Just as I was banishing my ignorance about how the forthcoming trial vaccine for H5N1 was produced, a trio of excellent articles from the Wall Street Journal and Fortune landed in my Inbox, facilitating my education.  The short story is that the virus grown in chicken eggs as the source of an attenuated vaccine is not actually H5N1.  The genes that cause the virus to be so fatal to eggs have been replaced with genes from less virulent strains, while the HA protein on the surface of the virus is modified so that it is more stable.

Alas, because the WSJ doesn't allow you to look at their list of stories in the print edition without a subscription, I can't even provide links to the stories.  Fortune, evidently, is more forthcoming.  Here are the titles, etc;

"A primer on the Threat of Avian Flu...", by Gautam Naik, and "Avian Flu Poses Challenge to Global Vaccine Industry...", by David Hamilton and Gautam Naik; both are from the 28 Feb, 2005 issue of the WSJ.  "The Coming War Against Bird Flu", by David Stipp, will appear in the 7 March, 2005 issue of Fortune.

The upshot of the three articles is that the vaccine is produced in sterile chicken eggs via a recombinant virus that is a modified version of H5N1.  This strategy requires a large number of those eggs, which are not easy to come by, and produces a vaccine that prompts the production of antibodies against a virus that may, or may not, be similar to the wild type H5N1.  That is what human trials will have to determine.

Thus my initial concerns (here and here) about this issue were not so far off target.  Stipp's article does an excellent job describing the production of the vaccine, and associated challenges.  It is pretty clear we need to come up with alternative means of producing vaccines, preferably rapid synthetic approaches that are deployable from a distributed infrastructure.

UPDATE (7 March 2005): I stumbled over this article in The Scientist, "H5N1 vaccine strain in a week", from 29 January 2004, which opens;

A prototype vaccine strain of the H5N1 flu virus causing havoc in Asia will probably be ready next week, John Wood of the UK National Institute for Biological Standards and Control (NIBSC) told The Scientist today (January 29). However, months of other hurdles remain before it may be ready for public health use.

The article describes several genetic manipulations of the H5N1 strain that will make it easier to produce in chicken eggs, beginning with the removal of, "a stretch of 4 or 5 basic amino acids at the hemagglutinin cleavage site that allows the virus to replicate in every organ of a chicken's body, rather than respiratory and gut tissue normally infected".

The article cites Klaus Stohr as saying, "The H5N1 virus kills chicken eggs, the normal medium for growing flu vaccine viruses, so the WHO laboratories are using reverse genetics to lower the pathogenicity of the virus to chickens and to get a high yield in the egg cultures", and describes the additional genetic manipulations; "Using other lab strain flu plasmids containing the other components of the viral genome, the team will then reassort the pieces into a nonpathogenic vaccine strain." 

Finally, the article suggests that, "Sufficient amounts of safety-tested prototype vaccine virus will probably be available for the necessary 1 to 2 months of clinical trials in the next 4 weeks".  The date of this article, again, was 29 January, 2004.

Looks like we are well on our way, circa January 2004, to producing a lovely vaccine against a bug that doesn't actually exist in nature.  We clearly need an alternative to attenuated (or killed) whole virus vaccines.  When I have time, I will post what I have been learning about DNA vaccines.