Genetics Led to Anthrax Researcher Wpost 8/6

FBI to Show How Genetics Led to Anthrax Researcher
By Marilyn W. Thompson, Carrie Johnson and Rob SteinWashington Post Staff WritersWednesday, August 6, 2008; A03
The FBI today will begin to unveil how it exploited the rapidly advancing science of genetics to link a single bioweapons researcher to samples taken from the victims of the 2001 anthrax attacks and to powder from the letters that killed them.
The bureau scheduled briefings with Senate leaders who were among the targets and with survivors and relatives of those who died after anthrax-laced mail passed through their hands. It also plans to release about 50 pages of documents offering some details of the case.
The FBI said it will share those details with members of the Senate Judiciary Committee, including Chairman Patrick J. Leahy(D-Vt.), who was the addressee on one of the letters that set off panic on Capitol Hill.
Former Senate majority leader Thomas A. Daschle (D-S.D.), who was also a target, received a phone call Monday from FBI Director Robert S. Mueller III to set up a meeting, one day after Daschle questioned "the overall caliber and quality of the investigation." Daschle said Mueller cited "grand jury limitations" in what he could discuss. It will be Daschle's first briefing on the attacks in five years.
Much of what the FBI will say will involve the scientific trail, which included 19 outside laboratories at a cost of $10 million, that led investigators to bacteriologist Bruce E. Ivins, a noted anthrax researcher at the Army's bioweapons laboratory at Fort Detrick, Md. The evidence gave them enough confidence to move toward charging Ivins with murder before he committed suicide last week. The Justice Department yesterday continued to discuss whether it can shutter one of the most perplexing investigations in FBI history and unseal the bulky case files.
"We crossed a number of scientific barriers in this case," said one senior FBI official who has been ordered not to talk about the case publicly. "We literally were inventing science as we went along."
Law enforcement sources and published scientific papers indicate that the investigation gained traction through technological and scientific advances that dramatically speeded up the process of differentiating the genetic makeup of hundreds of distinct but closely related strains of bacteria.
Coupled with a fresh scientific understanding of the subtle differences between the strains and a new system for analyzing them, the rapid "sequencing" machines made it possible to detect the minuscule differences and link the one used in the attacks to a single laboratory.
At the time of the attacks, the knowledge to accomplish this in less than decades of laborious work did not exist. But the science of reading and analyzing DNA was on the verge of an explosion, one that the anthrax attacks may have helped to speed up.
Bruce Budowle, an FBI scientist at its lab in Quantico, reported to an international conference in September 2003 that a new field of forensic science -- known as microbial forensics -- had evolved as a result of the investigation. The letter attacks, he said, showed the "need to enhance our capabilities for forensic attribution."
The FBI has boasted publicly only in general terms about the scientific accomplishments in the case. Laboratories and researchers involved in the work under FBI contracts signed agreements not to discuss their contributions, but some relevant insights have emerged in scientific papers published over the past six years as work progressed on decoding the genetic composition of Bacillus anthracis, the anthrax bacterium.
Still, many details of the FBI's work remain fuzzy. The bureau shared none of the details that its consultants reported back, even among the other trusted laboratories.
"I don't think anybody involved knew who all the partners were," said Claire M. Fraser-Liggett, a former president of the Institute for Genomic Research in Rockville and a top scientist in her field. Her lab provided information to develop new assays, or tests, that the FBI could use to match the strain used in the attack to samples elsewhere. She said she did not know how the bureau specifically used the information.
When the deadly letters first surfaced along the East Coast after passing through the U.S. Postal Service, geneticists had not yet decoded the full genetic code, or genome, of the spore-forming anthrax bacteria, usually found in animal hides. Timothy Read, a DNA researcher who worked with Fraser-Liggett, had begun work on a sample from Porton Down, a defense research center in Britain. His incomplete research soon took on urgency.
Authorities had learned that they were dealing with one of 89 strains of anthrax bacteria. They identified their culprit as the Ames strain, cultivated in Ames, Iowa, from a sample taken from a dead cow in Texas. They had learned this by performing autopsies on the victims, which was, in itself, controversial.
The victims in Florida, Washington, New York and Connecticut died from inhalation anthrax, the most serious form of anthrax disease, and performing autopsies in such cases is highly discouraged. Once an incision is made, bacterial spores can escape from a corpse and become airborne, threatening medical personnel with infection. Military doctors are warned that in the event of a biological assault on the battleground, they should leave corpses behind.
After much debate and precautions, doctors at the Centers for Disease Control and Prevention in Atlanta finally autopsied the first victim, Robert Stevens, a photojournalist from Florida. They sent samples to the Rockville genomics laboratory.
Sequencing samples from the other victims confirmed that the Ames strain was involved in all of them, narrowing the field of possible laboratories from which the material could have come. The U.S. Army Medical Research Institute for Infectious Diseases, the Fort Detrick research center, was on a short list of possibilities.
By 2003, researcher Read, who did not return phone calls seeking comment, had focused his genetic analysis on the Ames strain. He published a paper in the journal Nature that concluded that the Ames strain DNA included more than 5 million chemical "bases" or "letters" that could serve as identifiers. He further noted that a difference of just 11 letters separated two samples of Ames that he analyzed, one a sample from the bacteria used in the postal attacks.
Other projects done at Northern Arizona University at Flagstaff and Integrated Genomics in Chicago enhanced Read's findings. Several experts yesterday said Paul Keim of Northern Arizona probably played a crucial role in the investigation. In 2004, a team he led published a paper describing a three-step method of analyzing samples that allowed them to winnow 1,067 B. anthracis samples down to 476 genetic sub-subtypes that could be distinguished from one another. Keim did not return calls seeking comment, and a university spokesman referred queries to the FBI.
The bureau did other tests to narrow the field of possible sources to USAMRIID, then concentrated its energies on scientists working within the bacteriology division. They made unannounced visits to gather samples and equipment, leading to a heightened anxiety among the division workers.
The most time-consuming process came as the FBI, in a frenzy of genetic analysis, shipped to the outside laboratories thousands of Ames strain samples from around the world. The bureau thought that it had to be able to convince a jury that its analysis of the material was foolproof.
As the investigation continued, the time and cost of doing genetic analysis plummeted, allowing the flood of samples to be turned around more quickly.
J. Craig Venter, former head of the Institute for Genomic Research, said such investigation was impossible before the recent advances. "This is just applying that same technology to forensic purposes. It's more the use of it to solve a particular criminal problem rather than [to] make advances in science," he said.
As the investigation gained focus, the samples from USAMRIID scientists offered the first real chance of pinning the material in the lethal mail to a specific scientist or team. Scientists had concluded that the formulation in the letters contained a genetic anomaly -- a flipped DNA sequence -- indicating that it was made from a combination of materials. This offered a scientific fingerprint that allowed them to compare it to formulations prepared by individual scientists.
"Just as we as humans have slight genetic variations, if there were particular anomalies used by a particular researcher, then you might be able to produce a perfect match," said a law enforcement source involved in the case.
Sources have said that the genetic trail eventually led agents to Ivins, who prepared formulations for anthrax vaccine tests at USAMRIID and other Army labs. But as elaborate and painstaking as it was, the science leaves open the possibility that someone else had access to a flask of bacteria Ivins prepared.
Sources have said that as many as 10 people worked with Ivins and could have handled his material.