Inside the Plague Research Labs at the Heart of a Russian Mystery A Russian researcher, who died from an unknown illness, worked at a remote anti-plague facility. Few foreigners have visited these labs, which dot the former Soviet states, and are shrouded in secrecy.

A week after a 28-year-old researcher died from a mysterious infection while working in a Russian plague research laboratory, health officials around the world are still waiting for answers.

Darya Shipilova, a lab worker at the Irkutsk Anti-Plague Research Institute, was initially reported to have contracted pneumonic plague, raising concerns about the kinds of research being conducted at the facility and the safety measures employed there.

The Russian authorities have since ruled out pneumonic plague, a bacterial infection caused by the same pathogen as the better known bubonic plague, as the cause of Ms. Shipilova’s death, but have yet to confirm which pathogen was responsible for causing her pneumonia.

The incident, which led to denunciations by the United States and other governments, has exposed the international community’s lingering mistrust of Russian biomedical research, which harks back to the Soviet military’s once-robust programs for developing biological weapons.

The institute in Irkutsk never functioned as a military facility, but it was part of the broad yet secretive “Anti-Plague System.”At hundreds of field sites and labs across the Soviet Union, thousands of researchers were responsible for tracking emerging strains of plague and other endemic diseases, exterminating disease-causing rodents and developing vaccines. These facilities, experts said, had also provided pathogen samples to the military labs responsible for creating bioweapons during the Soviet era.

Most of these facilities are still functioning, and while those in Russia remain closely-guarded, some in former Soviet states have opened their doors to international researchers looking to learn about the fabled system.

The Anti-Plague System Although the Black Death of 14th-century Europe is the deadliest and best-known outbreak of the plague, a disease caused by the bacterium Y. pestis and carried by rodents, the illness has haunted Eurasia for thousands of years.

To put a stop to the frequent outbreaks in rural areas, where plague-harboring animals like rats, gerbils and marmots are endemic, the Soviet Union established a series of field sites and research institutes early in the 20th-century. They called it the “Anti-Plague System.”“The goal of their work was to be a central institute that surveils the vast areas around them, including the steppes that have large populations of burrowing wild rodents,” said Susan D. Jones, a veterinary historian at the University of Minnesota who in 2018 visited a former Soviet Anti-Plague Institute in what is now Kazakhstan.

In its early days, the program was rudimentary. Scientists would venture on horseback into plague hot spots, often staying in tents or renting rooms from local residents, and would spend their days exterminating rodents, digging up their burrows and burning their food supplies in an attempt to eradicate the diseases they carried.

Many of these expeditions were conducted without effective disinfectants or personal protective equipment, making the job of Anti-Plague workers a very dangerous one. And the eradication efforts didn’t stop the spread of the disease.

Between the 1920s and 1950s, however, the program shifted its focus from eradication to outbreak prevention, opening up a series of labs in cities around the U.S.S.R. By the middle of the 20th century, as an antibiotic to treat plague was developed, thousands of year-round employees staffed these labs, with hundreds more hired seasonally to collect samples in the field.

Inside the Soviet-Era Labs The research conducted at these Soviet-era facilities was “hidden behind a curtain of secrecy,” a former anti-plague researcher, Dr. Moisey Iosifovich Levi, wrote in a 1994 essay.

To avoid links being made between their work and the bioweapon development programs in military labs, workers at the plague labs were instructed never to mention anything specific about their work in their conversations.

Furthermore, the lab buildings themselves were built to look like normal housing units. Workers in many facilities maintained gardens, kept the lab windows open and walked around in normal clothing or even pajamas rather than wear white coats.

It wasn’t until one stepped inside the lab and saw scientific equipment — refrigerators full of pathogen samples, large sterilizers boiling used equipment and long tables dotted with microscopes — that the buildings’ true purpose became apparent.

Because of these unusual working conditions, “biosafety and biosecurity was very different from what we have in Western countries,” said Sonia Ben Ouagrham-Gormley, a biodefense researcher at George Mason University who has visited many anti-plague research institutes in former Soviet states.

In a series of anthologies entitled “Interesting Stories of the Events and People of the Anti-Plague System of Russia and the Soviet Union,” edited by Dr. Levi, authors describe dangerous conditions that included outbreaks among animals kept in the facilities, lab fires and lost pathogen samples.

In the final years of the Soviet Union, several facilities were provided with safer and more effective lab equipment. Household refrigerators were swapped for more secure versions and fume hoods replaced open windows. But funding for these changes was difficult to come by, so smaller and more remote facilities, including the institute in Irkutsk, struggled to keep up.

“In recent decades, much has changed at the Irkutsk Anti-Plague Institute, and not for the better. In contrast with other Anti-Plague institutes, it did not get attention,” wrote a former director of the institute, Igor Valerianovich Domaradsky, in an essay included in Dr. Levi’s anthologies.

“Therefore, the institute greatly lagged in acquiring new equipment and technology, which could not but affect the development of the institute,” he added. “What a shame.”The Facilities Today After the fall of the Soviet Union, most labs, from the advanced centers in wealthy cities to financially struggling rural facilities, remained open. And for decades, many were largely unchanged.

Dr. Ben Ouagrham-Gormley visited over 100 former-Soviet facilities in the early 2000s, alongside colleagues from the James Martin Center for Nonproliferation Studies. They found that entering one was like stepping into the past; tracking pathogen samples was done with pen and paper, and many vials were stored in oft-opened refrigerators, with wax seals used to indicate who had last opened them.

Many of the buildings, the researchers said, had no external security measures. And security inside was minimal, as well.

“We got there for a visit, and in the lab there was a table under a window that was wide open, because it was a summer, and there’s no air conditioning, and there were piles of plague cultures on the table,” Dr. Ben Ouagrham-Gormley said of one facility.

Over the next two decades, several facilities in former Soviet states were refurbished or rebuilt to accommodate updated scientific equipment, allowing some to become state-of-the-art centers visited by researchers from around the world.

“There are levels of containment within these buildings,” Dr. Jones said of the facility that she visited in Kazakhstan in 2018. “Once one is in the most high level of containment, one will be wearing full P.P.E. and all work is done in sealed containment facilities.”Because Russia has kept its Anti-Plague System facilities closed to international researchers and government officials, it’s difficult to say for certain whether facilities in that country have improved as much as those that benefited from international aid to other states after the breakup of the Soviet Union.

“I would assume that they have not improved much,” Dr. Ben Ouagrham-Gormley said. “But they probably had maintained their procedures of Soviet time and their methods, which were good to ensure biosafety and prevent accidents in spite of a lack of equipment.”About the facility in Irkutsk, little information is publicly available. However, Russian authorities have remained adamant that Ms. Shipilova’s death was not the result of unfollowed protocols or lapses in biosecurity at the facility.

K. R. Callaway is a science reporter and a member of the 2026-27 Times Fellowship, a program for journalists early in their careers.