Immunocompetent

If secondary sources are to be believed, such as this one, then CDC's PR hacks have sallied forth with a pack of lies about their patent claims on Indonesian, Thai, and other H5N1 genes, which were first brought into the public eye by this blog.

There are two main arguments that CDC has been quoted to me as making with respect to my article and related items that have come out in the press.  I will refute both of CDC's claims.

First, CDC is said to have rather remarkably claimed that they aren't part of the patent application.  This is patent bullshit, as I will show.  Secondly, and somewhat contradictorily, CDC's hacks are said to claim that the patent application is (to paraphrase), "for a vaccine and not a virus, so the Indonesian and other strains aren't claimed."  This too is wrong. To demonstrate that, I will walk readers through the text of one of the (many) claims, so you can read it for yourself.  The claims analysis is a bit tedious; but it's not rocket science.  Wade through it, and you will be rewarded with a clear explanation of why CDC is wrong.  We'll deal with the CDC arguments one by one:

First, CDC is said to have bizarrely claimed that they aren't part of the patent application. This would be a remarkable thing for the CDC hack to say, because CDC is indicated as a patent applicant on the first page of patent application (quoting directly):

APPLICANTS: THE GOVERMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES [US/US]; National Institutes of Health,, Office of Technology Transfer, 6011 Executive Blvd., Suite 325, Rockvillle, Maryland 20852-3804 (US) (All Except US).

THE GOVERMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES [US/US]; Centers for Disease Control and Prevention, 4770 Biford Hwy (K79), Atlanta, Georgia 30333 (US) (All Except US).

Clear as can be. Is there really a need to say more? There shouldn't be; but I'm afraid there is.

That's because an ancillary argument that the CDC hacks are said to be advancing is that the US National Institutes of Health (NIH) is really responsible for this and CDC should not be held accountable for its name on the patent. 

Off the top, I find it very hard to believe that a patent application can be submitted in CDC's name without CDC knowing about it. But more importantly, this CDC red herring needs to be put into context.  Both CDC and NIH are part of the US Department of Health and Human Services (i.e. the health ministry).  CDC hosts the WHO Collaborating Centre, and both it and NIH conduct flu research. And while it is true that most of the inventors listed in the application are from NIH, it's more than slightly disingenuous for CDC to try to beg off by foisting the blame on its HHS sister institute. In the international context, it's simply not credible to have one half of the health ministry (CDC) saying "no patents", while it is passing the material to the other half of the health ministry which is patenting away. So, in many senses, whether it is CDC or NIH or both is immaterial, because they are ultimately part of the same organzation (HHS) that has a WHO Collaborating Centre.

Turning to the claims analysis: CDC's hacks are said to have claimed that the patent application is (to paraphrase), "for a vaccine and not a virus, so the Indonesian and other strains aren't claimed."

The government spokesman bullshit detector of anyone with a whit of common sense would start ringing loudly just looking at the cover page of the patent (click it), which has an illustration of a genetic construct, claimed in the patent, that incorporates the "codon optimized" HA gene of A/Indonesia/5/05.  It even says so right on the picture.

Could it be any clearer?  Not really; but just be sure, we can turn to the most important part of patent, the claims, where the applicants specifically articulate the alleged invention that they are seeking patent for. Typically (but not always), the first claims are the most important in a patent.  Let's turn to Claim 1 of the CDC/NIH application:

	WHAT IS CLAIMED IS:

		1. A nucleic acid molecule comprising a polynucleotide encoding an influenza
	protein selected from the group consisting of hemagglutinin A (HA),
	neuraminidase (NA), M2 Protein, and nucleoprotein (NP), wherein said
	polynucleotide comprises
			 
	(a) a plasmid taken from Table 1 (or its insert), or
			 
	(b) an analog of said plasmid or insert having at least 95% identity thereto.
	 
	

The first thing to note about this claim is that it is a claim on matter.  That is, it is not merely a claim on the use of a particular type of matter (not that that would make it innocuous), it is a claim to the thing itself, full stop. Specifically this claim is for any polynucleotide (i.e. DNA or RNA) that encodes specific polypeptides (i.e. proteins), including some specific HA, NA, M2, and NP genes from influenza. And for good measure, anything 95% or more like them.

But which specific DNA or RNA is claimed, it's not spelled out explicitly in the quote above?  Good question.

And what does that phrase "or its insert" mean? Another good question. 

If you read the claim again, you will see that determining what specific DNA / RNA is claimed requires referring to "Table 1", and looking at the patent text in order to establish what "insert" means in the context of this patent application.

The meaning of insert can be quickly clarified. It is this:  The plasmids refered to in Claim 1 are longer DNA constructs designed as vaccines, and which are pieced together with genes from multiple organisms.  The picture on the cover page (click above) is one of these plasmids. The "insert" is/are the influenza pieces that are placed into the longer plasmid. Mostly "codon optimized" HA genes that have been copied into DNA from the viral RNA.

So, what's specified in Table 1?  I have extracted Table 1 from the patent application, and you can click here to read it yourself (PDF format).  It is 6 pages long, and includes no fewer than 151 150 separate genetic constructs claimed by NIH/CDC, most of which are either "plasmids" or "inserts". (Remember that the plasmids are claimed in their entirety, including the inserts... which are also claimed apart from the rest of the plasmid.)

If it's a plasmid or an insert in Table 1, then it is claimed.  On the first of the 6 pages of Table 1, there are 8 different constructs incorporating Thai H5N1 genetic material and one plasmid incorporating (i.e. with an "insert") of Indonesian genetic material. On the second page, there are 4 more constructs with Thai material. On the third page, there are 6 plasmids with Chinese (Hong Kong) genetic material, 2 with sequences from South Korea, and another Thai one. On the fourth and fifth pages there are 8 more with Thai genenic material. On the sixth page, there are 2 constructs with Thai genetic material, 6 with Hong Kong genetic material, and 2 with South Korean genetic materials.

The Indonesian construct ("VRC 9123") is the first listed and is the exemplary construct of the invention.  Also, because the Indonesian HA gene is an "insert", it is claimed both as part of the VRC 9123 plasmid and by itself, alone.  The same holds true for the other H5N1 inserts in Table 1.

Then NIH/CDC goes a step further, and says anything 95% or more like those genes is also claimed.

I hope that clarifies the nature and scope of CDC's patent claims.  If CDC representatives have been accurately quoted as saying that they are not part of the patent application and that the application in any event does not claim Indonesian (and other) H5N1 materials, then the CDC representatives are spreading clearly false information, and the leadership of CDC should be reprimanded for permitting them to do so.

[Edited for clarity - 27 Aug PM]