Further call for sequence database

Interesting promed post about genetic database stuff, covers some 
of the very real practical reasons why a less than ideal system 
exists at the moment.

I would agree that the world can do a lot more about this, but it will require a lot of
effort. Hopefully it will become politicly incorrect to withhold sequence data, so far
more samples will be made available far quicker.

Generally I dont think hat any human health issues should be seen as a marketplace and subject
to those rules of the game, but that is the world we live in. We cannot expect WHO and others
to behave any differently unless the world cahnges its attitude towards this stuff.
 
AVIAN INFLUENZA VIRUS: SEQUENCE DATABASE PROPOSAL
***********************************************
A ProMED-mail post
<http://www.promedmail.org>
ProMED-mail is a program of the
International Society for Infectious Diseases
<http://www.isid.org>

Date: Thu 9 Mar 2006
From: Ilaria Capua <icapua@izsvenezie.it>


A Proposal from Dr. Ilaria Capua
-------------------------------------
Avian Influenza infections caused by viruses of the H5N1 subtype are 
causing concerns about public and animal health, food security for 
developing countries and financial losses to the poultry industry. 
Evidence of infection in the African continent and in the 
Mediterranean open an unprecedented scenario with reference to virus 
adaptation mechanisms to different hosts within the animal kingdom.

The current H5N1 epidemic is characterized by spillover of infection 
to a variety of birds and mammals, and the range of hosts will 
increase as the virus affects new ecosystems.

[A worldwide list of species affected by H5N1, based upon referenced 
reports of highly pathogenic avian influenza H5N1 in animals, divided 
into 4 groups (wild, captive/sanctuary, domestic and experimentally 
infected), has been compiled by the National Wildlife Health Center, 
U.S. Grological Survey;
 <http://www.nwhc.usgs.gov/disease_information/avian_influ enza/affected_species_chart.jsp>. 
The list includes presently 9 mammal and 88 avian species, with 
common and scientific names. - Mods.AS/CP]

It is important to closely monitor the occurrence of adaptive 
mutations and compare genetic sequences of viruses obtained in other 
parts of the world. The OIE/ FAO Reference Laboratory for Avian 
Influenza at the Istituto Zooprofilattico Sperimentale delle Venezie 
in Padova, Italy invites other scientists to follow the line of 
conduct of Italian, UK, French, Croatian and Slovenian veterinary 
virologists to deposit H5N1 sequences into public databases as soon 
as they are available and expresses its gratitude to governments that 
grant permission to deposit sequences.

This increased availability of information in a timely manner appears 
to be the only tool available to attempt to understand the genetic 
implications of interspecies transmission and mechanisms of viral 
evolution in a rapidly changing scenario. Links to HA sequences of 
A/chicken/Nigeria/06 and A/swan/Italy/06 are currently available, and 
HA sequences of A/swan/Iran/754/06, A/duck/Niger/06 and 
A/swan/Slovenia/06 will be available shortly at the OFFLU website:
<http://www.offlu.net>.

--
Ilaria Capua
OIE/FAO and National Reference Laboratory for Newcastle Disease and 
Avian Influenza
Virology Department
Istituto Zooprofilattico Sperimentale delle Venezie
Viale dell'Universita' 10
35020 Legnaro
Padova, Italy
<icapua@izsvenezie.it>

[ProMED-mail welcomes the opportunity to support Dr. Capua's proposal.

The background to this proposal is provided in an article by Martin 
Enserink, which appeared in "Science" on 3 Mar 2006 (Vol. 311. no. 
5765, p. 1224 DOI: 10.1126/science.311.5765.1224) entitled: "As H5N1 
Keeps Spreading, a Call to Release More Data" the text of which reads 
as follows:

"PARIS: An impassioned call by a prominent Italian influenza 
scientist has renewed the debate about how to balance global health 
against scientists' needs to publish and countries' demands for 
secrecy. On 16 Feb 2006, Ilaria Capua of the Istituto Zooprofilattico 
Sperimentale delle Venezie in Italy asked more than 50 colleagues 
around the world to release all sequence data for the H5N1 avian 
influenza strain into the public domain. Comparing sequence data from 
every H5N1 isolate as soon as they become available is crucial for 
understanding how the virus moves and evolves, Capua argues.

Putting her money where her mouth is, Capua entered H5N1 sequence 
data from 2 recently infected countries, Nigeria and Italy, into the 
GenBank database the same day. She also rejected an offer by the 
World Health Organization (WHO) to join a select circle of 15 labs 
that share bird flu sequences on a password-protected Web site.

Capua's lab is a reference center for the U.N. Food and Agriculture 
Organization (FAO) and the World Organisation for Animal Health 
(OIE), and officials at those agencies say they support her call. But 
some scientists say sharing data instantly is complicated by the need 
for credit, and WHO argues that without some form of confidentiality, 
some countries would not submit samples at all.

Sharing information about H5N1 has been tricky from the start. WHO, 
FAO, and OIE encourage countries to send virus samples to specialized 
reference labs that can confirm the outbreak and study the virus 
further. Some have been reluctant to do so because they worry about 
intellectual-property rights or not receiving a fair share of the 
scientific credit; China, for instance, has not shared any avian 
samples for a year, a WHO spokesperson says. But even when reference 
labs do get their hands on a virus, they don't always release the 
data immediately.

For instance, in the past few months, H5N1 samples from about 15 
European countries have been sent to the Veterinary Laboratories 
Agency (VLA) in Weybridge, U.K., a reference lab for OIE and the 
European Union. Lab director Ian Brown says he's sharing sequence and 
other data with governments and the international agencies; to show 
support for Capua's campaign, he also submitted the sequence of a 
virus from an outbreak in Turkey that he says is a "progenitor to the 
European epidemic" into GenBank last week. However, until a paper 
about the European outbreaks -- which he says could be submitted in a 
matter of weeks -- has been accepted, Brown says he needs to hold on 
to the European sequences. "The staff in this institute is working 
24/7 to provide this service," he says. "I don't think it's 
unreasonable to expect ... for their endeavors." It also takes time 
to negotiate the conditions of release with dozens of individual 
governments, Brown says.

Capua counters that just isolating and sequencing a virus that comes 
in the mail does not give researchers the right to sit on the data, 
especially not at a government lab. "Most of us are paid to protect 
human and animal health," she says. "If publishing one more paper 
becomes more important, we have our priorities messed up." 
Governments can often be persuaded to release the sequences, adds 
Capua, who repeated her call at an OIE meeting in Paris on Monday [3 
Mar 2006?] and also plans to submit it to ProMED, an e-mail list 
about emerging infectious diseases.

WHO agrees that in an ideal world, scientists would share their data 
widely and voluntarily, says Wenqing Zhang of the agency's Global 
Influenza Programme. But because that's not happening, the agency 
created a special secured section at the Influenza Sequence Database 
at Los Alamos National Laboratory in New Mexico in 2004. Currently, 
some 15 labs have passwords to access these data, says Zhang, 
including WHO's 8 reference labs. The system is invaluable for WHO, 
she adds, as it helps the agency track the virus and adjust risk 
assessments if necessary.

Virologist Yi Guan of the University of Hong Kong, which has a huge 
H5N1 collection, says he would be prepared to release more data 
publicly before publication but is looking for WHO to establish a new 
policy. Until then, WHO's secure server at least ensures that 
policymakers and most of the scientists who advise them have access 
to vital information. But Capua says everyone with an interest should 
be able to browse all the data. When she was offered access in 
exchange for submitting her Nigerian sequence last month [February 
2006], she declined. And the system gets mixed marks within WHO as 
well. "Personally, I'm not in favor of it," says WHO scientist 
Michael Perdue.

Whether scientists' fears of being scooped are justified is difficult 
to say. In theory, once sequences are posted in the public domain, 
anybody could write a paper about them. In practice, journal editors 
will ask manuscript authors to get permission if they write a paper 
about unpublished data they did not submit to GenBank themselves, 
says Caroline Ash, who edits infectious diseases papers at Science. 
But Brown says he'd rather not take that risk."

- Mod.CP]
...................cp/msp/lm

Lets hoard all of the samples so only a few can make the decisions

Does that make sense to anyone here

The proper way to handle this is to let every scientis who would like to take a shot at take their shot. My god this is basic stuff, the more perspectives you have the better understanding of the problem you will have.

Why in gods name would you stop the research of something you can not to date control nor understand. I believe I have also seen these same concerns on the Recombination Wesite.

And another big problem is China, right now WHO is just taking their word for it on outbreaks and sequences.

NOT

Talk about super ego's at work!!!! Who the HE!! cares who gets the credit??? We are talking about human lives here....SCHEEESCH! Grow up! I thought we were all working for the betterment and survival of species here not who gets the credit!

Meewee

What do you mean elbows. You talk as thow these people, organizations, countries own the rights to the virus.

This is a no-brainer

The more qualified people you have in the loop will just help not hinder. Unless of-course you are not looking for help and really just trying to control.

yes I read the same on WTO.

Common sense needs to be injected into these organizations

The Human trait of control will probably be what sends everything out of Contol