раСПроСтранение Yersinia pestis СредневеКового Биовара в Северном, Северо-ЗаПадном ПриКаСПии и ПредКавКаЗье во второй Половине XX веКа 1 ФКУЗ «Российский научно-исследовательский противочумный институт «Микроб», Саратов, Российская Федерация; 2 РГП на ПХВ «Национальный научный центр особо опасных инфекций им. М. Айкимбаева» Министерства здравоохранения Республики Казахстан, Алматы, Республика Казахстан; 3 РГУ «Уральская противочумная станция» Комитета охраны общественного здоровья Министерства здравоохранения Республики Казахстан, Уральск, Республика Казахстан цель работы -установление происхождения штаммов Y. pestis, получивших распространение в природных очагах чумы северного, северо-западного прикаспия и предкавказья во второй половине XX века. материалы и методы. проведено исследование свойств и полногеномное секвенирование 22 штаммов Y. pestis, выделенных в 1923-2003 гг. в пяти природных очагах сусликового типа, расположенных в северном и северо-западном прикаспии и предкавказье. Филогенетический анализ выполнен по данным полногеномного SNP анализа на основе 1348 выявленных SNPs. поиск SNPs в коровом геноме проведен с помощью программы Wombac 2.0. для анализа филогенетических связей штаммов использована дендрограмма Maximum Likelihood, модель GTR. результаты и обсуждение. все исследованные штаммы из очагов северного, северо-западного прикаспия и предкавказья относятся к филогенетической ветви 2.MED1 средневекового биовара возбудителя чумы. по данным полногеномного SNP анализа выявлено наличие двух групп близкородственных штаммов, включающих штаммы 1923-1945 и 1962-2003 гг. предшественниками штаммов 1962-2003 гг. из северного, северо-западного прикаспия и предкавказья на филогенетическом дереве являются штаммы из северного приаралья 1945 г. это свидетельствует о том, что синхронная активизация группы природных очагов прикаспийской низменности и предкавказья в 1975-1979 гг., после длительных 20-37-летних перерывов, могла быть вызвана распространением штаммов из северного приаралья. данные эпизоотических наблюдений указывают на то, что активизация волго-уральского песчаного очага чумы в 60-х годах прошлого столетия предшествовала началу регистрации эпизоотий чумы на территории природных очагов сусликового типа в северном, северо-западном прикаспии и в предкавказье.Ключевые слова: возбудитель чумы, природные очаги прикаспия, штаммы, распространение.Abstract.
Objective of the work was to identify molecular-genetic peculiarities, to conduct whole genome sequencing and phylogenetic analysis of Yersinia pestis strains isolated inVietnam between 1962 and 1989.Materials and methods. We have studied the properties of 50 Y. pestis strains, carried out whole genome sequencing of 18 and fragment sequencing of 32 strains from Vietnam. Phylogenetic analysis was performed on the basis of whole genome SNPanalysis by 1391 identified SNPs. Whole genome SNP-analysis and search for marker SNPs were conducted applying Wombac 2.0 software package. Phylogenetic diagram construction was done using Maximum Likelihood algorithm.Results and discussion. Several phylogenetic branches and Y. pestis populations coinciding with geographical and historical dissemination of the strains have been distinguished. The major part of the strains from Vietnam falls under the branch designated by us as 1.ORI2v. Two strains form a separate branch together with the strain from India belonging to 1.ORI2 line, one more strain, 55-801 Saigon, is set among the strains of 1.ORI1 line. Based on the data obtained and evidence from the literature sources it can be assumed that introduction of plague into Vietnam occurred through several waves: Nha Trang city in 1898, by sea; north provinces of the country – 1908. The second wave of Y. pestis dissemination across the territory of Vietnam began in 1960s with the emergence of the strains from the natural plague focus in Yunnan province, China.
Objective of the study – comparative phylogenetic analysis of Yersinia pestis strains, isolated in Precaspian North-Western steppe focus in 1924–1926, 1972, and 1986–1990 to understand the causes of focal reactivation during different time periods of the XX century.Materials and methods. The work included 30 strains of Yersinia pestis from Precaspian North-Western steppe natural focus and adjacent plague foci. Whole genome sequencing of eight Y. pestis strains from the former was carried out. Also whole-genome sequences of 16 strains from neighboring natural foci were used. Whole-genome sequencing of Y. pestis strains was conducted in Ion PGM system (Life technologies). SNPs search across the core genome was performed using software package Wombac 2.0. Tree diagram Maximum Likelihood, HKU85 model, was constructed to analyze phylogenetic relations.Results and discussion. It is established that in early XX century (1924–1926), strains of phylogenetic branches 2.MED4 and 2.MED1, belonging to medieval biovar, main subspecies, circulated on Ergenin Upland in the Precaspian North-Western steppe natural focus. Later on they became extinct in the territory. It is shown that the strains, isolated on Ergenin Upland in 1972, constituted a common subcluster on the dendrogram with the strains from low-mountain and piedmont plague foci of Caucasus and Transcaucasia, dated the same time period. It was inferred that epizootic manifestations on Ergenin upland in 1972, after a long recess since 1938, were caused by importation of Y. pestis strains from low-mountain natural plague foci of Caucasus and Transcaucasia. It was noted that expansion of Caucasian strains was of short-term character, and plague infected animals have not been found on Ergenin Upland since 1974 (including modern period). It is established that Y. pestis strains isolated in the eastern part of Precaspian North-Western steppe focus between 1986 and 1990, do not have close genetic relation to the strains that circulated on Ergenin Upland in 1924–1926 and 1972. It is determined that each epizootic period (1913–1938 and 1972–1973) in Precaspian North-Western steppe natural focus culminated in the elimination of the circulating Y. pestis strains and rehabilitation of the focal territory.
Aim. The present paper provides a comparative analysis of the phylogenetic relationship between Yersinia pestis strains isolated in the Volga-Ural sandy natural focus during the periods of 1912-1945 and 1963-2003, which were characterised by different levels of epidemic activity, in order to identify the spatiotemporal patterns in the circulation of the plague pathogen in the North Caspian region. Materials and methods. We studied the properties and performed whole-genome sequencing of 18 Y. pestis strains from the Volga-Ural sandy focus, along with 12 strains from other foci in the North Caspian and North Aral regions, isolated from 1912 to 2003. The phylogenetic analysis was performed drawing on the whole-genome SNP analysis, which was conducted on the basis of 2188 SNPs identified in the core genome using the Wombac 2.0 program. Maximum Likelihood Dendrogram (GTR model) was used for the analysis of phylogenetic relationships between strains. Results and discussion. All studied strains from the foci of the North Caspian region belong to the main subspecies (biovar medievalis) of the plague pathogen. These are highly virulent and epidemiologically dangerous strains. The whole-genome sequencing and phylogenetic analysis of 30 strains from the Volga-Ural sandy focus, as well as adjacent plague foci, reveal that the strains (biovar medievalis) of two phylogenetic branches-2.MED4 and 2.MED1-were spread across the focus under study in the early 20th century. It is confirmed that 2.MED1 strains were the etiological agents of plague outbreaks in the Volga-Ural sandy focus during this period. The study revealed the presence of parallel evolutionary lines in 2.MED1 associated with plague outbreaks in the first half of the last century. In the second half of the 20th and early 21st centuries, the modern evolutionary line of 2.MED1 became widespread in the Volga-Ural sandy focus. The strains of this line are closely grouped, which indicates their close genetic relationship. Only sporadic cases of plague were recorded during this period. Modern strains from the Volga-Ural sandy focus (1963-2003), as well as the strains previously isolated there (1912-1945), do not originate from each other. These strains represent closely related, independent evolutionary branches, extending from the common trunk of 2.MED1. Modern strains originating from those of the North Aral desert focus (1945) form a separate cluster in the dendrogram. This suggests that, following a break in the 1950s, the Volga-Ural sandy focus was re-colonised by closely related strains from the North Aral region.
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