Pandemic News/Awareness - Thread 3

Human H7N2 Reassortant Sequences Withdrawn from Genbank

http://www.recombinomics.com/News/05280801/H7N2_Pulled.html

We were all wondering why it took over 4 years for the viral sequences to

be released on the Yonkers case. But, now that the research based on those

sequences has come out, the sequences have been withdrawn from Genbank

without explanation. No one knows why.

We might think that finding a bird flu virus capable of hospitalizing a human

in the middle of Yonkers, New York, of all places, with no known contact with

birds, would be a matter of concern after they realized it was efficiently

transmitted in other mammals. We also might think that they would be be willing

to share those sequences after the research finally appeared some four years

later, but we would be wrong.

There is something really wrong with this system. Why produce this research

and then take back the sequence information? They did not even release

the full sequences when they were available, only portions of them.

The world is waiting for this information. There is no time to be wasted when there

is not enough Tamiflu in the world, and no vaccine. What are they thinking?

Their own research is pointing out that another bird flu virus is adapting to mammals.

This research came out in PNAS this week:

Surprisingly, we found that recently isolated H7N2 and H7N3 viruses of the

North American lineage possess increased binding to 2–6 SA, with several

strains exhibiting preferential binding characteristic of human influenza viruses.

One of these was an H7N2 virus, A/NY/107/03, associated with respiratory

disease in an adult male, which we found to be capable of efficient direct

contact transmission in the ferret model.

"...the job of the media, everywhere, should be to comfort the afflicted and

afflict the comfortable" - Crawford Kilian

When peer reviewed journals fail to peer review, and the media doesn't even

notice, the world is a less healthy place for all of us.

The following link allows you to follow a conversational thread,

revealing a story about a failure of integrity by researchers, a govt agency,

science journals, and the media. You might not understand all of it, but I think

most will be able get that there are problems with how research gets reviewed

and reported. If you have been following the news on H5N1 then you already

know that viral sequences are being withheld by WHO affiliated labs including

the CDC, and that researchers treat this information as their own property. While

bird flu continues to spread, research continues at a leisurely pace as if there

were all the time in the world, and that the withheld sequences have no impact

elsewhere.

The GenBank sequence database is an open access, annotated collection of all

publicly available nucleotide sequences and this is where we would like all

of the privately held sequences to go.

E627K is a single nucleotide polymorphism called a snip [sNP] for short.

This SNP is found in all human seasonal influenza. It allows a flu virus to

have some selective advantage in targeting mammals like us because it

permits the virus to infect at the lower temperatures of the mammalian nose.

Birds have much higher body temperatures. If a bird flu virus has this SNP,

it has made an adaptive change by exchanging genetic material with another

flu virus, probably a human seasonal flu virus since all of them contain E627K.

This link tells the story about how the research involved in two different peer

reviewed papers on another group of bird flu viruses, the H7 viruses, has

been poorly covered. The information that was not covered was very important

to the preparedness effort. Maybe these were just honest mistakes, and the

researchers just goofed or maybe not...

At any rate the two journals, and the media have fallen down on the job.

http://www.flutrackers.com/forum/showthread.php?t=69641

UPDATE:

http://www.recombinomics.com/News/06020803/H7N2_Replaced.html

Looks like like they made an error, and have corrected it however, this still does not

excuse the peer reviewed journals or the media for not holding them accountable for

not releasing the accession numbers in their papers or the full gene sequences.

The PB2 sequence has not been released. Why are they not releasing the

sequences that their research is based upon, and why is this behavior condoned?

...the apparent reassortant was presumably due to submission errors for these four genes. The banner was removed from the three avian genes (HA, NA, NP), which were deposited in March and released in April.

The H7N2 isolate from a patient who was hospitalized in New York in 2002 attracted significant interest because of increased affinity for human receptors and transmission from ferret to ferret.

Release of the PB2 sequence would be useful.

... The sequences were never listed at either publication (J Virol last year or PNAS last week). The notices and replacements were all done at Genbank.

World Health Organization [WHO]

H5N1 avian influenza: Timeline of major events

http://www.who.int/csr/disease/avian_influenza/Timeline_08_05_20.pdf

They do not list every H5N1 event but give a good overview of what has

happened, enough that you can see the spread of the disease across the

planet. For anyone still thinking that this is just in southeast Asia, you are

going to be in for a surprise.

The UK

http://afludiary.blogspot.com/2008/06/uk-h7-outbreak-highly-pathogenic.html

All of the news lately seems to be about H7 viruses. Today we are hearing

about a highly pathogenic avian influenza [HPAI] occurring in poultry in

the UK. Humans can be infected with H7 viruses also which is why any

people at risk there will be offered Tamiflu not just for their own safety

but for everyone else as well. H7 viruses can be transmissible to others.

While outbreaks of H7 strains of bird flu have occurred in Britain before, they have always been characterized as `low pathogenic', or one that causes less mortality and morbidity among poultry.

Obviously, highly pathogenic viruses are of greater concern to the poultry industry and to public health officials. While the risk to humans from the H7 virus has historically been low, it is not zero.

Local health departments will reportedly track down contacts with the infected birds and offer antiviral medication where appropriate.

Arkansas - USA

http://www.recombinomics.com/News/06040801/H7N3_AR.html

H7N3 now being reported in Arkansas. Tyson Foods is spinning out

reassurances to the public that none of the birds have entered the

food chain. They are saying that they discovered the virus during

routine surveillance.

The...comments describe the detection of H7N3 antibodies in poultry flocks

in Arkansas. However, the reports also highlight surveillance failures

of finding H7N3 in wild birds prior to the outbreak, as well as H7N3 virus

prior to the development of antibodies in the affected flocks.

A recent report has raised questions about mismatched primers used to

detect H7 in wild birds. These primers do not match the H7 in the birds,

and therefore produce false negatives. It is unclear if this flawed approach

contributed to the failure to find H7 in the hens with H7N3 antibodies.

...the possibility of human infections in Arkansas is real, but unlikely to be

reported because of a fatally flawed surveillance program in North America,

which has failed to find H5N1 in wild birds, although PCR confirmed H5 was

reported in a dead gosling (in association with the death of all 3 goslings)

on Prince Edward Island.

The Difference Between Highly Pathogenic and Low Path Flu Viruses

http://www.flutrackers.com/forum/showpost.php?p=161500&postcount=22

A simplified explanation that is adequate for understanding these articles.

Remember though that with low path flu viruses, only a smaller percentage

of birds die or in some cases, there is no sign of infection, but the poultry will

always have to be culled because of the possibility that the virus might evolve

and become highly pathogenic.

The Silence from Indonesia Is Deafening

Here are a few links on what we are not hearing from there.

http://crofsblogs.typepad.com/h5n1/2008/05/who-relapses-in.html

On May 21, I posted this story: Indonesia confirms its 109th H5N1 death.

That was about the death of a 16-year-old girl with the beautiful name of

Istiqomah; she had died on May 12.

Ten days later, the World Health Organization has still not reported her death

as a confirmed H5N1 case. For that matter Indonesia's ministry of health hasn't

posted anything about it either, and Komnas FBPI has issued no follow-up.

Evidently, this is the same girl, and they will no longer be reporting these

deaths taking place in the country with more H5N1 victims than any other

nation.

http://crofsblogs.typepad.com/h5n1/2008/06/indonesia-anoth.html

A 15-year-old Indonesian girl died quietly of bird flu last month, but the health

ministry in the nation hardest hit by the disease decided to keep the news quiet.

It says it sees no benefit to formally announcing deaths linked to the H5N1 virus.

Confirmed: Supari is suppressing H5N1 death reports (updated)

http://crofsblogs.typepad.com/h5n1/2008/06/confirmed-supar.html

Please be aware that Indonesia is no longer allowing the release of information

on deaths from H5N1. This is also the same country that has been refusing to

allow viral samples to be sent to the WHO affiliated labs claiming that it is

intellectual property. By withholding these two pieces of information, Indonesia

places all of us in danger. We are now totally dependent on underground news

sources that risk the displeasure of Indonesian authorities to alert the world of

what is taking place there. The translators from the flu forums are now very

experienced at extracting information from the "boots on the ground" sources,

but the job is now more difficult than ever. Should a pandemic event arise from

that country, we might not have the early warning signals that we might otherwise

have had. This is very unfortunate and risky for the rest of the planet.

With permission from Recombinomics:

http://www.recombinomics.com/News/06060801/H5N1_Indo_H2H_Failures.html

Indonesia H5N1 Cluster Reporting Failures Increase Concerns

Health Minister Siti Fadillah Supari, who has clashed with the international

community and United States over her handling of health issues, on Thursday

said her ministry had changed its policy and would only report cases every

six months.

She did not say whether that reporting policy also included the World

Health Organization (WHO). But a health ministry official said on Friday that

the ministry had not decided yet whether it would report to the WHO every one,

two, or three months.

"We are obliged to report to WHO, we are also obliged to report it to the

public," said Nyoman Kandun, director-general of communicable diseases at

the health ministry, adding that the new policy was meant as a better way

to "package" the information.

The above comments are out of compliance with the 2005 revision of

the International Health Regulations, which specifically cite "human influenza

caused by a new subtype" as a notifiable disease which is to be reported to

WHO within 48 hours.

The comments on the new Indonesian policy, have been raised in response

to an H5N1 fatality that was not reported for over a month. The case

received considerable local media attention, because the brother of the

confirmed case had died days early with identical symptoms, including

cyanosis in extremities. There was little doubt that these fatalities represented

an H5N1 cluster, which followed two other clusters involving fatalities which

included H5N1 lab confirmed cases.

In each of these clusters, the index case was mis-diagnosed and the mis-

diagnosis was obvious because of the H5N1 lab confirmation in a fatally

infected relative. In one cluster the index case was said to have died

from respiratory disease. This cluster was only covered by the local media.

However, the second cluster was picked up by wire services, and Nyoman

Kandum was specifically asked about the death of the index case and he said

the brother died from dengue fever. This comment raised significant doubt

about H5N1 transparency in Indonesia linked to significant under-reporting of

cases and clusters.

The most recent cluster has still not been listed by WHO as a lab confirmed

case, although media reports indicate H5N1 has been confirmed by two or

more independent labs. The delay was said to be due to a consideration of

the new reporting policy. In this latest cluster, the brother's death was mis-

diagnosed as typhus.

These mis-diagnosis are obvious, and are usually corrected when H5N1 is

confirmed in a relative who has disease onset dates within days of the

earlier case. In all three of these clusters, the time differential in disease

onset dates strongly suggesting that these clusters represented human to

human transmission, yet none of the clusters have been acknowledged or

reported to WHO...

The decision to revise the reporting frequency, in clear violation of

International Health Regulations [iHR], is cause for concern, as is the WHO's

failure to investigate the index cases in each cluster. Although H5N1 clusters

are not new in general or to Indonesia in particular, the failure to investigate

these clusters has created conditions that allow for less transparency.

Although H5N1 infections have recently been reported at record levels in

India, Bangladesh, and South Korea, many media reports assume that the

decline in confirmed human cases reflects a reduced risk and a lower incidence

of human H5N1 infections. However, the limited number of human cases in the

above outbreaks, as well as the outbreak in Pakistan, is almost certainly due to

detection / confirmation / reporting failures.

These failures, and the WHO's acceptance of this lack of transparency,

encourages countries to conceal cases and / or announce new reporting policies

in clear violation of IHR.

The WHO has an obligation to enforce these regulations, which it has avoided

for some time, and reporting failures have been most obvious in recent months.

Bird flu mixed with human virus could form pandemic: research

http://www.abc.net.au/news/stories/2008/06/06/2267791.htm?section=justin

A new research paper has been published in the United States, proving that

bird flu, which has so far only killed people in its pure form, is capable of

combining with conventional human flu viruses.

A mutated virus combining human flu and bird flu is the nightmare strain

which scientists fear could create a worldwide pandemic. The pure bird flu

strain, called H5N1, has caused hundreds of deaths recently around the

world.

The research has emerged at the same time as other worrying news. The

Indonesian Government has announced it will stop reporting bird flu deaths

as they happen, apparently because it does not want bad news to spread.

Professor Anne Kelso from the World Health Organisation (WHO)

Collaborating Centre in Melbourne says such a move would hinder efforts to

contain any outbreak.

"The sharing of information and the sharing of viruses [for research] are the

two most important things that countries can do to help the world prepare for

a potential pandemic," she said.

"We don't need to know who the people are. It's very important we know

where the deaths are occurring and if possible to have access to the viruses

to compare with other viruses from around the world."

"The WHO on behalf of all the member states will have less warning if there

are changes happening that could lead to a pandemic," she said.

"In particular it's important to know whether the deaths are due to exposure

to viruses in poultry or whether there's evidence that they are being

transmitted from human to human."

The News from Hong Kong

http://www.flutrackers.com/forum/showpost.php?p=162295&postcount=9

Highly pathogenic avian influenza (HPAI), H5N1 was found during routine

surveillance that tested poultry droppings in a wet market. The birds did

not appear sick. That is why routine testing is now necessary. There is

no longer any guarantee that there would be any warning of infection

because the birds do not always show symptoms right away. Now they

will have to monitor the handlers, and put them on Tamiflu. They will

cull just these 2700 birds for now, and try to track where they came

from.

Why the concern? Check out this link on what happened in Hong Kong

in 1997.

In 1997, at least a few hundred people became infected with the avian

A/H5N1 flu virus in Hong Kong and 18 people were hospitalized. Six of the

hospitalized persons died. This virus was different because it moved

directly from chickens to people, rather than having been altered by infecting

pigs as an intermediate host. In addition, many of the most severe

illnesses occurred in young adults similar to illnesses caused by the 1918

Spanish flu virus. To prevent the spread of this virus, all chickens

(approximately 1.5 million) in Hong Kong were slaughtered. The avian flu

did not easily spread from one person to another, and after the poultry

slaughter, no new human infections were found.

This is from today in Hong Kong:

...our existing guideline is if there is one detection of H5N1 in one market,

we will cull the chickens in that market; but if we found another possible

detection in another market, we assume the risk is much higher and we

need to cull all the chickens in all the markets.

Reporter:

Is there a breakdown in the surveillance? And you've vaccinated all the

chickens in the market and why now you've found virus in the market?

Dr York Chow:

You are talking about two things.

Actually we are very grateful that we have such a strong surveillance that

enables us to detect the virus in the market this time.

You are talking about whether the biosecurity and the vaccination policy of

our poultry are functioning, and that is exactly what the concern is all about.

We cannot tell until we have done all the investigation and check where these

chickens came from, and whether these farms have complied with all our

requirements on vaccination and biosecurity measures.

So, we really have to trace to the source of this virus before we can tell

whether there is any change in the virus.

Reporter: Why genetic sequencing is important?

Dr York Chow: Genetic sequencing is important of course to see whether the

virus has transformed into any new type of virus which has different

pathogenesis. This is the sort of routine tests that we will do if we found any

possible virus in the environment.

Media Myths on H7 Transmission

http://www.recombinomics.com/News/06040803/More_H7_MM.html

Poultry companies, govt agricultural departments and the media tend

to downplay just how transmissible these H7 viruses are. It is true that

most human cases only come down with conjunctivitis but that is not the

point. Some people have ended up in the hospital with respiratory infections,

and there has been one death. Another reason for concern is that recent

studies are showing a tendency towards more adaptation to mammals. With

that adaptation could come a tendency towards increased virulence.

The last but not, least concern is that a co-infection with a more deadly virus

such as H5N1 could benefit H5N1 with the ability to become more transmissible

also.

Despite all the reassuring spin, the fact that contacts of the people that had

been exposed to the virus also were positive is just one more indication of just

how transmissible these viruses are.

Antibody testing is more accurate than PCR testing but takes longer. As

you can see, many cases that were really positive tested negative by PCR

originally.

The case for probable H2H transmission was significantly increased by follow-

up studies on H7 antibodies in the above cases and contacts. Over 1000 cases

were identified and 59% of culler contacts were positive, indicating the

sensitivity of the PCR testing was very low and H2H transmission was very

common.