Comparative Genetic Analysis of Yersinia pestis Strains Isolated on the Ukok Plateau and other Territories of the Altai Mountains

The aim of the study was molecular-genetic identification and analysis of the phylogenetic relationship of Yersinia pestis strains isolated on the Ukok Plateau in 2020, in order to establish the current boundaries of the natural mega focus of plague in the Altai Mountains in Russia and Mongolia.

Materials and methods. 37 strains of Y. pestis of the main subspecies isolated in the Tuva mountain and Gorno-Altai high-mountain plague foci and adjacent territories of Mongolia in 1971–2020 were studied. The whole genome sequencing of the strains was performed using the Ion S5 XL System (Thermo Fischer Scientific). Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 were used to process the data and assemble de novo the sequences of raw reads. The average size of the collected genome was 4.55 million base pairs. Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, then 28 SNP homoplasies were removed. The resulting set of SNPs contained only the core region of the genome (955 SNPs). The dendrogram was constructed using the Maximum Likelihood method applying the PhyML 3.1 program.

Results and discussion. The current population structure of Y. pestis of the main subspecies, antique biovar, phylogenetic line 4.ANT, endemic to the foci of the Altai Mountains in Russia and Mongolia has been determined. The presence of 4.ANT-21 clone, which became widespread in the territory of these natural foci of plague at the begining of the XXI century, was revealed. It is shown that three strains isolated on the Ukok Plateau in 2020 belong to clone 4.ANT-21. According to phylogenetic analysis, evidence of 4.ANT circulation on the Ukok Plateau before 2018 was obtained. The lesson that has been learned is that it is necessary to study the territories of Mongolia, Kazakhstan and China bordering the Ukok Plateau in order to establish the current boundaries of the 4.ANT mega focus. 

1. Onishchenko G. G., Kutyrev V. V., editors. [Natural Foci of Plague in the Caucasus, the Caspian Sea, Central Asia and Siberia]. Moscow: “Meditsina”; 2004. 191 p.

2. Kutyrev V.V., Eroshenko G.A., Nosov N.Y., Krasnov J.M., Kukleva L.M., Nikiforov K.A., Al’hova J.V., Oglodin E.G., Guseva N.P., Motin V.L. Phylogeny and classification of Yersinia pestis through the lens of strains from the plague foci of Commonwealth of Independent States. Front. Microbiol. 2018; 9:1106. DOI: 10.3389/fmicb.2018.01106.

3. Cui Y., Yu C., Yan Y., Li D., Li Y., Jombart T., Weinert L.A., Wang Z., Guo Z., Xu L., Zhang Y., Zheng H., Qin N., Xiao X., Wu M., Wang X., Zhou D., Qi Z., Du Z., Wu H., Yang X., Cao H., Wang H., Wang J., Yao S., Rakin A., Li Y., Falush D., Balloux F., Achtman M., Song Y., Wang J., Yang R. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl. Acad. Sci. USA. 2013; 110(2):577–82. DOI: 10.1073/pnas.1205750110.

4. Balakhonov S. V., Tsendzhav S., Erdenebat A. [New plasmidovars of plague pathogen strains isolated in Mongolia]. Moleculyarnaya Genetika, Mikrobiologiya i Virusologiya [Molecular Genetics, Microbiology and Virology]. 1991; 11:27–9.

5. Erdenebat A., Batbold J., Dashnyam B. Plasmid content and distribution of Y. pestis isolated in Mongolia. Scientific Journal. Center for Infectious Diseases with Natural Foci. 2001; 9:187–91.

6. Adyaasuren Z., Tserennorov D., Myagmar Zh., Gankhuyag Ts., Otgonbayar D., Bayar Ts., Verzhutsky D.B., Ganbold D., Balakhonov S.V. [The current situation in the natural plague foci of Mongolia]. Dalnevostochny Zhurnal Infektsionnoj Patologii. [Far Eastern Journal of Infectious Pathology]. 2014; 25:22–5.

7. Balakhonov S.V., Afanas’Ev M.V., Shestopalov M.Yu., Ostyak A.S., Vityazeva S.A., Korzun V.M., Verzhutsky D.B., Mikhailov E.P., Mishchenko A.I., Denisov A.V., Ivzhenko N.I., Rozhdestvensky E.N., Viskov E.N., Fomina L.A. [The first case of Yersinia pestis subsp. pestis isolation in the territory of Altai Mountain natural plague focus. Communication 1. Microbiological characteristics, molecular-genetic and mass-spectrometric identifica- tion of the isolate]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2013; (1):60–5. DOI: 10.21055/0370-1069-2013-1-60-65.

8. Kutyrev V.V., Popova A.Yu., Ezhlova E.B., Demina Yu.V., Pakskina N.D., Shchuchinov L.V., Mikhailov E.P., Mishchenko A.I., Rozhdestvensky E.N., Bazarova G.K., Denisov A.V., Sharova I.N., Popov N.V., Kuznetsov A.A. [Infection of an individual with plague in the Gorno-Altaisk high-mountain natural focus in 2014. Communication 1. Epidemiological and epizootiological peculiari- ties of plague manifestations in the Gorno-Altaisk high-mountain (Sailyugemsky) natural plague focus]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2014; (4):9–16. DOI:10.21055/0370-1069-2014-4-9-16

9. Balakhonov S.V., Popova A.Yu., Mishchenko A.I., Mikhailov E.P., Ezhlova E.B., Demina Yu.V., Denisov A.V., Rozhdestvensky E.N., Bazarova G.K., Shchuchinov L.V., Zarubin I.V., Semenova Z.E., Madenova N.M., Dyusenbaev D.K., Yarygina M.B., Chipanin E.V., Kosilko S.A., Noskov A.K., Korzun V.M. [A case of human infection with plague in the Kosh-Agach region of the Republic of Altai in 2015. Communication 1. Clinical-epidemiological and epizootiological aspects]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2016; (1):55–60. DOI: 10.21055/0370-1069-2016-1-55-60.

10. Korzun V.M., Balakhonov S.V., Denisov A.V., Chipanin E.V., Kosilko S.A., Rozhdestvensky E.N., Mikhailov E.P., Mishchenko A.I., Bazarova G.Kh., Yarygina M.B. [Introduction of the plague pathogen of the main subspecies into the settlements of the gray marmot in the South-Eastern Altai]. Meditsinskaya Parazitologiya i Parazitarnye Bolezni. [Medical Parasitology and Parasitic Diseases]. 2017; 4:20–9.

11. Popova A.Yu., Balakhonov S.V., Shchuchinov L.V., Matrosov A.N., Mikhailov E.P., Mishchenko A.I., Denisov A.V., Shefer vV.V., Shestakov V.A., Rozhdestvenskly E.N., Chipanin E.V., Korzun V.M., Kosilko S.A., Innokent’yeva T.I., Yarygina M.B., Sbitneva S.V., Tagyzova S.L., Arkhipov G.S., Shcherbakova S.A., Toporkov V.P., Kuklev E.V., Razdorsky A.S., Kuznetsov A.A., Sludsky A.A., Popov N.V., Ermakov N.M., Kutyrev V.V. [Organization of plague control and prevention measures on the ter- ritory of Kosh-Agach district of the Altai Republic and estimation of their effectiveness]. Infektsionnye Bolezni [Infectious Diseases]. 2018; 16(4):5–15. DOI: 10.20953/1729-9225-2018-4-5-15.

12. Balakhonov S.V., Shchuchinov L.V., Mishchenko A.I., Matrosov A.N., Denisov A.V., Rozhdestvensky E.N., Korzun V.M., Kosilko S.A., Tagyzova S.L., Toporkov V.P., Popov N.V., Shcherbakova S.A., Kutyrev V.V. [Organization of preventive, antiepidemic measures to reduce the risk of complications of the epide- miological situation on plague in the territory of the Altai Republic]. Zhurnal Mikrobiologii, Epidemiologii, i Immunobiologii [Journal of Microbiology, Epidemiology and Immunobiology]. 2018; 6:85–94. DOI: 10.36233/0372-9311-2018-6-85-94.

13. Eroshenko G.A., Popov N.V., Krasnov Y.M., Nikiforov K.A., Kuznetsov A.A., Matrosov A.N., Kutyrev V.V. [Natural megafocus of Yersinia pestis main subspecies, antique biovar, phylogenet- ic line 4.ANT in Gorny Altai]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2018; (2):49–56. DOI: 10.21055/0370-1069-2018-2-49-56.

14. Morelli G., Song Y., Mazzoni C.J., Eppinger M., Roumagnac P., Wagner D.M., Feldkamp M., Kusecek B., Vogler A.J., Li Y., Cui Y., Thomson N.R., Jombart T., Leblois R., Lichtner P., Rahalison L., Petersen J.M., Balloux F., Keim P., Wirth T., Ravel J., Yang R., Carniel E., Achtman M. Yersinia pestis genome sequenc- ing identifies patterns of global phylogenetic diversity. Nat. Genet. 2010; 42(12):1140–3. DOI: 10.1038/ng.705.

15. Balakhonov S.V., Yarygina M.B., Gladkikh A.S., Mironova L.V., Feranchuk S.I., Bochalgin N.O., Rozhdestvensky E.N., Vityazeva S.A., Natsagdorzh B., Tserennorov D., Tsogbadrakh N., Kosilko S.A., Korzun V.M. [Molecular-genetic characteris- tics of Yersinia pestis strains isolated in the Mongolian territory of transboundary Sailyugem natural plague focus]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2019; (3):34–42. DOI: 10.21055/0370-1069-2019-3-34-42.

16. Altantugs B., Byambasuren D., Maralmaa G., Naranbaatar R., Saltanat S., Uuganjavkhaa B., Erdenechimeg L., Altantogtokh D. Epidemiology of human plague in Mongolia. Current issues on zoonotic diseases. Ulaanbaatar. 2017; 22:26–33.

17. Popov N.V., Eroshenko G.A., Karnaukhov I.G., Kuznetsov A.A., Matrosov A.N., Ivanova A.V., Porshakov A.M., Lyapin M.N., Korzun V.M., Verzhutsky D.B., Ayazbaev T.Z., Lopatin A.A., Ashibokov U.M., Balakhonov S.V., Kulichenko A.N., Kutyrev V.V. [Epidemiological and epizootic situation on plague in the Russian Federation and forecast for its development for 2020–2025]. Problemy Osobo Opasnykh Infektsii [Problems of Particularly Dangerous Infections]. 2020; (1):43–50. DOI: 10.21055/0370-1069-2020-1-43-50.

18. Chipanin E.V., Denisov A.V., Korzun V.M., Kholin A.V., Shestakov V.A., Roshchupkin S.E., Bazarova G.H., Mishchenko A.I. [Results of epizootiological survey of hard-to-reach areas of the Gorno-Altai high-mountain natural plague focus in 2019]. Dalnevostochny Zhurnal Infektsionnoj Patologii. [Far Eastern Journal of Infectious Pathology]. 2019; 37:52–3.

19. Onishchenko G.G., Kutyrev V.V., editors. [Laboratory Diagnostics of Particularly Dangerous Infectious Diseases. Practice Guidelines]. Moscow: CJSC “Shiko”; 2013. 560 p.

20. Harbeck M., Seifert L., Hänsch S., Wagner D.M., Birdsell D., Parise K.L., Wiechmann I., Grupe G., Thomas A., Keim P., Zoller L., Bramanti B., Riehm J.M., Scholz H.C. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague. PLoS Pathog. 2013; 9(5):e1003349. DOI: 10.1371/journal.ppat.1003349.