07 August 2008

Would Ivins Really Have Been Allowed in the Hot Suite After Stopping the Special Immunization Program?

At Emptywheel, Marcy Wheeler has assembled another of her very impressive timelines, in which she has integrated information from yesterday's document dump with other facts from the investigation of the anthrax attacks of 2001. Of particular interest are two early entries on the timeline:

Spring 2001: Ivins taken off Special Immunization Program

September 7, 2001: Ivins put back on Special Immunization Program

From the documents, it is clear that Bruce Ivins was taken off the Special Immunization Program in the spring of 2001 and then immunizations re-started on September 7. That information is impossible to rectify with the chart in the first search warrant attachment, where the government lays out the case for Ivins spending extra time in the laboratory around the time that the materials in the mailings could have been prepared. Note the discussion of Suite B3:
USAMRID containment Suite B3 is a Biological Safety Level-3 (BSL-3) suite of laboratories used by USAMRIID Bacteriology personnel for research on dangerous animal and human pathogens. The flask identified as RMR-1029 was stored in Suite B3 at the time of the letter attacks. Suite access is obtained via a Security Access Control (SAC) badge reader at the door to the cold-side change room, which is secured by a magnetic-lock. A central security system monitors and records a time stamp for each SAC badge and keypad request.

A review of Dr. Ivins's laboratory access records for Building 1425 was assessed to determine trends in working hours and evening times (after 6 p.m.) spent in Suite B3. His regular working hours on average consisted of a 7:30 a.m. to 4:45 p.m. shift, but he would periodically return in the evenings, presumably to check on the status of various experiments. Beginning in mid-August 200 1 ; however, there was a noticeable spike in Dr. Ivins's evening access to the B3 hot Suite.
If Ivins was taken off of the Special Immunization Program, he should not have had access to the "hot Suite". Here is a chart with a detailed summary of Ivins' after-hours activity from the same document:
As stated above, if Ivins was taken off the Special Immunization Program, it makes no sense that he would have retained access to Suite B3. If that is the case, how can there be access records, after hours, for him to have been in B3 when he was off the immunization program? From the chart, it appears he did not enter the suite after hours in March or May of 2001 and only briefly in April. After hours activity began to build in June and July and then went very high in August, peaking in September and then continuing in October through December. The August time is especially troubling, since he would have been off the immunization program for several months by that time.

Here is a portion of an email in the same document that supports the information above:
September 7,2001, "I was taken off the Special Immunization Program because of what happened last spring, and I've just gotten back on it, getting my anthrax and Yellow fever shots. We are currently finishing up the last of the AVA, and when that is gone, there's nothing to replace it with. I don't know what will happen to the research programs and hot suite work until we get a new lot.
This email confirms that anthrax vaccination was part of the Special Immunization Program. I repeat: How could Ivins have had access to the hot suite while he was off the program?

06 August 2008

The First Search Warrant in the Ivins Case; Updated

The Department of Justice has just released documents in the case against Bruce Ivins as the anthrax killer. In this post, I want to address just the genetic and other technical issues relating to the attack material and whether it can appropriately be linked to Ivins. I will rely only on the first search warrant in the release, other relevant information may be lurking in the other documents.

The CDC examined isolates of the Bacillus anthracis extracted from the powder contained in the letters and compared it to body fluid samples collected from the five decedents. The CDC has determined that the strain of Bacillus anthracis found in each of the decedents' bodies is the same strain of anthrax found in the threat letters mentioned above. This particular strain is commonly known as the Ames strain of Bacillus anthracis.
Determination of Origin of Anthrax Contained in 2001 Mailings

The mail attacks are believed to have occurred on two separate occasions, which are delineated by the postmark dates of the recovered letters. Letters used in the first attack were postmarked on 09/18/2001 and were focused to media establishments located in the New York area. Three weeks later, letters postmarked 10/09/2001 were sent to two U.S. Senators in Washington, DC.

In order to fully characterize the threat letters and their contents, the Task Force has conducted numerous physical (phenotypic) and genetic (genotypic) analyses. Physical comparison of the spore powders taken from the Post and Brokaw letters versus the Senator Leahy and Senator Daschle letters reveals obvious differences. The spore powders recovered fiom the Post and Brokaw letters were granular and multicolored in consistency, while the Senator Leahy and Senator Daschle letters contained fine spore powders that were uniform in color.

Microscopic examination of the evidentiary spore powders recovered from all four letters identified an elemental signature of Silicon within the spores. This Silicon signature had not been previously described for Bacillus anthracis organisms.

Much more information is needed here on the physical description of the attack material. See the immediately preceeding post for the information especially relating to "silicon". Professor Matthew Meselson of Harvard has told the FBI that silicon is present in closely related spores. The information in the search warrant is not sufficient to determine whether the Daschle and Leahy samples especially were treated with advanced materials using advanced techniques to make them more deadly. The FBI needs to release electron mircrographs of the attack material, of known highly purified spores and of spores which have been "weaponized" by the scientists at Dugway. Similarly, they need to provide raw X-ray spectrometry data of these three types of samples, as well. This will go a long way toward understanding the expertise involved in preparing the attack material.

Genetic Analysis of the Anthrax Used in the Attacks

Upon visual inspection of the Bacillus anthracis organisms used in the mail attacks, researchers have discovered numerous phenotypic variations, which distinguish it fiom the original Ames anthrax isolated in 1981, which is the earliest known sample. The phenotypic variations were identified as differences in morphology (i.e. shape, color, texture) fiom the original Ames anthrax. Changes in morphology can be attributed to individual genetic mutations within the Bacillus anthracis DNA. As a whole, the collection of all of the genetic mutations found in the anthrax used in the 2001 mailings, serve to provide a "DNA fingerprint" which can, and has been used to investigate other Ames isolates collected from laboratories possessing the Ames strain. Four individual, highly sensitive, and specific molecular assays capable of detecting four of the genetic mutations discovered in the Bacillus anthracis used in the mail attacks have been developed and validated.

Following the mailings, sixteen domestic government, commercial, and university laboratories that had virulent Ames strain Bacillus anthracis in their inventories vrior to the received Arnes strain Bacillus anthracis isolates or samples from all sixteen domestic laboratories, as well as, fiom laboratories in Canada, Sweden, and the United Kingdom. All total, the Task Force has obtained more than 1000 isolates of the Ames strain of Bacillus anthracis fiom these laboratories and archived these isolates in the FBI Bacillus anthracis Repository (hereinafter "FBIR").

The four aforementioned molecular assays have been applied to each of the more than 1000 Bacillus anthracis samples contained within the FBIR. Of the more than 1000 FB'R samples, only eight were determined to contain all four genetic mutations.

The Task Force investigation has determined that each of the eight isolates in the FBIR is directly related to a single Bacillus anthracis Ames strain spore batch, identified as RMR-1029. RMR-1029 was stored in the B3 biocontainment suite within Building 1425 of the United States Army Medical Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland. Access to the suite is afforded only to those personnel who are approved by the USAMRIID Security, Safety, and Special Immunizations Program to have the required background check, training, and medical protection (vaccination or personal protective equipment (PPE)). Dr. Bruce Ivins has unrestricted access to the suite and has been the sole custodian of RMR-1029 since it was first grown in 1997.
The language of that first paragraph is very hard to decipher. The "phenotypic" variations they are describing here (shape, color, texture) I think must be referring to the bulk properties of the samples being analyzed and would depend far more on the culture conditions and post-culture processing than on the underlying genetics of the sample. However, the discussion does then move on to actual genetics. It appears that after original DNA sequencing of the attack material identified it as the Ames strain, the FBI then found 16 domestic and several foreign sources of live Ames strain. They then obtained over a thousand different isolates from these sources and carried out a detailed sequence analysis of all of these isolates. They report a combination of four unique mutations that are specific to the attack material. It appears that only 8 of the individual isolates in the analysis shared the four mutations with the attack material. Each of these 8 isolates appeared to have been derived from a single flask, designated RMR-1029, produced in 1997. Bruce Ivins was the sole custodian of this flask from the time it was produced.

The search warrant goes on:

Bacterial contaminant found in attack letters

Both of the anthrax spore powders recovered from the Post and Brokaw letters contain low levels of a bacterial contaminant identified as a strain of Bacillus subtilis. The Bacillus subtilis contaminant has not been detected in the anthrax spore powders recovered from the envelopes mailed to either Senator Leahy or Senator Daschle. Bacillus subtilis is a nonpathogenic bacterium found ubiquitously in the environment. However, genomic DNA sequencing of the specific isolate of Bacillus subtilis discovered within the Post and Brokaw powders reveals that it is genetically distinct from other known isolates of Bacillus subtilis. Analysis of the Bacillus subtilis from the Post and Brokaw envelopes revealed that these two isolates are identical.

Phenotypic and genotypic analyses demonstrate that the RMR-1029 does not have the Bacillus subtilis contaminant found in the evidentiary spore powders, which suggests that the anthrax used in the letter attacks was grown from the material contained in RMR-1029 and not taken directly from the flask and placed in the envelopes. Since RMR-1029 is the genetic parent to the evidentiary spore powders, and it is not known how the Bacillus subtilis contaminant came to be in the Post and Brokaw spore powders, the contaminant must have been introduced during
the production of the Post and Brokaw spores. Taken together, the postmark dates, the Silicon signature, the Bacillus subtilis contaminant, the phenotypic, and the genotypic comparisons, it can be concluded that, on at least two separate occasions, a sample of RMR-1029 was used to grow spores, dried to a powder, packaged in an envelope with a threat letter, and mailed to the victims. '
Several crucial pieces of information are missing here. First, we don't have the amount of material that is in RMR-1029 or its status in terms of processing with regard to purity or possible processing to weaponize it. In later sections of the warrant, Ivins is said to also refer to this flask interchangeably as "Dugway Ames Spores -- 1997", so it is entirely possible that the spores in RMR-1029 are treated with advanced materials. Notice also that this description does not have the previously leaked information regarding carbon-14 dating showing that the attack material was produced in the previous two years before the attack. Nevertheless, the presence of B. subtilis in the attack material is taken as evidence that RMR-1029 was the parent material for the attack material. That simply doesn't follow--if RMR-1029 contained sufficient material, the attack material could have been taken from that flask and mixed with other material, including the B. subtilis. Only with age data could one conclusively determine which sample is the parent. The presence of B. subtilis in one set of samples and its absence in another is also used to argue that RMR-1029 was sampled twice to obtain starter cultures. This also does not follow, as the two sets of attack material, if started from RMR-1029, simply could be from different stages in a purification process after culturing. Finally, the silicon content is referred to with regard to attack material but doesn't appear to be described for the RMR-1029 flask material.

The bottom line is that this search warrant does not solve many of the mysteries surrounding the nature of the material distributed through the mail. Most importantly of all, it is silent on the original source of RMR-1029. These are the critical questions that MUST be answered regarding RMR-1029:

1. Who grew that culture?
2. How large was the culture?
3. Who harvested the culture?
4. How was the material processed?
5. Where was RMR-1029 produced?
6. It it was produced at Dugway, does RMR-1029 contain all of the material produced in that batch?

Sadly, this search warrant leads to more questions than it answers with regard to the source of the anthrax attack material.


I have just noticed that the introductory "Overview" section of the warrant includes this:
At the time of the attacks, he was the custodian of a large flask of highly purified anthrax spores that possess certain genetic mutations identical to the anthrax used in the attacks;
So we do know that the material in RMR-1029 is highly purified. We still don't know if it is treated in any way to make it more dangerous. We also know that the flask is "large" but still have no idea how much material is there.

04 August 2008

More Speculation on the Source of the Spores in the 2001 Anthrax Attacks

In multiple comments over the past several days on Glenn Greenwald's blog and at Emptywheel, I have stated a belief that the material in the anthrax attacks of 2001, especially in the letters sent to Senators Daschle and Leahy, could only have come from the Army's Dugway Proving Grounds facility operated by Battelle Memorial Institute. However, after reading an article posted in a link in comments last night at Emptywheel, I now am much more open to the possibility that the material could have been produced outside of a sophisticated facility.

There are two key components to this change in my thinking. First, the article in Chemical and Engineering News by Lois Ember calls into question the early reports that the Dashcle material contained silica. It appears that the scientist in that report mis-spoke and that while silicon was detected, silica was not. Relaying information from Professor Matthew Meselson of Harvard, Ember further points out that closely related bacterial spores are reported to contain silicon, so the silicon in the early analysis may not have been from a source other than the spores themselves. Even more importantly, Ember reports that Meselson and another unnamed scientist have seen electron micrographs of the the attack material and there is no evidence that the spores have been treated with either silica or bentonite, as various media reports over time have suggested. In addition, Meselson and "Ken Alibek" (who previously worked for the Soviet bioweapons program) published a letter in the Washington Post, reprinted here, that makes the same contention.

To illustrate this point, and how straightforward the interpretation would be when looking at electron micrographs, I have copied some images from this website. I can't vouch for the authenticity or provenance of the photos, but they do serve to illustrate the points under discussion.

This photo is purported to be an anthrax spore coated with fumed silica and prepared at Dugway:
Note the "fuzzy" appearance of the spore and that, from the scale bar, it is in the 1 micron size range for a single spore of anthrax. Compare that to another photo said to be from the same publication from Dugway, where there is a clump of uncoated spores:

Note that the uncoated spores have a much smoother appearance. Also note that the scale is different here, as the bar is two microns instead of one. Also, the spores in the upper right part of the clump appear to have a little bit of the coating on them. Now compare these coated and partially coated spores with the following photo:
The photo above is specially important in another way. This appears to be a very clean, "pure" sample of spores labeled as anthrax and coming from USAMRIID (which is at Ft. Detrick). Clearly, it is possible to produce very clean preparations of anthrax spores, if the provenance of the photo is correct.

Any person with a significant amount of training in microbiology, sterile technique and basic biosafety standards, in my opinion, could produce highly purified anthrax spores that are untreated, using only equipment costing a few thousand dollars. Only if the spores are treated with a sophisticated material such as fumed silica does the requirement for an advanced facility and more advanced biosafety protocols come into play. The silica itself is highly dangerous to work with and would require much more sophisticated practices to protect the person preparing the material.

Also reported by Ember and elsewhere, is that DNA sequence information has definitively linked the attack material as genetically identical to the strain used at Ft. Detrick and that the water used to grow and/or process the material came from the northeastern US.

However, if the attack material is not treated in a way that requires sophisticated equipment, then anyone who had access to the Ft. Detrick strain could have produced the attack material without being detected. Further, they did not necessarily have to do the work in the northeastern US, since sterile filtered water from a company formerly named Bethesda Research Laboratory (Bethesda, MD) can be purchased. In fact, someone working on their own, without a sophisticated facility, possibly would find it easier to purchase sterilized water to work with, although they also could rely on simple filter sterilization of local water, as well.

If the FBI closes the antrhax case and releases its information in the next few days, it will be crucial to examine their evidence on the analysis of the attack material. If the material was simply purified, untreated spores, it will be very important to see how they connect this material with Bruce Ivins. The amount used in the attacks was millions of times more than he would have used in his experiments, so it is unlikely he would have produced it at Ft. Detrick without his colleagues noticing. This is especially important since producing this amount would begin to run up against the treaty prohibitions against producing amounts that could be used offensively, so he would have had to do it secretly outside the lab.

Further, there needs to be an explanation of the targeting of Senators Daschle and Leahy, with their letters being mailed after the first fatality was known. That mailing is most easily described as trying to get approval for the Patriot Act, and there has been no introduction of evidence that Ivins was even paying attention to that issue. The first death, even if unintended, should have been sufficient to bring attention to the need for an improved anthrax vaccine such as the one Ivins was working on, and thus fulfilling the motivation most have ascribed to his actions if he were the one behind the attacks.

01 August 2008

Connecting Some Dots

As first announced this morning by the Los Angeles Times, a new suspect in the 2001 anthrax attacks is dead of an apparent overdose of prescription pharmaceuticals. Like previous suspect Dr. Steven Hatfill, Dr. Bruce Ivins worked at the US Army Medical Research Institute of Infectious Diseases at Ft. Detrick, MD. Reports in the press are now saying that Ivins' rationale for releasing the anthrax was to test an anthrax vaccine on which he had been working.

It turns out that the US government got behind that idea of testing the vaccine in a very big way. As reported in the New York Times on September 18, 2006, the government, in response to the anthrax attacks, embarked on
Project BioShield, a $5.6 billion effort to exploit the country’s top medical and scientific brains and fill an emergency medical cabinet with new drugs and vaccines for a host of threats.
What is interesting about BioShield is that one company, Vaxgen, was awarded a contract for $877.5 million to produce a large amount of an anthrax vaccine. That vaccine was described in this way:
VaxGen's rPA102 vaccine is composed of a purified protein called recombinant Protective Antigen (rPA) and an aluminum salt routinely used in many vaccines. This design produces a vaccine that is expected to be well characterized and consistent across manufacturing runs. Recombinant Protective Antigen induces antibodies shown to neutralize anthrax toxins. rPA102 cannot cause anthrax infection.
rPA102 is based on work conducted at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). VaxGen has exclusive, worldwide rights to develop and commercialize a recombinant anthrax vaccine candidate based on patented technology developed by USAMRIID.
And yes, Dr. Ivins is an author of a publication in the journal Vaccine titled "Defining a serological correlate of protection in rabbits for a recombinant anthrax vaccine."

Looking further, Ivins is the first listed inventor of patent number 6,387,665 "Method of making a vaccine for anthrax", which does specifically reference rPA102.

So, the pieces do fit that the anthrax attacks did result in testing of Ivins' vaccine. However, it remains to be proven conclusively that Ivins is indeed responsible for the attacks. What is abundantly clear, however, is that the United States government wasted no time in putting nearly a billion dollars into testing Ivins' vaccine.