Genetic sequences
revere | November 21, 2009The Norwegian Institute of Public Health is reporting sporadic occurrences of a mutation in a portion of the flu virus that is involved with the process by which it attaches to cells. I use the word "sporadic" because at this point there is no evidence that the cases where the genetic change has been found are epidemiologically linked. Therefore we don't see it spreading from person to person but rather arising in people after they have been infected. At least that's how it appears from reports, but we have only preliminary information at this point. According to WHO, the mutation has been…
revere | October 5, 2008An article in The Straits Times from newswire Associated Press (AP) drew my attention to a festering disagreement between proponents of an innovative global sharing initiative for influenza information and the World Health Organization, the official UN Agency that has run the global influenza surveillance system for more than a half century. The new system, The Global Initiative on Sharing Avian Influenza Data (GISAID), began midway through 2006 and has made rapid progress. It came into being to deal with dissatisfaction with the existing system wherein WHO allowed influenza gene sequence…
revere | October 2, 2008Scientists have been using genetic data to estimate when species first appeared for some time. The basic idea is to use differences between species and a guess as to how fast sequences change as a molecular clock, running it backward until they show the same sequence. The same trick can be done with viral genetic information. If you know the genetic sequence of a virus at one point in time and then at a later time you can make an estimate of how fast the clock is ticking. An analysis along these lines has just been done with a newly found lymph node sample from Kinshasa (Democratic Republic…
revere | May 15, 2008Last week WHO's flu maven, Keiji Fukuda, said what we and others have been saying for a long time. Flu scientists need to change their research ethics. The world of flu virology has developed a mandarinate that is impeding progress for its own benefit. And their bad behavior is enabled and imitated by some public health agencies, like CDC. Researchers and CDC are sitting on H5N1 genetic and other flu sequences of public health importance. They treat their data as proprietary, to be used for their own benefit in scientific publications.
This isn't unusual. It is the normal way of doing…
revere | April 25, 2008For years we have been naming flu viruses in a particular way. Now Declan Butler has a news article in Nature observing that the system is being modified for bird flu to be more "politically correct." What is the system that's being modified (still in use for seasonal flu)?
It starts off with the type of influenza virus, either A, B or C. The type was originally based on a broad class of antibody response but now is related to genetic markers in two of the eleven proteins (matrix M1 or nuceoprotein, NP). The three types have a common ancestor but only types A and B are of public health…
revere | February 23, 2008Indonesia is providing bird flu specimens to WHO again. And Indonesian Health Minister Dr Siti Fadilah Supari has just published a book declaring the 50 year plus history of global influenza surveillance is part of a conspiracy by the developed world to control the rest of the world:
"Developed countries become richer because they have the capability to develop the vaccine and control the world," she writes.
Dr Supari also expresses alarm at WHO laboratories sharing bird flu virus data with the United States National Laboratory in Los Alamos, New Mexico, where nuclear weapons are developed.
"…
revere | February 5, 2008Bangladesh is a country with more than its share of woes. Now there is H5N1 galloping through its poultry. Bangladesh needs all the help it can get. Which also means it needs to help others, too. How can a resource poor country like Bangladesh help other nations? They can start by sharing the genetic sequences of the viruses isolated from their poultry:
Bangladesh has refused to share the genetic details of its H5N1 bird flu virus with India. In a blow to India's efforts to find the origin of the highly pathogenic avian influenza strain that is presently wreaking havoc in West Bengal,…
revere | January 29, 2008Since the antiviral agent oseltamivir (Tamiflu) has been touted as the global savior should a bird flu pandemic materialize the idea has been haunted by the specter of Tamiflu resistance. What if H5N1 becomes resistant to the drug? Is all lost? Now it is being reported in the media that the European Centre for Disease Control and Prevention has found that the predominant circulating seasonal flu virus in Europe this year, H1N1, is showing an unexpectedly high rate of Tamiflu resistance (19/148 isolates tested). This is much more than what has been seen in the past and was from patients not…
revere | December 30, 2007After spending more time than I wished "defending" WHO against what I considered a particular kind of scurrilous attack (it also seemed to raise the hackles of some unintended as targets, but the dialog with them was at least rational) -- after all that, I now have to turn around and complain about WHO (again). Let me be constructive and offer their spokesperson, John Rainford (or whoever writes the statements he mouths), a little biology lesson. A mutation of a virus is a technical term that describes a replicable change in the sequence of bases that constitute the virus's genetic blueprint…
revere | December 20, 2007Nature's senior correspondent, Declan Butler, was one of the first to raise the profile of a pandemic threat in the scientific community and has had done some superb reporting since, including several stories on sharing gene sequences. The problematic actors in his earlier stories were respected scientists and the business-as-usual way they were approaching release of genetic sequences even as the world worried that the virus they were studying, influenza A, was inexorably searching for the right recipe to enhance its own raison d'etre, to make still more copies of itself, potentially with…
revere | December 10, 2007The debate about how much wild migratory birds contribute to the spread of highly pathogenic influenza/A H5N1 goes on. According to a sensible Commentary in Nature (Dec. 6) it needn't. We should have taken steps some time ago to answer an answerable question. But we didn't and still haven't initiated those steps:
Two years ago, some believed that H5N1 viruses were poised to spread around the globe on the wings of migrating wild birds. A massive effort was mounted to track their movement but, as of September 2007, very few positive birds have been found in tests of over 300,000 healthy wild…
revere | November 26, 2007Indonesia's health minister, Siti Fadilah Supari, has answered the question whether the recently concluded Geneva summit on sharing of influenza viruses had produced sufficient agreement to induce that country to begin sharing again. Her answer seems to be "no":
Indonesia's health minister reiterated Sunday that she would not send bird flu specimens to the World Health Organization, saying poor nations needed assurances that any pandemic vaccines developed from the virus would be affordable.
Siti Fadilah Supari made the comments on her return from Geneva, where the WHO held an…
revere | November 24, 2007As you will see from the account below the fold, the flu summit was a contentious and complicated affair. Only time will tell if it was even a qualified success, but there are reasons to be hopeful. Tip of the hat to Ed Hammond, one of the NGO participants, who provided the public health community with his perspective at a time when no one else was talking. This involved late hours for him at the end of long days. We are grateful.
Here's his wrap-up:
Influenza Meeting Ends in Qualified Success
At the end of contentious meetings like the one on policies for sharing flu virus it is tempting to…
revere | November 24, 2007Yesterday was the fourth and final day of the important Geneva summit on sharing flu virus isolates. Like premature news of Mark Twain's death, the Reuters report the meeting had failed was exaggerated. On the contrary, the summit appeared to have moved things forward. We have the latest, below. You can find previous happenings and background here, here, here and here.
Status mid-day, Day 4 (3:26 pm Geneva time, November 23), as reported by Ed Hammond:
Some Things That Happened in the Night Session of Day 3 and Morning Session of Day 4
These sessions were the final negotiations before…
revere | July 17, 2006An interesting Commentary on the problem of releasing the flu sequences has been posted on the blog Anthropologique by its proprietor, J. F. Brinkworth. I disagree with it, but he makes some pertinent points.
Brinkworth believes WHO is not at fault for failure to release the Indonesian sequences and he provides some information of which I, and probably most others, are not aware:
Indonesia has very, very stringent nucleic sequence I.P. laws. All genetic material recovered there is their property. Their Convention of Biological Dviersity Law No.5 (1994) and Cultural Practices Law No. 12 (1992…