR) - 4 (3,6) - 5 (3,6) - 0.155 - 4 (3,6) - 0.244
  • Male gender - 87/123 (71%) - 67/119 (56%) - 0.019 - 1937/3486 (56%) - 0.001
  • Any Co-existing chronic medical conditions - 42/105 (40%) - 11/104 (11%) - <0.001 - 748/3485 (21%) - <0.001
  • Chronic heart disease - 12/105 (11%) - 1/102 (1%) - 0.001 - 147/3457 (4%) - 0.003
  • Chronic lung disease - 10/105 (10%) - 6/100 (6%) - 0.344 - 305/3397 (9%) - 0.849
  • Chronic renal disease - 1/105 (1%) - 1/102 (1%) - 0.984 - 91/3450 (3%) - 0.221
  • Chronic liver disease - 5/105 (5%) - 1/101 (1%) - 0.092 - 27/3478 (1%) - 0.002
  • Chronic neurological disease - 3/105 (3%) - 0/39 (0%) - 0.166 - 55/3472 (2%) - 0.356
  • Diabetes - 18/105 (17%) - 1/100 (1%) - <0.001 - 185/3470 (5%) - <0.001
  • Asthma - 0/105 (0%) - 0/0 - NA - 102/3442 (3%) - 0.013
  • Immune compromise - 2/105 (2%) - 1/100 (1%) - 0.586 - 86/3433 (3%) - 0.685
  • Hypertension - 51/105 (49%) - 2/41 (5%) - <0.001 - 366/3479 (11%) - <0.001
  • Malignancy - 6/105 (6%) - 1/41 (2%) - 0.375 - 92/3468 (3%) - 0.096
  • Pregnancy - 2/105 (2%) - 5/106 (5%) - 0.246 - 400/3436 (12%) - <0.001
  • Smoking history - 26/105 (25%) - 10/88 (11%) - 0.015 - 541/3431 (16%) - 0.02
  • Obesity (BMI ≥30) - 3/45 (7%) - 0/10 (0%) - 0.265 - 175/2018 (9%) - 0.623
_________

Any Co-existing chronic medical conditions is any of the following: Asthma, Diabetes, Chronic respiratory disease, Chronic heart disease, Chronic renal
disease, Chronic hepatic (liver) disease, Chronic neurological disease, Immune compromise (see Supplementary materials for definitions).

(...)


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

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

(...)

Table 5. Laboratory results on admission*

[Median (inter-quartile range) - H7N9 (ref group) - H5N1 - P-value - pH1N1 - P-value]

  • White cell count - 4.5 (2.9,6.2) - 3.9 (2.5,7.1) - 0.805 - 6 (4.2,8.8) - <0.001
  • Lymphocyte count - 0.5 (0.3,0.7) - 0.9 (0.6,1.4) - <0.001 - 1 (0.6,1.5) - <0.001
  • Neutrophil count - 3.3 (2.2,5.4) - 3 (1.5,5.4) - 0.203 - 4.3 (2.6,6.9) - 0.004
  • Platelet count - 114 (82,147.5) - 126 (86,196) - 0.203 - 173 (132,229.8) - 0.004
  • Aspartate aminotransferase - 53 (38,96.5) - 100 (47,233) - 0.076 - 40 (26.4,68.5) - <0.001
  • Alanine aminotransferase - 35.5 (24,64.5) - 48.5 (29.5,99.5) - <0.001 - 24 (15.6,44) - <0.001
  • Serum creatinine - 70.7 (58.3,85) - 83 (54,100) - 0.028 - 62 (45.4,81) - <0.001
  • CK - 195 (96,562) - 552 (126.5,939.8) - 0.255 - 120 (62,304) - <0.001
  • CRP - 65 (25,113) - 51 (14.2,118.3) - 0.191 - 25.4 (7.9,75.5) - <0.001
  • LDH - 498 (388,661) - 1025 (334.8,1832.5) - 0.525 - 307 (217,491) - <0.001
[n/N (%)]

  • Leukopenia - 48/105 (46%) - 54/107 (50%) - 0.489 - 736/3305 (22%) - <0.001
  • Lymphopenia - 88/99 (89%) - 54/98 (55%) - <0.001 - 1601/2891 (55%) - <0.001
  • Neutropenia - 13/103 (13%) - 24/97 (25%) - 0.027 - 221/2891 (8%) - 0.086
  • Neutrophilia - 5/103 (5%) - 15/97 (15%) - 0.011 - 477/2891 (16%) - <0.001
  • Thrombocytopenia - 80/104 (77%) - 69/105 (66%) - 0.073 - 1106/3066 (36%) - <0.001
  • Elevated aspartate aminotransferase - 54/103 (52%) - 41/54 (76%) - 0.004 - 1165/3197 (36%) - 0.001
  • Elevated alanine aminotransferase - 34/100 (34%) - 25/52 (48%) - 0.093 - 668/3167 (21%) - 0.003
  • Elevated serum creatinine - 11/103 (11%) - 9/62 (15%) - 0.469 - 201/3054 (7%) - 0.129
  • Elevated CK - 48/98 (49%) - 13/20 (65%) - 0.188 - 1018/2951 (34%) - 0.004
  • Elevated CRP - 83/92 (90%) - 9/12 (75%) - 0.162 - 1193/1708 (70%) - <0.001
  • Elevated LDH - 89/98 (91%) - 17/21 (81%) - 0.218 - 1617/2922 (55%) - <0.001
* Or earliest available time point after admission. NC = collected.

(...)

[AST / ALT = Liver enzymes
Creatinine = Kidney function
CK (creatin - kinase) = heart & Muscle pathology
CRP (Protein C reactive) = systemic infection / inflammation
LDH (lattico dehydrogenase) = ards / acute lung injury / systemic illness . gm]

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

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

Likely our contributor is referring to the mechanism of recombination, an event not fully undestood and debated in the mainstream flu research establishment.

But it is out of any reasonable doubt that H1 IS interfering with avian flu viruses since it is dominant in Young people.

How can a virus isolated in thousands of samples not influence the H7N9 epidemiology:

Please click on attached image
 

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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+

while things are "unknown", they are not completely unknown, so to speak.
We have some hints. We have (subjective) probability estimates.

----------------------------------------------------------------

H7N9 is different from H5 and pH1 in:
Median age - 63
Male gender - 87/123 (71%)
Diabetes - 18/105 (17%)
Hypertension - 51/105 (49%)
Smoking history - 26/105 (25%)
CK - 195 (96,562)
CRP - 65 (25,113)
Lymphopenia - 88/99 (89%)
Neutrophilia - 5/103 (5%)
Thrombocytopenia - 80/104 (77%)
Elevated LDH - 89/98 (91%)
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

The high number of H7N9 cases is a worrying signal but the world has decided to take the risk well ahead when the H5N1 was downgraded.

The Canadian nurse Death is only a reminder.

Mainstream media, journalists & flublogia should answer a certain number of questions:

1) Why does H5N1 suffer a such dramatic change in human epidemiology? Since a couple of years ago, dozens of confirmed & suspected cases were spotted in several countries, like Egypt and Indonesia; now, only very few of these cases are being reported;

2) How does H5N1 manage this sudden change in its zoonotic behaviour, causing little damage to poultry in endemic regions?

3) What kind of improvement in poultry farming has been achieved in disadvantaged countries like Bangladesh, Nepal, Pakistan, Indonesia and Egypt in order to avoid explosive animal outbreaks?

4) H7N9 caused so far at least 300 recognized human cases, but H5N1 may have caused also a lot of cases, although not in cluster or in community h2h transmission in the region where it is supposed to be endemic; is it possible for Nepal to have had hundreds of poultry outbreaks and not a single human case? The same thing is true for India & Bangladesh. What is the host determinant that make humans 'immune' to H5N1 in some regions?

5) A such dramatic change in zoonotic and epidemiological behaviour should be carefully investigated. It is important to understand the hidden mechanism of this switch from a universal scourge to a little bug of no importance.

6) H1N1pdm09 remained in swine population for decades before to start to rapidly change its genetic constellation until it reached the match an efficient for human spread. H5N1 - now fallen into oblivion - is doing the same: lurking and changing silently in animals and possibly human.

7) Is it safe to take as true the statements from endemic countries that no further human cases are being detected?

8) Are flublogia doing right to take this lull (?) in cases' detection as a sign that H5N1 was indeed a hype?

I want to make clear that I am not dismissing the H7N9 risk but H5N1 out there and wild suggest me an uneasy comfort...
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

Thank for not having answered to my (sarcastic) questions!
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

Scientific debate is crucial to science. Civil discourse is crucial to keeping our citizens informed. We are at at a crossroads. It is very likely humanity will in the future move into a pandemic phase. We have novel flu strains popping up all over the place. Some of them are closing in on us. As most of us do not have a background in gene sequencing we are dependent on the few of us who do understand that very narrow field. However, many of us are scientists or, well informed laypersons. Regardless, ALL of us here at FT are dedicated to furthering information about emerging disease especially the flu to anyone and everyone. We have thousands of dedicated followers. Many visit every day. They come from all walks of life, from doctors, to government insiders, to housewives. They come from Azerbaijan to the Vatican. They depend on our staying up to date about disease developments. Many also expect our prognosticating to some degree about future developments. We can't do that if we are not willing to be a little more polite to one another. If things get worse, as I personally believe they might, then working together is critical. Questioning is going to be part of the process. Questioning is expected in every field of science. None of us has the whole picture. For that reason, we expect that each person who regularly posts at FT will help to inform others who do not understand. Therefore, it is imperative we remain civil and as helpful as we possibly can. Please take a deep breath and remember who we are posting for, why we are posting in the first place, and why this matters personally to you. You wouldn't be posting here at all, if you didn't want to keep others informed.
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

1) Why does H5N1 suffer a such dramatic change in human epidemiology? Since a couple of years ago, dozens of confirmed & suspected cases were spotted in several countries, like Egypt and Indonesia; now, only very few of these cases are being reported;

## I think it evolves in poultry only now, too special for the ducks

2) How does H5N1 manage this sudden change in its zoonotic behaviour, causing little damage to poultry in endemic regions?

## increasing immunity ?

3) What kind of improvement in poultry farming has been achieved in disadvantaged countries like Bangladesh, Nepal, Pakistan, Indonesia and Egypt in order to avoid explosive animal outbreaks?

4) H7N9 caused so far at least 300 recognized human cases, but H5N1 may have caused also a lot of cases, although not in cluster or in community h2h transmission in the region where it is supposed to be endemic; is it possible for Nepal to have had hundreds of poultry outbreaks and not a single human case? The same thing is true for India & Bangladesh. What is the host determinant that make humans 'immune' to H5N1 in some regions?

## behaviour, customs

5) A such dramatic change in zoonotic and epidemiological behaviour should be carefully investigated. It is important to understand the hidden mechanism of this switch from a universal scourge to a little bug of no importance.

6) H1N1pdm09 remained in swine population for decades before to start to rapidly change its genetic constellation until it reached the match an efficient for human spread. H5N1 - now fallen into oblivion - is doing the same: lurking and changing silently in animals and possibly human.

## swine are more human than chickens

7) Is it safe to take as true the statements from endemic countries that no further human cases are being detected?

## 80%

8) Are flublogia doing right to take this lull (?) in cases' detection as a sign that H5N1 was indeed a hype?

## not a hype, we couldn't have known. With the decreasing dynamics of spread the perceived danger decreased

I want to make clear that I am not dismissing the H7N9 risk but H5N1 out there and wild suggest me an uneasy comfort...[/QUOTE]

## IMO more dangerous are humans because of research and reverse genetics
 
Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

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

Thank GSGS.

I remain skeptical about the complete disappearance of H5N1 from human in Egypt, Indonesia and the never detected cases in India, Nepal...
 
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