Phylogeny of <i>Yersinia pestis</i> strains of the 4.ANT lineage from the Tuva mountains and adjacent plague foci
Introduction. The Tuva mountain plague focus (TMPF) in Russia has been continuously epizootically active since its discovery in 1964. The strains of Yersinia pestis isolated in this focus belong to the phylogenetic lineage 4.ANT of the antique biovar of the main subspecies. They are highly virulent...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | Russian |
| Published: |
Central Research Institute for Epidemiology
2025-07-01
|
| Series: | Журнал микробиологии, эпидемиологии и иммунобиологии |
| Subjects: | |
| Online Access: | https://microbiol.crie.ru/jour/article/viewFile/18773/1607 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Introduction. The Tuva mountain plague focus (TMPF) in Russia has been continuously epizootically active since its discovery in 1964. The strains of Yersinia pestis isolated in this focus belong to the phylogenetic lineage 4.ANT of the antique biovar of the main subspecies. They are highly virulent and epidemically significant. The use of modern molecular genetic technologies will make it possible to determine the population structure of 4.ANT strains in the TMPF.
The aim of the study was to analyze the phylogenetic and population structure of Y. pestis strains of the 4.ANT lineage from the TMPF according to the data of whole-genome SNP (single nucleotide polymorphism) typing and MLVA25 (multiple locus variable number tandem repeats analysis) typing.
Materials and methods. Whole-genome nucleotide sequences of 68 Y. pestis strains, including 60 strains of the 4.ANT lineage, were analyzed. Sequencing of strains was performed on the MGI platform. SNP-analysis was performed by sequence alignment in the Snippy v. 4.6 program with subsequent construction of a Maximum Likelihood dendrogram based on the identified core SNPs in the SeaView program. SNPs, being markers for strains of the 4.ANT lineage, were detected using the MEGA11 program. MLVA-genotyping of Y. pestis strains of the 4.ANT lineage was performed by searching loci and then counting the number of tandem repeats in the Tandem Repeats Finder program. MLVA-dendrogram construction was performed by UPGMA method in the BioNumerics v. 7.6.3 program.
Results. According to SNP-analysis of Y. pestis strains of lineage 4.ANT from the TMPF, the presence of 4 phylogeographic groups was established: T1 (Saglinsky, Tolaylyg and Barlyk mesofoci, 1971–1987), T2 (Karginsky mesofocus, 2014–2024), T3 (Karginsky mesofocus, 1977–2009), T4 (Karginsky, Tolaylyg and Boro-Shai mesofoci, 2006–2013). Eight MLVA-genotypes of strains of 4.ANT lineage from Tuva and variable VNTR loci were identified: yp1290ms04, yp1935ms05, yp0559ms15, yp4042ms35, yp4425ms38, yp1108ms45, yp4280ms62, yp1580ms70.
Discussion. Among the strains analyzed, the earliest representatives of the 4.ANT branch are strains of the T1 cluster from the TMPF. The population of strains from the Altai Mountains and Mongolia and the population of strains from the TMPF (1977–2024) are represented as separate sub-branches on the tree. The latter population is represented by polytomy and is characterized by pronounced clustering according to the spatial and temporal principle.
Conclusion. The presence of 4 main phylogeographic groups in the population of 4.ANT lineage in the TMPF was determined and genetic differences between them were established, which can be used for in-depth molecular-genetic differentiation and typing of Y. pestis strains in this focus. |
|---|---|
| ISSN: | 0372-9311 2686-7613 |