Declan Butler, reporter

April 4, 2007

Nature launches avian flu site

Filed under: avian influenza,Uncategorized — admin @ 3:33 pm

Nature helped launch interest in addressing the risks of a flu pandemic back in 2005. One of may favourites still is the fictional blog I wrote; The flu pandemic: were we ready?

Since then awareness of the threat has grown and there is extensive blog and media coverage on developments, as well as governmental and other sites providing information.
As an archive of reliable scientific information, Nature has now brought all its avian flu content together on one site, with almost all on free access. Here’s the link.

December 10, 2006

Google Earth avian flu maps updated

Filed under: avian influenza,GIS,Google Earth,Open data — admin @ 11:08 pm

I’ve updated the flu maps to this weekend — link here.. Since August, the spread of avian flu, as reported, has shown a lull, with only a few animal outbreaks, reported, in Indonesia, Vietnam, Cambodia, Egypt, China and South Korea. Over the same period there have been 10 human cases in Indonesia, and 1 in Egypt.
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November 15, 2006

Article on WHO’s new DG — Margaret Chan

Filed under: avian influenza,Uncategorized — admin @ 10:26 pm

With the death penalty trial in Libya and the Nature supplement on Islam & Science, I’ve had to put avian flu and the World Health Organization (WHO) on the backburner over the past few weeks.

In this week’s Nature, though I take at look at Margaret Chan’s election as director general of WHO, and what this might mean for global health.
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September 17, 2006

The spread of avian flu with time; new maps exploiting Google Earth’s time series function

Filed under: avian influenza,GIS,Google Earth — admin @ 8:44 pm


Google Earth last week introduced new functionality that allows one to map events against time. Clearly this is the ideal way to view the spread of avian flu worldwide, so I have adapted my existing flu maps to it. Only the new maps will be updated. The new link for the time-enabled maps is this one (the KML file).

You WILL NOT be able to view these maps correctly using the standard Google Earth client. You MUST FIRST install the latest GE 4.0 beta — download link here.

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August 30, 2006

More on flu data access scheme

Filed under: avian influenza,Neglected diseases,Open data,Standards — admin @ 7:33 pm

Nature has an Editorial in this week’s edition — ‘Boosting access to disease data’ — on the Global Initiative on Sharing Avian Influenza Data (GISAID) — see previous post. It also has a short news story — ‘Plan to pool bird-flu data takes off.’

Some excerpts from the Editorial:
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August 24, 2006

Global Initiative on Sharing Avian Influenza Data

Filed under: avian influenza,Open data — admin @ 1:45 pm

In a Correspondence published online today by Nature, 70 top flu scientists and health officials, including six Nobel laureates, back a plan to end secrecy over avian flu data. The published letter is available on free access here, and the signatories here.

An accompanying news article — Bird flu data liberated — describes this Global Initiative on Sharing Avian Influenza Data (GISAID), which is intended to encourage scientists and nations to share data rapidly with other scientists worldwide.

I’ve compiled some links to recent related events and Nature coverage here.

I will post related media and blog articles to the Connotea social bookmarking service under the GISAID tag

August 1, 2006

FAO reiterates data sharing policy on H5N1

Filed under: avian influenza — admin @ 9:41 pm

Last week I revealed that since summer 2005 almost no avian flu poultry isolates have gone from Indonesia to the joint network of national and international reference laboratories run by the UN Food and Agriculture Organization (FAO) and the World Organization for Animal Health (OIE).

I therefore found it interesting that today the FAO issued a statement reiterating the policy on data sharing which it announced earlier this year. I’ve pasted its statement below.
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July 28, 2006

International community driving blindfolded in Indonesia flu battle

Filed under: avian influenza,Neglected diseases — admin @ 7:17 pm

Indonesia is the world’s current hotspot of avian flu, with the concomitant risk of emergence of a pandemic flu strain. Despite this risk, almost no avian flu poultry isolates have gone from Indonesia to the joint FAO/OIE network of national and international reference laboratories since summer 2005, I reveal in a short article tonight.

Some excerpts from the article:

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July 25, 2006

More ‘Aaargh plop;’ cat flu in Iraq

Filed under: avian influenza — admin @ 10:02 pm

Back in March I reported on what we know, and don’t know, about the avian flu virus H5N1 in cats. The issue has new resurfaced with a paper in Emerging Infectious Diseases reporting avian flu in cats in northern Iraq — see my story today; “More cats found with bird flu“.

The earlier post commented on the fact that cat infections were more common than recognized:
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July 20, 2006

WHO’s in charge?

Filed under: avian influenza,Neglected diseases — admin @ 9:42 pm

That’s the title of an editorial in this week’s Nature looking at the shift in balance of governance in global health away from the World Health Organization, prompted by the plethora of new actors, including the G8 (see the Saint Petersburg communiqué on infectious diseases) the Global Fund to fight AIDS, Tuberculosis and Malaria and the Bill & Melinda Gates Foundation.

Some excerpts
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July 15, 2006

Media pickup of Indonesia sequences

Filed under: avian influenza,Open data — admin @ 11:19 pm

My article on the Indonesia flu mutations has generated a fair bit of press coverage, making the front page of Google News — see here. Reuters, and many other media outlets, have picked up on it also, but the best article I’ve seen so far I think is this one, which gives balanced credit to both WHO’s core data needs in handling outbreaks, while also discussing its difficulties in making data more widely available. Le Monde also has good coverage — in French, as has CIDRAP.

The article has also generated considerable discussion in the blogosphere — see for example, the comments here.
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July 12, 2006

Indonesia cluster mutations

Filed under: avian influenza,Open data — admin @ 10:54 pm

Just a quick signpost to an article I’ve published in Nature tonight revealing the full mutations in the recent Indonesian cluster where human to human transmission occurred. Some abbreviated excerpts:

A strain of avian flu that spread through a family in Indonesia, killing seven of the eight people infected, was accumulating mutations as it spread from person to person, according to confidential sequence data seen by Nature. The functional significance of the mutations isn’t clear — most of them seem unimportant. But influenza researchers say the finding reiterates the need for sequence data to be made more widely available, if the virus is to be better understood.
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July 6, 2006

Congress members call to free H5N1 gene sequences

Filed under: avian influenza,Open data — admin @ 9:10 pm

I mentioned in a previous post that:

“Dennis Kucinich (Democrat, Ohio) and Wayne Gilchrest (Republican, Maryland) are circulating a letter in the House of Representatives that calls on Michael Levitt, the US health secretary, to require H5N1 sequences and other publicly funded research data “to be promptly deposited in a publicly accessible database, such as GenBank”.

The letter has now been sent, signed by 16 members of Congress: you can read it here.

June 29, 2006

The time for sitting on flu data is over.

Filed under: avian influenza,Uncategorized — admin @ 9:12 pm

Nature has a short but strong editorial today on the problem issue of access to flu data, which I’ve already blogged about here and here. It follows up on our much longer March editorial on the issue — Dreams of Flu Data.

Here are a few excepts, from today’s:
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May 31, 2006

Breaking the silence: “If this was a test to see whether Indonesia could contain a virus, they failed miserably”

Filed under: avian influenza — admin @ 10:10 pm

The latter quote is from a front-page article I’ve published in Nature tonight on what the experience of the large human cluster of avian flu cases in Indonesia says about the realities of attempting to slow the spread of, much less extinguishing at source, an emerging pandemic in the context of a developing country, with poor health infrastructure.
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May 30, 2006

Map update

Filed under: avian influenza — admin @ 11:09 pm


I’ve posted a quick update to the maps. Obvious things to note are the large cluster of human cases in Indonesia, widely discussed in the media, and the less obvious spread of animal outbreaks, almost entirely confined to Europe, over the past two weeks. I’ll have a detailed article on the Indonesian cluster coming out in Nature tomorrow night, and will post about that then.
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May 16, 2006

Map update

Filed under: avian influenza,Google Earth — admin @ 11:24 pm


H5n1 maps have been updated — link here. You will notice that there has been a large decrease in the number of outbreaks reported over the last month.
We had a couple of pieces in last week’s Nature on the threat of H5N1 to the Americas — all free access- see :
Avian Flu and the New World
How might it get there?
and
State’s flu response raises concern.
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April 16, 2006

Easter avian flu map update


Map update

This weekend’s update adds a minor change to make it easier to see the latest human cases and animal outbreaks. The initial screen will by default only show — in yellow — those events that have occured since the last map update (see screenshots below). Download the new maps directly to Google Earth by clicking here. For a more detailed explanation of the new maps, click here.
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April 6, 2006

Avian flu map weekly update

Filed under: avian influenza,GIS,Google Earth — admin @ 6:37 pm


Last weekend’s scheduled weekly update to the flu maps finally went up tonight, after I found the bug that was causing export errors in the update. Download map directly here.

This week’s update, including the first bird case in Scotland, will go up this weekend.

Featured image from this week: Egypt
(Circles = animal outbreaks; triangles = human cases)
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March 24, 2006

Mapping avian flu in almost real-time using Google Earth

Filed under: avian influenza,GIS,Google Earth,Neglected diseases,Open data — admin @ 11:53 pm


UPDATE — SEPT 2006; the links below are to the old maps; to see the new time-enabled versions, click HERE – UPDATE

New Google Earth maps of avian flu spread

This is the new beta of an operational service designed to provide Google Earth maps of avian flu spread on a weekly basis for the first time. As well as mapping human cases and poultry outbreaks, the maps also provide additional data on each event, and additional datasets, such as poultry densities worldwide, to let you explore avian flu.

The fact that the maps can now be regularly updated has been made possible largely through technical improvements in the initial beta map computing infrastructure , and new volunteer support in data management.
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March 9, 2006

Cat flu — ‘aaargh plop’ , and next-generation GIS

Filed under: avian influenza,GIS,Google Earth — admin @ 12:31 am

I’ve a short article in Nature tonight summarising the situation on H5N1 and cats. I first raised this issue in an article a month back, before the first cases of cat infections in Germany and Austria.

Thought you might enjoy this excerpt.
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March 1, 2006

Reinventing the world’s disease surveillance system

Filed under: avian influenza,Uncategorized — admin @ 11:50 pm

Quick post; I’ve a 2-page article in Nature tonight on the need to reinvent the world’s disease surveillance systems, in particular with respect to avian flu. The problem is so large, that it could have been 15 pages, or a book.

I have my thoughts on what are the roles and responsibilities of international agencies such as WHO, FAO, and OIE, and their own agendas, and their diplomatic and other constraints, and also what are the glaring elements lacking in the current international system, but I’ll save that for a later date in Nature… And yes we can also talk about cats and H5N1; see my article from two weeks ago on this risk.

Here are a few excerpts from tonight’s article:
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February 22, 2006

Collection of several hundred bookmarks on virtual globes, science, and GIS

Filed under: avian influenza,GIS,Google Earth,Open data,Social bookmarking — admin @ 2:04 pm

Journalists researching articles come across many interesting web resources, but whereas a few key ones might be linked to in the final published articles, most remain on the journalists’ hard drives, never used or exploited again by themselves, let alone others. During my research into scientific applications of virtual globes, such as Google Earth — articles linked to here — I checked out many web resources. Given that these resources might be useful to others, I’ve now made them all public on Connotea, the free social bookmarking service for science professionals.

In a sense, I’m sharing with everyone some of my effort put into researching the topic, with the thinking that my link collection might provide starting points that are an alternative, and more select, starting point than a Google search for virtual globes and science.
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February 13, 2006

Avian flu — Africa, Thai dogs, catching up

Filed under: avian influenza — admin @ 10:40 pm

Some quick pointers/quick catch up.
I’ve published tonight a piece showing the first scientific evidence of possible widespread infection of dogs with the avian flu virus H5N1; in Thailand: see “Thai dogs carry bird-flu virus, but will they spread it?
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January 19, 2006

More on Turkey mutations

Filed under: avian influenza — admin @ 5:01 pm

Just a pointer to a long article I’ve published in Nature today on the three mutations found in human cases of H5N1 in Turkey — “Alarms ring over bird flu mutations.
It’s a follow up to last week’s article “Bird flu mutation sparks concern.

For more avian flu news, see my flu ‘thin’ blog or sign up to its RSS feed.

January 13, 2006

Turkey updates to avian flu maps

Filed under: avian influenza,GIS,Google Earth — admin @ 11:00 pm


Given the current interest in the outbreak of H5N1 in Turkey, I’ve exceptionally manually updated the Google Earth global avian flu outbreak maps to show the location of the latest human cases in Turkey (red dots), and links to relevant WHO updates.
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January 11, 2006

BBC Radio 5 has a piece on the Google Earth flu maps

Filed under: avian influenza,GIS,Google Earth,Uncategorized — admin @ 12:07 am

Here’s the link

January 4, 2006

Google Earth featured in Nature’s podcast

Filed under: avian influenza,GIS,Google Earth — admin @ 11:21 pm


This week’s Nature podcast features a short interview with me on Google Earth.

Avian flu maps in Google Earth

Filed under: avian influenza,GIS,Google Earth — admin @ 8:16 pm


[2007: NOTE THAT THE MAP BELOW IS NOW OLD: MORE RECENT AND UPDATED TIME SERIES MAPS ARE AVAILABLE AT THIS LINK -- http://declanbutler.info/blog/?p=58 ]

Nature has a Google Earth map of avian flu outbreaks online tonight.

Download the network link directly from here.

It accompanies an article I’ve published in Nature: “Mashups mix data into global service.” The article also has a box on methods; a shorter version of this post: “Nature gets mashed up.”

The visualization of avian flu outbreaks is the first online map, to my knowledge, of each of the more than 1800 individual outbreaks of avian flu in birds that have been reported over the past two years. It also provides a geographical overview of confirmed human cases of infection with the H5N1 influenza virus.
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December 8, 2005

More on threatened Indonesian flu lab closure

Filed under: avian influenza — admin @ 9:43 pm

Scientific American today reported on the threatened closure of Namru-2 in Indonesia (see previous post). Associated Press also report that the laboratory may now be given a stay of execution, and that this may be tied to financial terms of any vaccine produced from Indonesian viral samples.
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December 7, 2005

Indonesia threatens closure of US military lab that’s key to avian flu fight

Filed under: avian influenza — admin @ 10:41 pm

In tomorrow’s issue of Nature, I’ve a short exclusive on Indonesia seeking to close down Namru-2, a US military lab which has played a key role in helping build the country’s influenza surveillance and testing infrastructure.

Here’s a couple of snippets:
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‘Thin blogs’, RSS and ‘social bookmarking’

Filed under: avian influenza,Blogging — admin @ 7:45 pm

Journalists are information professionals. We handle, and select, huge amounts of information every day, and add to it through our own investigations. That’s what we are paid for. But can we use new technologies to help us share our research better, rather than leaving it in notebooks and on our hard drives? I think so; here I kick off with just some personal reflections on bookmarks and web resources.
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