Here are some comments about the GSK adjuvant announcement, the expansion of vaccine candidates by the WHO, H5N1 evolution in the lab and in the wild, and sequence data sharing.

GlaxoSmithKline announced recently that through the use of a proprietary adjuvant they have dramatically reduced the amount of egg-grown vaccine required to produce a decent antibody response in humans. 

A news story at CIDRAP explains that, "The GSK vaccine was made from an inactivated H5N1 virus collected in Vietnam in 2004, according to Jennifer Armstrong, a GSK spokeswoman in Philadelphia," and then notes that, "It is uncertain, however, how effective the vaccine would be against H5N1 strains other than the one it was made from. [Albert Osterhaus of Erasmus Unversity in the Netherlands] told the AP, "This vaccine will only give protection against this particular H5N1 strain and possibly other strains.""

This last statement may be true, but in my view it may also give false hope.  Aside from criticisms others have raised about GSK announcing science by press release, instead of waiting until a publication is ready, or alternatively just releasing the data, we already know that there are H5N1 variants in the wild that kill humans but don't cross prime immune systems.

In response to this development, the WHO recently advised work begin on vaccines based on clade 2 isolates from Indonesia.  (Here is CIDRAP's take, and here is the original WHO announcement.)  Note that this does not mean we will immediately have vaccines in production against these isolates; as far as I know the reference vaccine is still solely based on the original Vietnamese isolate.

As is fairly widely understood at this point, it is not at all clear that vaccines made from either the Vietnamese or Indonesian isolates will protect humans against potential pandemic strains that arise in nature.  Some effort at discerning the threat from certain potential strains was reported in PNAS in early August.  A news story in Nature describes the results with the headline, "Bird flu not set for pandemic, says US team" (subscription req.).

I find that headline very confusing, because the work in question has very little to do with whether H5N1 is "set for [a] pandemic."  Instead, the research explored the effects on ferrets of a exposure to a small number of recombinant viruses consisting of components from H5N1 and H3N2.  The text following the headline is clearer: "The scientists who conducted the work, at the [CDC], say it suggests that the H5N1 virus will require a complex series of genetic changes to evolve into a pandemic strain...  The study [does not] address whether H5N1 could evolve into a pandemic strain by accumulating mutations."

In fact, only very limited conclusions can be drawn from the paper in question, "Lack of transmission of H5N1 avian-human reassortant influenza viruses in a ferret model" (Mains, et al., PNAS, vol 103, no 32).  The first and last paragraphs of the discussion section show the authors are relatively circumspect in interpreting the data:

If H5N1 viruses acquire the ability to undergo efficient and sustained transmission among humans, a pandemic would be inevitable. An understanding of the molecular and biologic requirements for efficient transmissibility is critical for the early identification of a potential H5N1 pandemic virus and the application of optimal control measures. The results of this study demonstrate, that unlike human H3N2 viruses, avian H5N1 viruses isolated from humans in 1997, 2003, or 2005 lack the ability to transmit efficiently in the ferret model. Furthermore, reassortant viruses bearing 1997 avian H5N1 surface glycoproteins with four or six human virus internal protein genes do not transmit efficiently in ferrets and thus lack the key property that predicts pandemic spread.

Although these findings do not identify the precise genetic determinants responsible for influenza virus transmissibility, they provide an assessment of the risk of an H5N1 pandemic strain emerging through reassortment with a human influenza virus. Our results indicate that, within the context of the viruses used in this study, H5N1 avian-human reassortant viruses did not exhibit properties that would initiate a pandemic. Nevertheless, H5N1 viruses continue to spread geographically, infect a variety of mammals, and evolve rapidly. Therefore, further evaluation of the efficiency of replication and transmissibility of reassortants between contemporary H5N1 viruses and circulating human influenza viruses is an ongoing public health need. The ferret transmission model serves as a valuable tool for this purpose and the identification of molecular and biologic correlates of efficient transmissibility that may be used for early detection of a novel virus with pandemic capability.

It is certainly true that this sort of work is vital for figuring out how influenza works, and in particular vital for trying to sort out how reassortant viruses arise, how they change during passage between animals, and how they kill mammals.  Reassortment was historically important in some flu pandemics.  However, the genetic changes seen in nature in the present H5N1 outbreak appear to be solely due to mutation.  In particular, a cluster of cases in Indonesia in April and May -- the first clear example of human-to-human transmission of H5N1, according to the WHO -- allows tracking sequence changes between viruses that infected eight family members.

In "Family tragedy spotlights flu mutations" (subscription req.), Declan Butler writes that;

Viruses from five of the cases had between one and four mutations each compared with the sequence shared by most of the strains. In the case of the father who is thought to have caught the virus from his son -- a second-generation spread -- there were twenty-one mutations across seven of the eight flu genes. This suggests that the virus was evolving rapidly as it spread from person to person.

[While] many of the genetic changes did not result in the use of different amino acids by the virus...experts say they cannot conclude that the changes aren't significant. "It is interesting that we saw all these mutations in viruses that had gone human-to-human," says one scientist who was present at the Jakarta meeting but did not wish to be named because he was commenting on confidential data. "But I don't think anyone knows enough about the H5N1 genome to say how significant that is."

So there is considerable mutation occurring, even between viruses present in different family members, and we don't yet know enough about H5N1 in humans to say whether this is significant with respect to evolving into a pandemic strain.  But even more interesting, there are so many differences between the viruses that they look like different clades.  Again, from Dr. Butler:

Elodie Ghedin, a genome scientist at the University of Pittsburgh School of Medicine in Pennsylvania, says she's surprised that the virus from the father had so many mutations compared with others in the cluster, apparently arising in just a few days. "I have a hard time believing that the father acquired the virus from his son," she says, adding that the nine mutations in one gene in the father's virus are almost identical to those in viruses isolated from human cases in Thailand and Vietnam in 2004.

One possibility is that the father simply caught a different strain of virus from birds, although other mutations in his virus are similar to those in the strain isolated from his son. Or perhaps the virus from the son reassorted with another flu strain circulating in his father at the time, Ghedin says.

Perhaps, but it would seem that if the father was also carrying a virus from Thailand or Vietnam that there should be signs in birds or other humans.  I was unable to find out whether the father was in a position to pick up a virus from another clade, which would be a good check on the likelihood of reassortment.

Dr. Butler goes on to note that a simple lack of information is a significant factor in the slow progress:

Part of the reason the picture is so unclear, say virologists contacted by Nature, is that the continued withholding of genetic data is hampering study of the virus. None of the sequence data from the Indonesian cluster has been deposited in public databases -- access is restricted to a small network of researchers linked to the WHO and the US Centers for Disease Control and Prevention in Atlanta, Georgia.

Fortunately, this has changed and the Global Initiative on Sharing Avian Influenza Data (GISAID) is now in place.  I'll have something more later on the sharing plan after I digest all the information.  It looks like a nice step forward, but, as always, we'll have to see what comes of it.