Pisarenko Sergey V, Evchenko Anna Yu, Kovalev Dmitry A, Evchenko Yuri М, Bobrysheva Olga V, Shapakov Nikolay A, Volynkina Anna S, Kulichenko Alexander N
Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
Stavropol Research Anti-Plague Institute, 355035 Stavropol, Russian Federation.
Genomics. 2021 Jul;113(4):1952-1961. doi: 10.1016/j.ygeno.2021.04.021. Epub 2021 Apr 20.
Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries.
We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2.
On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y. pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.
鼠疫是一种极具危险性的媒介传播传染病，在人类历史上留下了深刻印记。高加索地区有13个自然鼠疫疫源地，分布在俄罗斯联邦、阿塞拜疆、亚美尼亚和格鲁吉亚境内。我们对在高加索和外高加索自然疫源地分离出的鼠疫耶尔森菌菌株进行了全基因组测序。利用全基因组单核苷酸多态性（SNP）分析数据和贝叶斯系统发育方法，我们对鼠疫病原菌现代种群进行了进化-系统地理学分析，以确定来自高加索地区的鼠疫耶尔森菌菌株与其他国家菌株之间的系统发育关系。
我们使用345个鼠疫耶尔森菌基因组，基于全基因组SNP分析构建了该物种的全球进化系统发育重建。本研究对16株分离株的基因组进行了测序，其余329个基因组来自GenBank数据库。核心基因组分析揭示了3315个可用于区分菌株的SNP。进化系统地理学分析表明，所研究的鼠疫耶尔森菌菌株属于遗传谱系0.PE2、2.MED0和2.MED1。结果表明，在东高加索高山、外高加索高山和里亚拉克辛斯基低山鼠疫疫源地分离出的鼠疫耶尔森菌菌株属于所有现存遗传谱系中最古老的——0.PE2。
基于对345株鼠疫耶尔森菌菌株的全基因组SNP分析，我们描述了鼠疫病原菌的现代种群结构，并明确了在高加索和外高加索自然疫源地分离出的菌株在鼠疫耶尔森菌全球种群结构中的位置。通过对病原菌当前种群的回顾性进化-系统地理学分析，我们确定了鼠疫耶尔森菌遗传谱系分化的可能时间框架，并提出了鼠疫病原菌历史传播的可能路径。
