The department hasn't determined whether samples containing plague bacteria and specimens of the deadly virus were shipped from its labs, Cook said.
"One of the things they're doing right now is trying to assess whether any of these substances, first of all, pose any sort of threat; second of all, whether these substances were shipped to any other laboratories," he said.
He said the Centers for Disease Control and Prevention determined there is no risk to the health of workers or the public.
Pressed by reporters for more answers about the investigation at a briefing Thursday, Cook said he was revealing everything he could.
"We're trying to be as forthcoming as we can be right now without alarming the public," he said.
Labeling, storage raise concerns
The latest investigation started after CDC inspectors found a sample of the plague in a freezer outside of a containment area on August 17 at the Edgewood Chemical Biological Center in Maryland, Cook said.
Investigators are working to determine whether the sample posed an "infectious threat," Cook said. Army tests found it was not infectious.
"That's the scientific work that's being done at this particular time, determining exactly what happened there, and whether or not ... there was mislabeling," he said.
Investigators are also looking into whether samples of equine encephalitis were labeled properly in logs, he said.
Anthrax shipments sparked inquiry
Earlier this year the Defense Department began an investigation after determining live anthrax samples had been shipped from Pentagon labs to 86 research facilities in the United States and at least seven foreign countries over the last several years.
Last week, the secretary of the Army directed an immediate review of safety procedures at all Defense Department labs
and facilities involved in the handling of toxic agents, such as anthrax.
The review ordered by Secretary John McHugh follows the discovery of anthrax contamination at a facility in Utah along with instances of incomplete record keeping at two other facilities in the United States.
Bacteria, virus can be deadly
Cook didn't provide details about the samples in question. A report in USA Today
said the investigation involved specimens of Yersinia pestis
, the bacteria that causes plague, and also two viruses that can cause serious illnesses: Eastern equine encephalitis
and Venezuelan equine encephalitis.
Yersinia pestis, the same type of bacterium that was responsible for the plague pandemic that wiped out 60% of the European population between the 14th and 17th centuries, maintains a foothold in the United States
and around the globe in rodents and the fleas that live on them. Today, the infections are treatable with antibiotics if they're caught early enough. Since 1970, there have been anywhere from a few to a few dozen cases of plague every year in the United States, most of them occurring in Western states, according to the Centers for Disease Control and Prevention.
Eastern equine encephalitis and Venezuelan equine encephalitis
are viruses that can be spread to humans by mosquitoes. According to the CDC, only a few cases of the illness are reported in the United States each year, but it's one of the most severe mosquito-transmitted diseases in the country, resulting in death in roughly a third of cases and causing significant brain damage in most survivors.