Inside the Irkutsk Plague Institute

Mongolia, Marmots, Golden Eagles, and the ongoing plague investigation

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Washington DC · Dr.s Robert W. Malone and Jill Glasspool Malone

Plague is endemic along the Saylyugem mountain range, which runs along the border between the Russian Altai and western Mongolia. This is not a historical concern. Yersinia pestis (the Plague agent) circulates in wild animals across the region, and Russian and Mongolian teams find it there regularly.

The plague zone covers about twenty-nine thousand square kilometers, roughly sixty percent on the Mongolian side. The ground is high, dry, and treeless. The main animal hosts are grey marmots, long-tailed ground squirrels and pikas, along with the fleas that carry the bacterium between them.

Every summer, Russian and Mongolian anti-plague teams survey the region together. They trap rodents, collect and test their fleas, sample carcasses and examine remains found beneath raptor perches.

Golden eagles hunt this country, feeding on hares, marmots and corsac foxes. Upland buzzards hunt the same slopes for pikas, ground squirrels and young marmots. What the birds leave accumulates beneath their perches. The Russian surveillance term translates as “the remains of the table of birds of prey.” Field workers collect these remains fresh and mummified because a marmot that died of plague and was carried off can still yield the organism. A pair of eagles can cover more ground in a week than a trapping line covers in a season. We found no literature on whether golden eagles are susceptible to plague or act as vectors for its transmission, but we believe this issue should be examined.

In 2025, on the Russian side in the Kosh-Agach district of the Altai Republic, field workers collected material on the 14th and again on the 18th of August. Three samples came from grey marmots, including scavenger remains and a carcass. Another came from a long-tailed ground squirrel. Cultures came up on August 22, 27 and 29: four strains of Yersinia pestis, all of the main subspecies, the fully virulent form responsible for the historic pandemics.

Four strains are a productive season. Across the entire Russian Federation in 2025, the anti-plague service examined 41,559 rodent hosts and 124,380 vectors, including 110,960 fleas, and isolated thirteen strains. Plague cultures come from a handful of places, and few people handle them.

This year, the same teams worked the same ground from August 14 through 31 and studied more than two hundred samples of field material. On September 5, Rospotrebnadzor announced that the focus was showing high epizootic activity.

In the last week of September, Darya Shipilova fell ill. She was a laboratory technician at the Irkutsk Anti-Plague Research Institute of Siberia and the Far East, which holds the reference collection of cultures from this borderland. She was hospitalized on September 29 and died on October 2.

We cannot establish what she was handling. Nobody outside the institute can. Most reporting on her death treats the institute as a black box, even though its territory, collection, seasonal workflow and diagnostic capabilities are published. Placing her death within the institute’s system for collecting, processing and storing plague specimens is more useful than speculation.

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A More Dangerous Plague Strain is Discovered

Two years before Shipilova died, Sergey Balakhonov published a warning about those mountains. He directs the Irkutsk Institute. His paper appeared in the proceedings of the Seventeenth Interstate Scientific-Practical Conference of CIS member states, held in Irkutsk in October 2024, which he edited jointly with Anna Popova, the head of Rospotrebnadzor.

The Gorno-Altai high-mountain focus had been under Russian surveillance since 1961. For half a century it yielded one organism, Y. pestis of the Central Asian subspecies, which kills marmots reliably and people rarely. In 2012 the main subspecies turned up there for the first time. It had come from Mongolia across the mountains, and it spread through the grey marmot population across much of the plague region.

Three residents of Kosh-Agach contracted bubonic plague between 2014 and 2016. Balakhonov’s assessment states that the borderland warrants maximum attention. It records extraordinarily high epizootic activity in the neighboring Tuva focus since 2012, marmots included, and names the risk drivers as uncontrolled marmot hunting and new settlements built directly on the foci.

What this anti-plague institute is

The Soviet Union built a system that no Western country has an exact counterpart to. Plague is endemic in rodent populations across a wide belt of Central Asia and southern Siberia, and the Soviet state responded by creating a standing scientific and field service dedicated to it. Research institutes sat at the top. Below them sat anti-plague stations, permanently staffed, assigned to specific natural regions, going out every summer to trap, comb and culture. Russia inherited the system intact and still runs it under Rospotrebnadzor.

The Irkutsk institute covers the Siberian and Far Eastern federal districts, which is to say roughly half of Russia by area. It operates anti-plague stations at Chita and Khabarovsk directly, and it directs the scientific and methodological work of the stations on the southern Siberian foci, among them the Altai station at Gorno-Altaysk and the Tuva station at Kyzyl.

The stations perform the fieldwork and primary isolation. The institute maintains the reference collection and performs the characterization: subspecies identification, molecular typing, and antibiotic susceptibility testing. Each year, the pattern is to collect in the second half of August, isolate within one to two weeks at the station, then refer confirmed cultures upward. Autumn is when the reference bench in Irkutsk receives the season’s work.

Between 1961 and 2023, the service isolated 2,621 plague cultures from the Gorno-Altai region: 2,438 of the Central Asian subspecies and 183 of the main subspecies. In Tuva, 1,793 cultures were isolated between 1964 and 2023 from roughly 201,000 small mammals screened. A published paper from the institute describes Gorno-Altai as the most active focus in the Russian Federation and notes that cultures are isolated there every year.

The Mongolian half

Mongolia classifies seventeen of its twenty-one provinces as plague-risk territory. Two people died there in 2019, in Bayan-Olgii province along the Russian border, after eating marmot. On July 25 of this year, the Mongolian National Center for Zoonotic Diseases confirmed another human case by bacteriological testing in Khovd province.

The Mongolian side is where the organism is thickest. In 2018, a joint expedition surveyed 2,668 square kilometers of the Mongolian part of the focus, in the Saylyugem and Kharlankhuu ranges at altitudes between 2,400 and 2,800 meters. The team examined 282 mammals and 261 ectoparasites, 257 of them fleas, along with fresh and mummified remains from raptor feeding sites. It isolated forty-seven strains of Y. pestis of the main subspecies, all from grey marmots and their fleas.

Forty-seven strains from one Mongolian expedition. Thirteen from the entire Russian Federation in 2025. The concentration of plague activity on the Mongolian side is striking.

The expedition was conducted jointly by the Irkutsk institute and Mongolia’s national and Bayan-Olgii zoonotic disease centers. The same Irkutsk institute that coordinates this cross-border plague surveillance employed Shipilova.

The other route

There is a way into this that does not involve a laboratory bench at all.

The institute’s territory contains active plague foci, and its people go into them. Everyone named in this story so far who caught plague caught it outdoors: the three in Kosh-Agach, the two in Bayan-Olgii, the Mongolian case in July. None of them worked in a laboratory.

A worker infected in the field rather than at the bench would present differently and would also reconcile the official language. Natural plague begins as the bubonic form. It becomes pneumonic secondarily, when the organism reaches the lungs, and only then does it transmit from person to person. That sequence would account for a contact list weighted toward a hospital rather than a laboratory, which is what the Irkutsk contact tracing produced.

Early reporting pointed that way. Shipilova was described as having returned from a work trip shortly before falling ill, and Alexey Tsydenov, who heads the neighboring Republic of Buryatia, wrote that she had died of plague before amending the post to say she possibly had.

On October 3, Tsydenov stated, citing Rospotrebnadzor, that Shipilova had not visited Buryatia and that there were no known areas of plague activity in the republic. The 2025 surveillance data support that statement. The nearest documented plague activity was in Tuva and the Altai Republic.

In the same sentence denying the Buryatia connection, he called her the woman who died of plague.

Nobody has said whether Shipilova traveled to Tuva or the Altai Republic, where plague activity was documented both this year and last.

What the institute can do

The central point is simple: the Irkutsk institute has sophisticated technology for detecting plague, including unusual strains that simpler tests might miss. Whether those tests could conclusively determine what infected Shipilova depends on what specimens were collected, when they were collected, and whether antibiotics had already been started. None of that has been disclosed.

In 2025, the institute issued a methods manual on rapid detection of pathogenic biological agents. For plague, it specifies commercial Russian polymerase chain reaction systems that test several genetic targets at once. One detects locus 3a on the bacterial chromosome, the caf1 gene on the pFra plasmid and the pla gene on the pPCP1 plasmid. A second real-time test detects pla, caf1 and lcrV. The manual states that virulent strains can be distinguished from avirulent ones by their plasmid profile.

That matters because Y. pestis can lose plasmids. Strains that no longer produce the F1 capsular antigen occur naturally, have been isolated from sick people and can escape tests that depend on F1, including rapid antigen tests and standard serology. A Rostov institute study of twenty-one such strains concluded that when culture and F1 testing are doubtful or negative, investigators should continue testing with chromosomal targets. The Irkutsk system does exactly that, testing a chromosomal target alongside plasmid targets.

Timing matters as well. Antibiotics can quickly reduce the likelihood of recovering live Y. pestis by culture. If appropriate specimens were not collected before treatment began, a later negative culture would not necessarily exclude plague. Molecular testing does not require living bacteria, but its ability to answer the question still depends on what specimen was available, when it was collected and what test was performed.

Rospotrebnadzor has stated only that no microorganisms associated with Shipilova’s professional activity were identified. It has not disclosed what specimens were collected, whether they were obtained before or after antibiotics, what tests were performed, or the PCR results, if PCR was performed.

The issue is therefore not whether the institute possesses the technology to investigate a suspected plague infection. It clearly does. What remains unknown is what samples were available, what tests were run, and what those tests found.

The Plague Vaccine Problem

One argument has run through much of the coverage, and we raised it in our earlier analysis. Anti-plague institute personnel are vaccinated against plague. Russia uses a live attenuated vaccine, the EV line, and vaccination of personnel who handle the organism is routine and longstanding. If Shipilova was vaccinated, the argument goes, plague should have been unlikely to kill her.

The institute’s own published data complicate that assumption.

Between 2016 and 2017, its scientists studied sixty previously unvaccinated volunteers in Kosh-Agach, at the center of the Gorno-Altai plague region. All received the domestic live plague vaccine produced at the Stavropol institute. Ninety-one percent showed seroconversion one month later. By six months, antibody titers had fallen significantly and no longer exceeded the diagnostic threshold. The same was true at twelve months.

Revaccination performed little better. Sixteen percent exceeded the threshold one month afterward and seventy-six percent at three months, with more than thirty-nine percent still above it at six months.

The vaccination schedule is annual. The institute’s own measurements therefore show that antibody levels can fall substantially well before the next scheduled dose. An independent study of vaccinees in Kazakhstan found a similar pattern, with protective titers in twenty-six percent at four months, fifteen percent at eight months and eleven percent at twelve.

Vaccination therefore does not rule out plague as the cause of Shipilova’s death. More broadly, the published data raise an important question about how much protection the vaccine provides throughout the full year between doses. It appears most vaccinated people may be unprotected for most of the year. That question remains relevant regardless of what ultimately killed Shipilova.

Plague is Treatable

Institute scientists tested fifty-one Y. pestis strains from the Gorno-Altai collection against eight antibiotics. They found no resistant strains.

The important finding is straightforward: the plague strains tested from this region are susceptible to antibiotics. That raises another unanswered question about Shipilova’s death. Was she treated for plague, and if so, when? If she was not, why not?

She worked at one of Russia’s principal plague institutes and became critically ill during the season when plague cultures from the surrounding regions were being collected and processed. The institute’s own research showed that protection from the vaccine could wane well before the next annual dose. If plague was suspected, effective antibiotics were available. If it was not suspected until too late, that raises a different question: how was the diagnosis missed?

We do not know whether treatment came too late or never came at all.

The Evidence Russia Has Not Released

The Irkutsk institute will host the eighteenth scientific conference of the Commonwealth of Independent States (CIS), the regional organization formed by former Soviet republics, on October 21 and 22. Delegations have been invited from ten capitals, including Beijing and Ulaanbaatar. The conference has a budget of roughly $160,000 and has not been canceled.

An institute capable of convening an international conference can release a PCR result. Difficulty is not the obstacle.

No international mechanism can compel it to do so. The Biological Weapons Convention has no verification regime, a limitation Under Secretary of State Thomas DiNanno described plainly in Geneva last December. The International Health Regulations require notification of events that may constitute an international public health concern, but the state itself determines whether an event meets that threshold. Russia has made no such notification.

That leaves a remarkable gap. From the institute’s own publications, an outsider can reconstruct its territory, plague collection, seasonal workflow, diagnostic capabilities, vaccine performance and antibiotic susceptibility data. What we cannot see are the clinical and laboratory records that would answer the simplest questions about Shipilova: what specimens were collected, when they were collected, what tests were performed, what those tests found, and whether she was treated for plague.

For decades, this system has trapped infected animals, isolated Y. pestis, characterized the strains and preserved the cultures. It can tell us when a plague strain was collected from a marmot in the Altai, what subspecies it belonged to and whether it was susceptible to antibiotics.

What it has not told us is what killed one of its own laboratory technicians.

End

*Dr. Robert Malone is a U.S.-nominated Qualified Expert on the roster of the United Nations Secretary-General’s Mechanism for Investigation of Alleged Use of Chemical and Biological Weapons (UNSGM), whose experts may be called upon to participate in UN investigations of alleged chemical, biological, or toxin weapons use.

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References

Arsenyeva, T. E., A. L. Trukhachev, E. A. Vasilieva, I. V. Morozova, and S. A. Lebedeva. 2014. “Osobennosti shtammov vozbuditelya chumy, ne produtsiruyushchikh osnovnogo kapsulnogo antigena F1, i aprobatsiya otdelnykh metodov ikh detektsii.” Universum: Khimiya i Biologiya. Rostov-on-Don Anti-Plague Institute. https://7universum.com/ru/nature/archive/item/1513.

Balakhonov, S. V., and A. Yu. Popova, eds. 2024. Aktualnye voprosy sanitarnoi okhrany territorii i snizheniya riskov rasprostraneniya chumy i drugikh opasnykh infektsionnykh boleznei. Proceedings of the XVII Interstate Scientific-Practical Conference of CIS Member States, Irkutsk, October 8 and 9. https://irknipchi.ru/mat_conf_0809102024.pdf. Includes Balakhonov et al. on the Central Asian plague natural focal zone, the 2012 arrival of the main subspecies in Gorno-Altai from Mongolian territory, culture counts for the Gorno-Altai and Tuva foci, and joint Russian-Mongolian anti-plague teams.

DiNanno, Thomas G. 2025. “Modern Tools for Modern Threats: Towards Strengthening BWC Implementation, Verification, and Assurance.” Remarks at a Biological Weapons Convention Meeting of States Parties side event, Geneva, December 15. https://geneva.usmission.gov/2025/12/16/remarks-on-msp-side-event-modern-tools-for-modern-threats-towards-strengthening-bwc-implementation-verification-and-assurance/.

Irkutsk Anti-Plague Research Institute of Siberia and the Far East. 2025. Ekspress- i uskorennye metody spetsificheskoi indikatsii patogennykh biologicheskikh agentov. Educational manual. https://irknipch.ru/express_2025.pdf. Specifies the multiplex PCR panel for Y. pestis: locus 3a, caf1, pla, and lcrV.

Korzun, V. M., S. V. Balakhonov, A. V. Denisov, E. N. Rozhdestvensky, E. G. Tokmakova, et al. 2019. “Epizooticheskaya situatsiya v Mongolskoi chasti transgranichnogo Sailyugemskogo prirodnogo ochaga chumy v 2018 g.” Problemy Osobo Opasnykh Infektsii. https://journal.microbe.ru/jour/article/view/1153. Irkutsk institute with Mongolia’s National Center for the Study of Zoonotic Infections and the Bayan-Olgii Center for Zoonotic Infections. Source for the 2018 survey area, specimen counts, raptor feeding-site remains, and the forty-seven main-subspecies strains.

Khvoinova, E. G., E. G. Tokmakova, O. D. Zakhlebnaya, S. A. Vityazeva, and S. V. Balakhonov. 2017. “Izuchenie antibiotikochuvstvitelnosti kollektsionnykh shtammov Yersinia pestis v Gorno-Altaiskom vysokogornom prirodnom ochage.” In Sovremennye problemy epidemiologii, mikrobiologii i gigieny, 149. Rospotrebnadzor IX All-Russian Conference of Young Scientists. https://irknipchi.ru/conference-materials.pdf.

Korytov, K. M., V. V. Voitkova, V. I. Dubrovina, S. L. Tagyzova, and S. V. Balakhonov. 2017. “Serologicheskii monitoring u lyudei, vaktsinirovannykh protiv chumy i prozhivayushchikh v Gorno-Altaiskom vysokogornom prirodnom ochage chumy.” In Sovremennye problemy epidemiologii, mikrobiologii i gigieny, 69. https://irknipchi.ru/conference-materials.pdf.

Mongolia National Center for Zoonotic Diseases, via Xinhua. 2026. “Suspected Bubonic Plague Case Confirmed in Mongolia.” July 25. https://english.news.cn/asiapacific/20260725/52ed7127c5df463bbf87b8dd272f6e13/c.html.

Popov, N. V., and L. D. Shilova, comps. 2026. “Epizooticheskaya aktivnost prirodnykh ochagov chumy na territorii Rossiiskoi Federatsii v 2025 g.” Appendix, reference materials. Russian Research Anti-Plague Institute “Microbe,” Saratov. https://www.microbe.ru/files/Plag_foc_2025.pdf.

Tsydenov, Alexey, via i38.ru. 2026. “V Buryatii ochagov chumy net.” October 3. https://i38.ru/obschestvo-obichnie/v-buryatii-ochagov-chumi-net. Head of Buryatia, citing Rospotrebnadzor, that the deceased had not visited the republic and that Buryatia contains no plague foci.

Toktarov, M., et al. 2019. “Human Response to Live Plague Vaccine EV, Almaty Region, Kazakhstan, 2014-2015.” PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0218366.

Zab.ru. 2026. “Na granitse s Mongoliei i Rossii zafiksirovali vysokuyu aktivnost ochaga chumy.” September 5. https://zab.ru/articles/8801. Rospotrebnadzor announcement of high epizootic activity in the Saylyugem focus, sampling window August 14 to 31.