Caspian Sandy Natural Focus: Phylogenetic History and Origin of <i>Yersinia pestis</i> Strains

The purpose of the work was to analyze the phylogenetic relations and origin of Yersinia pestis strains isolated in different periods of epizootic activity of the Caspian sandy natural focus (CSNF) of plague in the XX–XXI centuries.Materials and methods. We used 40 Y. pestis strains from CSNF and adjacent plague foci, isolated in 1922–2015. Carried out was whole genome sequencing of 19 Y. pestis strains from CSNF. Phylogenetic analysis was performed using whole genome SNP analysis based on 1914 identified SNPs. The search for marker SNPs was conducted using the Snippy 4.6 software. The phylogenetic tree was constructed using the Maximum Likelihood algorithm, the GTR nucleotide substitution model.Results and discussion. The whole genome SNP analysis has revealed that Y. pestis strains of the medieval biovar from CSNF belong to 2.MED1 phylogenetic lineage and fall into two major branches. One of them circulated in the focus in the first half of the XX century, and the other – in the second half of the XX – early XXI centuries. It is shown that strains of the first branch were the cause of outbreaks and individual cases of plague in the CSNF in the first half of the XX century. They are closely related to strains from the Caspian North-Western steppe and Volga-Ural sandy natural plague foci, which caused numerous outbreaks with high mortality rate in the same period. Y. pestis strains from the CSNF of the second half of the XX and early XXI centuries belong to the second phylogenetic branch of the 2.MED1 line, at the node of which the strains from the Northern Aral Sea region of 1945 lay. The latter were the predecessors of all strains isolated in the CSNF after a long inter-epizootic period that occurred in the middle of the XX century. There can also be traced a genetic relation between the strains from CSNF and the Dagestan plain-foothill focus

Variability of <i>pgm</i>‑Region Genes in <i>Yersinia pestis</i> Strains from the Caspian Sandy and Adjacent Plague Foci

The aim of the study was to compare the nucleotide sequences of pgm‑region genes in Yersinia pestis strains isolated on the territory of the Caspian sandy and adjacent plague foci in 1925–2015. Materials and methods. 65 Y. pestis strains from the Caspian sandy and adjacent plague foci were used in the work. DNA isolation was performed using the PureLink Genomic DNA Mini Kit. Whole genome sequencing was conducted in Ion S5 XL System (Thermo Fischer Scientific). Data processing was carried out using Ion Torrent Suite software package 3.4.2 and NewblerGS Assembler 2.6. To compare the obtained sequences with the NCBI GenBank database, the Blast algorithm was used. The phylogenetic analysis was performed according to the data of whole genome SNP analysis based on 1183 identified SNPs. The search for marker SNPs was performed using the Snippy 4.6 program. The phylogenetic tree was constructed using the Maximum Likelihood algorithm, the GTR nucleotide substitution model. Results and discussion. The nucleotide sequences of pgm‑region genes of 65 Y. pestis strains from the Caspian sandy and adjacent plague foci have been assessed. Single nucleotide substitutions have been identified in Y. pestis strains from the Caspian sandy and Kobystan plain-foothill foci in the hmsR, astB, ybtS, ypo1944, ypo1943, ypo1936 genes, as well as a deletion of 5 bp in the ypo1945 gene, which is characteristic of strains of one of the phylogenetic lines of Y. pestis from the foci of Caucasus and Transcaucasia, isolated in 1968–2001. The data obtained can be used to differentiate Y. pestis strains from the Caspian sandy focus, as well as to establish the directions of microevolution of the plague pathogen in this region and adjacent foci

SNP-Profiles of <i>Yersinia pestis</i> Strains of the Medieval Biovar from the Caspian Sea Region Plague Foci

The SNP-typing method based on the detection of stable genetic markers in the genome, i.e., single nucleotide polymorphisms, is successfully used for genotyping of pathogenic microorganisms and can be applied for SNP-profiling of Yersinia pestis strains and molecular-genetic certification of focal areas. The aim of the study was to determine the SNP profiles of Y. pestis strains of the medieval biovar isolated in the Caspian Sea region plague foci in 1912–2015 and to develop a method for identifying unique SNPs using the Sanger sequencing for molecular-genetic certification of these territories. Materials and methods. A comprehensive study of the phenotypic and genotypic properties of 190 Y. pestis strains from plague foci in the Caspian Sea region was carried out. Phylogenetic reconstruction by the Maximum Likelihood method (GTR model) in the SeaView 5.0.4 software was performed on the basis of 1621 SNPs identified among 50 Y. pestis strains according to WG-SNP analysis in the snippy 4.6 program. Primers for PCR amplification of the SNP loci selected as target were calculated using the Vector NTI program. Sanger sequencing of SNPs loci was conducted on an ABI PRISM 3500XL genetic analyzer (Applied Biosystems, USA). Results and discussion. According to phenotypic characteristics, all studied strains from the Caspian foci belonged to a highly virulent and epidemically significant medieval biovar of the main subspecies of Y. pestis. According to the results of the WG-SNP analysis, 9 SNP genotypes were identified based on the polymorphism of single nucleotides of 24 genes characteristic of the main phylopopulations, which include strains isolated during various periods of epidemic and epizootic activity in the Caspian plague foci. Determining of SNP genotypes of Y. pestis strains of the medieval biovar, obtained over a hundred years in the Caspian foci, creates the prerequisites for defining the canonical SNP profile (canSNP) and for developing an algorithm for molecular epidemiological monitoring of the foci in which this highly virulent biovar circulates

Фено- и генотипический портрет штаммов Yersinia pestis филогрупп 2.MED4 и 2.MED1 – этиологических агентов вспышек чумы ХХ века в Прикаспийском регионе

We performed a comparative analysis of the phenotypic and genotypic characteristics of strains of the plague pathogen of phylogroups 2.MED4 and 2.MED1 of the medieval biovar of the main subspecies from epidemically active plague foci in the Caspian Sea region in the XX century. According to the results of the analysis, biochemical properties, nutritional requirements and plasmid profile of strains of phylogroups 2.MED4 and 2.MED1 of the medieval biovar of Y. pestis were determined. Genetic variability in the hemS, caf1M, and ssaJ genes associated with the virulence in strains of the 2.MED lineage was revealed. The data obtained on the phenotypic and genotypic characteristics of the medieval biovar of the plague microbe can be used in laboratory diagnostics of the plague microbe and will contribute to the study of genome changing in the process of microevolution of this highly virulent biovar.Проведен сравнительный анализ фенотипических и генотипических характеристик штаммов возбудителя чумы филогрупп 2.MED4 и 2.MED1 средневекового биовара основного подвида из эпидемически активных в ХХ веке очагов чумы Прикаспийского региона. По результатам анализа определены биохимические свойства, питательные потребности и плазмидный профиль штаммов филогрупп 2.MED4 и 2.MED1 средневекового биовара Y. pestis. Выявлена генетическая вариабельность в генах hemS, caf1М и ssaJ, ассоциированных с вирулентностью, у штаммов линии 2.MED. Полученные данные по фенотипическим и генотипическим характеристикам средневекового биовара могут найти свое применение в лабораторной диагностике чумного микроба и внесут вклад в исследование преобразований генома в процессе микроэволюции этого высоковирулентного биовара

Electronic structure, linear, nonlinear optical susceptibilities and birefringence of CuInX2 (X = S, Se, Te) chalcopyrite-structure compounds

The electronic structure, linear and nonlinear optical properties have been calculated for CuInX2 (X=S, Se, Te) chalcopyrite-structure single crystals using the state-of-the-art full potential linear augmented plane wave (FP-LAPW) method. We present results for band structure, density of states, and imaginary part of the frequency-dependent linear and nonlinear optical susceptibilities. We find that these crystals are semiconductors with direct band gaps. We have calculated the birefringence of these crystals. The birefringence is negative for CuInS2 and CuInSe2 while it is positive for CuInTe2 in agreement with the experimental data. Calculations are reported for the frequency-dependent complex second-order non-linear optical susceptibilities . The intra-band and inter-band contributions to the second harmonic generation increase when we replace S by Se and decrease when we replace Se by Te. We find that smaller energy band gap compounds have larger values of in agreement with the experimental data and previous theoretical calculations.Comment: 17 pages, 6 figure