Abstract

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.

Highlights

  • 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

  • Core SNPs were detected by aligning the contigs of Y. pestis strains on the CO92 genome using the Snippy 4.6 program, 28 SNP homoplasies were removed

Read more

Summary

Original articles

Сравнительный генетический анализ штаммов Yersinia pestis, выделенных на плато Укок и других территориях Горного Алтая. Цель исследования – молекулярно-генетическая идентификация и анализ филогенетического родства штаммов Yersinia pestis, выделенных на плато Укок в 2020 г., для установления современных границ природного мегаочага чумы в Горном Алтае в России и Монголии. Исследовано 37 штаммов Y. pestis основного подвида, выделенных в Тувинском горном и Горно-Алтайском высокогорном очагах чумы и смежных территориях Монголии в 1971–2020 гг. Определена современная популяционная структура Y. pestis основного подвида античного биовара филогенетической линии 4.ANT, эндемичной для трех очагов Горного Алтая в России и Монголии. Выделенных на плато Укок в 2020 г., к клону 4.ANT-21. Сделан вывод о необходимости обследования пограничных с плато Укок территорий Монголии, Казахстана и Китая для установления современных границ мегаочага 4.ANT.

Оригинальные статьи
Материалы и методы
Результаты и обсуждение
Очаг и место выделения Focus and site of isolation
Координаты Coordinates
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call