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The paper describes a developed comprehensive system for molecular-genetic identification of Yersinia pestis strains according to their appurtenance to certain subspecies, biovars, phylo-geographic populations, using realtime PCR (RT-PCR), allele-specific RT-PCR, and multiplex PCR with hybridization fluorescent registration of results on a solid substrate. Application of this system makes it possible to establish the appurtenance of Y. pestis strains to the following phylogenetic branches: 0.ANT1, 0.ANT2, 0.ANT3, 0.ANT5, 3.ANT, 4.ANT of antique biovar of the main subspecies; 2.MED0, 2.MED1, 2.MED2, 2.MED3, 2.MED4 of medieval biovar of the main subspecies; 1.IN1, 1.IN2, 1.IN3 of intermedium biovar of the main subspecies; 1.ORI1, 1.ORI2, 1.ORI3 of oriental biovar of the main subspecies; 0.PE3 (angolica subspecies), 0.PE7 (tibetica subspecies) and 0.PE10 (qinghaica subspecies). The first stage of the studies within the frames of the developed system is indication of plague agent using registered diagnostic drugs. The second stage is the determination of belonging to individual subspecies through RT-PCR or by the method of multiplex PCR system with hybridization-fluorescent registration of results on a solid substrate, which also allows for establishing to which biovars of the main subspecies and the main phylogenetic lines of the ancient biovar the strains belong. The third stage is the identification of strain appurtenance to phylogenetic branches by the AS-RT-PCR method. The designed complex system for molecular-genetic identification of Y. pestis strains can be applied at the regional and federal levels of the laboratory network of the Russian Federation for diagnostics of infectious diseases. Its use will considerably facilitate and increase the efficiency of intraspecific differentiation of Y. pestis strains within the framework of the epidemiological investigation of outbreaks or importation of strains of plague pathogen into the territory of the Russian Federation or during the certification of strains in collection activities.

The aim of the work was to assess the epidemic situation on plague in the world and epizootic activity of natural plague foci of the Russian Federation in 2022. Following the implementation of comprehensive preventive interventions plans, there was a decrease in the epizootic activity of the Gorno-Altai high-mountain and Tuva mountain natural foci, the cessation of plague epizootics in the Central Caucasian high-mountain focus. The total area of epizootics in the Russian Federation in 2022 reached 248.3 km2, which is 7 times less than in 2021. Infected animals were not found in the Tersko-Sunzhensky low-mountain, Dagestan plain-piedmont, Caspian North-Western steppe, Volga-Ural steppe, Trans-Baikal steppe, Volga-Ural sandy, Caspian sandy, East Caucasian high-mountain natural foci. Persistence of tense epizootiological situation in 2023 is predicted for the territory of the Altai Republic and the Republic of Tuva. The prospects of using the GIS portal of the Russian Anti-Plague Institute “Microbe” of the Rospotrebnadzor for an operational assessment of the actual epidemiological situation in natural plague foci are substantiated.

The aim of the study was to develop methodological approaches to assessing the economic damage associated with the incidence of hemorrhagic fever with renal syndrome (HFRS) and to calculate the economic damage by the example of an outbreak of HFRS in the Saratov region in 2019. Materials and methods. The paper analyzes the economic indicators of the Federal State Statistics Service; data on the incidence of HFRS in the Russian Federation for the period of 2019–2022. To calculate the cost of outpatient and inpatient medical care, as well as the costs associated with the medical follow-up of convalescents, the indicators of the Program of state guarantees of free provision of medical care to citizens for 2022 and for the scheduled period of 2023 and 2024 were used. The calculation of economic losses associated with the payment of temporary disability benefits was carried out according to the equation provided in the Federal Law No. 255-FZ dated December 29, 2006 (as amended on October 07, 2022). Economic losses associated with premature death at an economically active age were calculated based on the value of unproduced GDP due to lost years of life in the corresponding age group. Results and discussion. The costs of treatment, rehabilitation and payment of temporary disability benefits for 1 case of HFRS at the age of 0 to 56.5 years for the female population and from 0 to 61.5 years for the male population amount to 140 495 rubles; over the age of 56.5 years for the female population and 61.5 years for the male population – 95 412 rubles, respectively. Each fatal case of HFRS aged 0 to 16 years among the male population costs the state 38 976 231 rubles; among the female population – 34 708 331 rubles; in active working age – the value of economic damage varies depending on the age of the person who died of HFRS. The economic damage of the outbreak of HFRS in the Saratov Region (2019), taking into account the direct expenditures of the healthcare system and indirect losses of the country’s economy amounted to 441 453 432 rubles. It is of note that the structure of the main damage is dominated by indirect losses in the economy caused by the premature death of people in economically active age.

The aim of the study was to test the feasibility of long-term survival and preservation of the properties of Yersinia pestis in association with soil amoeba Acanthamoeba castellanii. Materials and methods. Y. pestis strains and acanthamoeba isolated in the common area of the Gorno-Altai high-mountain plague focus were used for the study. The systematic affiliation of protozoa was determined through analyzing the 18S rRNA gene fragment sequencing data, followed by alignment with amoeba sequences from the NCBI GenBank database. A fluorescent Y. pestis strain was obtained by electroporation using the pTurboGFP-B plasmid. Co-cultivation was carried out in saline buffer in the absence of nutrients for the cells of plague pathogen. The influence of co-culturing with protozoa on Y. pestis properties was determined using microbiological, biological, and molecular-genetic methods. Results and discussion. The cell viability preservation for 22 months of the experiment in Y. pestis strain belonging to the main subspecies of the antique biovar, the 4.ANT phylogenetic line in co-culture with amoeba cells in the absence of additional nutrients has been established. Co-cultivation with amoebae did not lead to a change in the cultural, morphological, genetic and virulent properties of the plague pathogen strain. The data obtained confirm the possibility of using Acanthamoeba castellanii by the plague microbe to persist in soil biocenoses and open up the prospect of studying the mechanisms of plague pathogen surviving during extended inter-epizootic periods.

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.

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.

The paper contains the data on international cooperation of the Republican Center of Quarantine and Particularly Dangerous Infections of the Ministry of Health of the Kyrgyz Republic and the Russian Research Anti-Plague Institute “Microbe” of the Rospotrebnadzor to combat plague and other dangerous infections over the period from 2016 to 2022. Areas of cooperation include conducting joint epidemiological monitoring of plague foci in the Kyrgyz Republic; exchange of up-to-date information on the state of natural foci of the two countries; equipping the anti-plague service of the Republic with modern equipment and mobile laboratories, diagnostic tools and technologies; conducting joint exercises to ensure biological safety and prompt response to emergencies; provision of advisory and methodological assistance; training and strengthening of professional personnel; conducting joint scientific researches, conferences; publication of scientific works. Data on the complex characterization of properties and phylogeographic analysis of Yersinia pestis strains isolated during field studies in the Kyrgyz Republic in 2012–2020 are summarized. The prospects for carrying out joint cartographic, molecular-genetic and paleomicrobiological work in the natural foci of the Kyrgyz Republic are outlined.

The review presents the data on domestic and foreign phenotypic classifications of Yersinia pestis strains developed in the XX century; genetic classifications of the XXI century; as well as on the genealogy of ancient strains of the plague microbe, reconstructed using paleogenomic technologies. Since the discovery of the plague agent in 1894, many classifications were created that corresponded to the level of development of microbiology at that time. The intraspecific classification schemes of the XX century were based on three principles: phenotypic differences between strains, features of the species composition of carriers, and geographical affiliation. With the development of molecular microbiology early on in the XXI century, a genetic nomenclature of the branches of the pathogen evolution was developed and a number of classifications based on the analysis of the population structure of Y. pestis were created. Through the prism of the genetic diversity of Y. pestis strains from natural plague foci in Russia, near and far abroad countries, an improved classification with a division into seven subspecies has been developed: pestis, tibetica, caucasica, qinghaica, angolica, central asiatica, ulegeica, which allocates the subspecies according to the phylogenetic principle and epidemic significance. With the advancements in paleomicrobiology, prehistoric lineages of evolution have been included in the genealogy of Y. pestis, which expand the data on the intraspecific diversity of the plague microbe.

The most important component of strengthening the potential for responding to biological threats both at the national and interstate levels is the formation of a unified system for monitoring and responding to emergencies (ES) of sanitary-epidemiological nature in the CIS territory.The aim of the work was to review the systems for monitoring and responding to emergencies of sanitary-epidemiological character in the CIS countries by the example of the Russian Federation, the Republic of Belarus, the Republic of Kazakhstan and the Kyrgyz Republic, to characterize the main areas of international cooperation on countering biological threats and coordinating international response measures in the CIS countries.Materials and methods. Information and analytical materials provided by organizations responsible for epidemiological surveillance and control in the CIS countries, Internet sources, and publications were used for the study.Results and discussion. The organization and functioning of the systems for monitoring and responding to emergencies in the CIS countries is a state function. It includes, as a rule, the national, regional (sub-national) and territorial (local) levels, which have horizontal and vertical connections. The legal framework is made up of documents of the legislative level. Interdepartmental interaction in response to emergencies is carried out both at the republican level and in administrative territories; the basis for interaction is the integrated planning of preventive and anti-epidemic measures and the functioning of the relevant organizational structures on an ongoing basis. Since 2015, with the support of the Government of the Russian Federation, programs have been implemented aimed at assisting partner countries in the implementation of the International Health Regulations (2005) in order to increase national response capacity and form a unified sanitaryepidemiological emergency response system in the CIS countries. The main areas of collaboration are strengthening the material and technical base and human resources of specialized institutions and scientific cooperation. As a result of the program implementation, a unified system for monitoring and prompt response to emergencies in the field of public health of sanitary-epidemiological nature has essentially been formed in the CIS countries to date, uniting more than 15 specialized institutions from 8 CIS countries.

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.

A comprehensive analysis of the accumulated epidemiological and epizootiological data in combination with results from phylogenetic analysis of Yersinia pestis strains creates the basis for establishing patterns of spatialtemporal distribution of the plague pathogen and opens up the prospect of long-term forecasting of natural plague foci activation. Previously, we traced the distribution pathways of Y. pestis, medieval biovar, in the plague foci of the Northern and Northwestern Caspian Sea regions in the 20th and early 21st centuries.The purpose of this work was to identify the regularities of circulation of Y. pestis, medieval biovar, in four natural plague foci located in the Eastern Caspian Sea region.Materials and methods. A complex study of the phenotypic and genetic properties of 16 Y. pestis strains isolated in the Ustyurt, Mangyshlak, Karakum and Kopetdag autonomous desert plague foci in 1926–1985 was carried out. They were compared with strains from other natural plague foci in Eastern Europe and Central Asia obtained in 1917–2003. Whole-genome sequencing of 12 of those strains was performed. Phylogenetic analysis included the genomes of other 19 Y. pestis strains that we had sequenced earlier. Based on the 1717 polymorphic nucleotides (SNPs) identified in the core genome, a dendrogram of the relations of the studied strains was constructed.Results and discussion. All 16 Y. pestis strains from the Ustyurt, Mangyshlak, Kopetdag, and Karakum desert foci belong to the 2.MED1 branch of the medieval biovar. All investigated strains from the first three foci and most of the strains from the Karakum focus are in the Caspian 2.MED1 branch, and three strains from the Karakum desert focus are included in the Central Asian one. We have revealed several waves of dissemination of the strains under the 2.MED1 phylogenetic branch of Y. pestis of the medieval biovar in the Eastern Caspian Sea region in the 20th century.

The most common anthropozoonoses on the African continent are coxiellosis and Rift Valley fever. It is known that detection of specific IgG antibodies in the blood sera of farm animals is one of the indicators of the pathogen circulation in a certain territory. The aim of the work was to identify specific IgG antibodies in the blood sera of farm animals collected on the territory of the Republic of Guinea to pathogens of zoonotic infectious diseases: coxiellosis, brucellosis, glanders, CCHF, West Nile and Rift Valley fevers, using enzyme immunoassay (ELISA). Materials and methods. A panel of 970 samples of blood sera from farm animals inhabiting all landscape-geographical zones of Guinea was compiled for the work. Identification of specific antibodies was carried out using enzyme immunoassay with preparations recommended for veterinary studies. Results and discussion. Specific antibodies to zoonoses were detected in 700 out of 1074 samples (65.2 % of the total), including: to Coxiella burnetii – in 172 (16.0 %); to Brucella spp. – in 212 (19.7 %); viruses of Rift Valley fever – 85 (7.9 %); CCHF – in 139 (12.9 %) and West Nile fever – in 92 (8.6 %). Antibodies to Burkholderia mallei were not found in the tested material. Positive samples were registered in all landscape-geographical zones. Thus, an urgent task is to continue studying the circulation of pathogens of zoonoses and anthropozoonoses in the territory of the Republic of Guinea and to organize regular monitoring over the spread of zoonotic infectious diseases in collaboration with veterinary services, which will allow timely forecasting and coordinating prophylactic (anti-epidemic) measures to prevent cases of diseases.

The aim of the work was to conduct phylogenetic analysis of Y. pestis strains, biovar altaica ssp. central asiatica, isolated in Gorno-Altai high-mountain and Sailyugem natural plague foci on the territory of Russia and Mongolia in 1965–2020, by full-genome sequencing data.Materials and methods. To determine the population structure of the biovar altaica ssp. central asiatica, 34 whole genome sequences were used (including 20 Y. pestis strains of the biovar altaica, 18 of which were sequenced by us). To isolate DNA from the Y. pestis strains, a PureLink Genomic DNA Mini Kit (Invitrogen, USA) was applied. Sequencing of the nucleotide sequences of Y. pestis strains was carried out in Ion PGM system Lifetechnologies. The analysis and processing of the obtained data were performed with the help of Newblergs Assembler 2.6 and IonTorrent Suite software package, 3.4.2. The search for SNPs was performed using the Wombac 2.0 program. The Maximum Likelihood dendrogram was built in the PhyML 3.1. The dendrogram was visualized using the FigTree 1.4.3 software.Results and discussion. Based on the data of whole genome analysis, taking into account the 1871 revealed polymorphic nucleotides, the spatial structure of the biovar altaica ssp. central asiatica has been determined. It includes several phylogeographic branches: the Kurai-Tarkhatinskaya (cluster 0.PE4a-1) and the Ulandryk-Mongolian (0.PE4a-2), which is in agreement with the geographical regions of the isolation of strains forming these branches in the Altai Mountains. The Kurai-Tarkhatinskaya branch is further divided into the Kurai (sub-cluster 0.PE4a-1-1, formed by the strains of 2009–2018) and Tarkhatinskaya (subcluster 0.PE4a-1-2, formed by the strains of 2012–2020) sub-branches, while the Ulandryk-Mongolian branch of evolution is split into sub-branches represented by strains from the Ulandryk meso focus (sub-cluster 0.PE4a-2-2, strains 1965–2010) and the Sailyugem focus of Mongolia (sub-cluster 0.PE4a-2-1, strains 1964–1990).

The aim of the research was to assess epizootic activity of natural plague foci in the Russian Federation in 2021 and provide a prognosis for 2022. Activation of epizootic process has been detected in Central-Caucasian high-mountain natural plague focus after a recess since 2007. Local epizootics persist to develop in Tuva Mountain and Gorno-Altai highmountain plague foci. Total area of epizooties in Russia in 2021 amounted to 1649.5 km2. 28 plague microbe strains were isolated. Animals infected with plague were not found in Tersko-Sunzhensky low-mountain, Dagestan plain-piedmont, Precaspian north-western steppe, Volga-Ural steppe, Trans-Baikal steppe, Volga-Ural sandy, Caspian sandy and EastCaucasian high-mountain natural plague foci. It is demonstrated that epidemiological welfare as regards plague in Russia in 2017–2021 was achieved through annual epizootic monitoring of plague-enzootic territories, timely epizooty detection and preventive activities aimed at reducing the risk of infection. Substantiated has been the forecast for tense epidemiological situation on the territory of Karachay-Cherkessia, Kabardino-Balkaria, Altai Republic and Tuva Republic in 2022. A new Epitracker application has been proven to be prospective for rapid assessment of actual epidemiological situation in natural plague foci.

The aim of the study was to develop a test system that allows for detecting plague pathogen DNA in clinical and biological samples, environmental objects with the simultaneous determination of its appurtenance to the main and non-main subspecies, differentiation of the altai biovar central asiatica subspecies separately. Materials and methods. Primer sets for specific genetic markers have been selected using the VectorNTI 10 software, optimal conditions for PCR were determined for RotorGene devices. To assess the specificity and sensitivity of the developed set of reagents, 44 strains of microorganisms were used, of which 19 were Yersinia pestis strains and 25 strains of heterologous microorganisms. The diagnostic sensitivity of “GenPest-subspecies/Altai-RGF” is 98.6 % with a confidence level of probability of 91 %. The diagnostic specificity of “GenPest-subspecies/Altai-RGF” is ≥ 99 % with a confidence level of 91 %. Results and discussion. A medical product “A set of reagents for the detection and differentiation of plague pathogen strains of the main and non-main subspecies (altai biovar, subspecies central asiatica exclusively) by the polymerase chain reaction with hybridization-fluorescent registration of results in real-time mode (GenPest-subspecies/Altai-RGF)” has been developed. The set of reagents passed the state registration in accordance with the established procedure. The use of the developed set of reagents is relevant for the Gorno-Altai high-mountain plague focus of the Russian Federation and the adjacent part of Mongolia.

For many years, arbovirus infections have been a global health problem and one of the urgent threats to the sanitary and epidemiological well-being of the population. Climatic conditions, species diversity and abundance of vectors, epidemiological and demographic factors are of fundamental importance for the emergence and persistence of natural foci of arbovirus infections. In the Socialist Republic of Vietnam (SRV) and other countries of the Asia-Pacific region, the most complex epidemiological situation is observed in regard to a number of arboviral infectious diseases transmitted by mosquitoes, inter alia to dengue fever. In this review we analyzed the literature data to identify the features of the circulation of some arboviruses in Vietnam, such as dengue virus, Zika, Chikungunya, Japanese encephalitis virus, Dabie virus, and the routes of their transmission and spread. It is shown that the climatic, ecological, epidemiological and demographic conditions existing on the territory of Vietnam contribute to the spread of pathogens of many arboviruses. Areas of more active circulation and ways of spreading pathogens of arbovirus infections have been identified. Based on the data obtained, it is necessary to conduct annual epidemiological and epizootiological survey of the territory of the SRV in order to identify markers of pathogens and determine the boundaries of natural foci of arbovirus infectious diseases which will enhance and increase the effectiveness of preventive and anti-epidemic measures.

Objective of the study was to perform a comparative analysis of molecular-genetic properties in non-toxigenic Vibrio cholerae O1 strains biovar El Tor, isolated in the Republic of Kalmykia and on cholera endemic territories and to reveal their phylogenetic relations to toxigenic isolates.Materials and methods. We have carried out bio-information analysis of whole genome sequences of 60 cholera vibrio strains from endemic as regards cholera regions and from Kalmykia. The presence of pathogenicity and endemicity islands in their genomes has been determined. Specifed have been the sequence-types of the examined strains and whole genome SNP-analysis conducted.Results and discussion. Non-toxigenic El Tor vibrios circulating in Kalmykia are clustered into two major genotypes: ctxA–tcpA+VPI-2+VSP– and ctxA–tcpA–VPI-2Δ+VSP–, where VPI-2 Δ+ signifes the presence of deletions of varying length in the genome of this pathogenicity island. Only the latter one is found in regions endemic for cholera. In addition, ctxA– tcpA+VPI-2+VSP+ populations circulate in cholera endemic foci, not found in Kalmykia. 17 sequence-types were identifed among the studied strains (by seven housekeeping gene loci). Phylogenetic analysis performed using SNP-typing demonstrated the absence of close genetic relation between the ctxA–tcpA+VPI-2+VSP– vibrios from Kalmykia and both toxigenic and non-toxigenic vibrios with different composition of pathogenicity and pandemicity islands in the genome. At the same time, genetic proximity of ctxA–tcpA–VPI-2Δ+VSP– cholera vibrios from endemic cholera foci with those isolated in Kalmykia was detected, which may indicate the possibility of their recurrent importation into the territory of Russia. Non-toxigenic V. cholerae strains found in the territory of Kalmykia are characterized by a high genetic diversity. Circulation of the strains with unique sequence-types suggests their potential for long-term persistence on this territory. At the same time, phylogenetic closeness and identity of certain strains with strains from endemic territories can be an evidence of repeated importation.

The aim of the study was a comprehensive analysis of the phenotypic and genetic properties of Yersinia pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci of the Tien Shan in 2019–2020; determination of the present-day population structure and areal of these highly virulent strains of the plague pathogen.Materials and methods. Studies of biochemical properties (fermentation of carbohydrates, nutritional requirements), virulence (in vitro and in laboratory animals), molecular-genetic analysis and whole genome sequencing of Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 have been carried out. We used Y. pestis strains from the foci of the Tien Shan and Pamir-Alai dated 1928–2016 for the comparison. Whole genome sequencing was performed using the Ion S5 XL System. Phylogenetic analysis was performed on the basis of 1443 identified core SNPs in 36 Y. pestis strains of various phylogenetic lines included in the analysis. The construction of dendrograms was carried out using the Maximum Likelihood algorithm, PHYML program, HKY85 model.Results and discussion. It is established that all Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 belong to the 0.ANT5 phylogenetic branch of the ancient biovar of the main subspecies. Genome-wide sequencing revealed the presence of two 0.ANT5 clones, the first of which consists of strains from the basin of the river Kooylu in the Sarydzhaz focus, dated 2020. The second powerful clone includes the strains of 2012–2020 isolated in the Sarydzhaz and Upper-Naryn foci. The high virulence of the isolated strains has been shown. It was concluded that further study of the territories of the highmountain foci of the Tien Shan and Pamir-Alai is necessary to establish the current boundaries of the 0.ANT5 areal, as well as to identify the circulation areas of Y. pestis of other phylogenetic lineages.

The aim of the review was to consider the principles and criteria for the formation of funds of service microbiological collections and the specialized State collection of pathogenic bacteria (SCPB) at the RusRAPI “Microbe”. The rapid pace of characterization, study, and use of microbial diversity makes the development of criteria for the selection of microorganisms for permanent storage in collections particularly relevant. The number and format of these criteria are determined by the tasks the collection centers of different levels and specialization are facing. Service collections form their funds by depositing or acquiring type, reference, educational strains. In recent years, the practicability of expanding the range of strains, the deposition of which is desirable in service collections, has been recognized. These are strains characterized by phylogenetic, genomic, metabolic, ecological uniqueness; with a fully sequenced genome; known and emerging plant, animal and human pathogens that caused disease outbreaks; used in international research projects; having biotechnological and economic significance. The main task of the SCPB as a specialized state collection of pathogenic bacteria of groups I–II is to preserve strains characterizing the intraspecific diversity and populations of pathogens circulating in natural foci or in certain territories of the Russian Federation, isolated during epizootics, local or epidemic outbreaks. The selection criteria for strains for permanent storage are their ecological, phenotypic, and genetic peculiarities. The preservation of such a collection is important for future research using new technologies and tracking the evolution of pathogenic bacteria – causative agents of particularly dangerous infectious diseases.

Emergence of various genovariants of the SARS-CoV-2 virus, which are characterized by a higher ability to spread and a more severe clinical manifestations compared to the initial variants, require molecular-genetic monitoring of strains circulating in the Russian Federation.The aim of the work was to identify the VOC SARS-CoV-2 genovariants in the territory of the Republics of Bashkortostan, Tatarstan, Udmurtia, and Samara, Penza, Saratov, Ulyanovsk, and Orenburg Regions.Materials and methods. The identification of genovariants and the determination of the type of mutations was carried out by the Sanger fragment sequencing method.Results and discussion. The study examined 298 samples of clinical material obtained from the Centers for Hygiene and Epidemiology in the Republics of Bashkortostan, Tatarstan, Udmurtia, Samara, Penza, Saratov, Ulyanovsk, and Orenburg Regions. In 17 % of cases, the variability of the SARS-CoV-2 virus was observed for one or more markers: in three samples, a new coronavirus of the B. 1.1.7 line (“British”) was detected; in a number of cases, only one mutation was detected in the virus found in samples – deletion Y144 or substitution D138Y, E484K, N501Y, and very rarely two mutations – deletion Y144 and substitution E484K. The presence of the L141-G142-V143 deletion localized in the recurrent deletion region RDR2 of the S-gene was shown in 10 % of the cases. The data obtained indicate the heterogeneity in macroorganism of the population of the new coronavirus with the deletion L141-G142-V143, which leads to a change in the antigenic structure of the virus, which probably allows the virus to evade the immune response.

The aim of the work was to substantiate the forecast of the epidemiological and epizootiological situation in natural foci of plague in the Russian Federation, countries of the near and far abroad for the year of 2021. Characteristics of the distribution of Yersinia pestis strains of the main subspecies (subspecies pestis) of medieval and antique biovars, Caucasian (ssp. caucasica) and central Asian (ssp. central asiatica) subspecies by 45 natural foci of the CIS countries are presented in the paper. The persistence of a multidirectional trend in the dynamics of epizootic activity of natural foci of the CIS countries with the circulation of Y. pestis pestis strains of the medieval biovar of the 2.MED1 phylogenetic branch and the antique biovar of the 0.ANT5, 4.ANT phylogenetic branches in the current decade has been outlined. For the Russian Federation, the development of epizootics is predicted in the Gorno-Altai highland and Tuva mountain natural foci caused by the circulation of Y. pestis pestis strains of the antique biovar 4.ANT and Y. pestis of the Altai biovar of the Central Asian subspecies 0.PE4a in 2021. For the Republic of Kazakhstan, there is a high probability of preserving epizootic activity in the North Aral, Aral-Karakum, Balkhash, Mojynkum, Taukum desert and Ili intermountain natural foci with the circulation of Y. pestis pestis strains of the medieval biovar of the phylogenetic branch 2.MED1. For the Kyrgyz Republic, the forecast for the development of plague epizootics caused by Y. pestis pestis strains of the antique biovar 0.ANT5 phylogenetic branch in the Sarydzhaz and Upper Naryn high-mountain natural foci has been substantiated. A high epidemic risk of epizootic manifestations caused by highly virulent strains of Y. pestis pestis of antique biovars 0.ANT5, 4.ANT and medieval biovar 2.MED1 for the entire territory of the CIS countries is noted. The relevance of implementing forecasts of the epidemiological situation into practice, taking into account the molecular-genetic and epidemiological characteristics of Y. pestis strains circulating in areas of expected epizootic manifestations of plague, is highlighted.

The aim of the study was to develop and assess the efficacy of a method for Lujo virus RNA detection in clinical and biological samples using one-step real-time RT-PCR.Materials and methods. In order to select the conservative regions of the genome, we utilized the available in GenBank database Lujo virus sequences (https://www.ncbi. nlm.nih.gov/genbank) aligned in BioEdit 7.2.5 software package ( (IbisBiosciences, USA). To conduct one-round RTPCR, reverse transcriptase and TaqF-polimerase were used. Recombinant Escherichia coli strain, XL1-Blue, containing pGEM-T plasmid with inserted synthetically-generated fragment of the virus genome, was produced to make positive control sample (PCS). Constructed recombinant plasmids were used for creating RNA-containing PCS with protective protein shell of MS2-phage. Determination of specificity of the developed method was performed with the help of control panel of RNA and DNA of 23 viral strains related to 10 families; the sensitivity – the panel of biological samples artificially contaminated with PCS. Further testing was carried out at the premises of laboratory of the Russian-Guinean Center for Epidemiology and Prevention of Infectious Diseases (Kindia, Republic of Guinea) on 265 blood sera from practically healthy persons, 110 blood sera of cattle, 83 suspensions of ticks, and 165 suspensions of organs of small mammals collected in the territory of Guinea.Results and discussion. Two conservative polymerase gene fragments have been chosen as targets for Lujo virus RNA detection using RT-PCR. The combination of primers and probes has been experimentally selected, optimum composition of reaction mixture for PCR and mode of RT-PCR set-up established, as well as control samples C+, internal control, positive control sample developed. Sensitivity of the proposed method is 5·103 GE /ml, specificity – 100 %.

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.

The global community is experiencing one of the largest infectious disease outbreaks in the 21st century. In the Saratov Region, the first case of new coronavirus infection was confirmed on March 19, 2020.The maximum increase in cases was noted between May 15 and June 30, during that time the total number of infected people in the region increased from 1526 to 6444. Since July 2020, a stable incidence level of new coronavirus infection has been observed in the Saratov Region, without a steady decline.The aim of the study was to assess the status of population immunity to the SARS-CoV-2 virus among residents of Saratov and the Saratov Region under the COVID-19 epidemic.Materials and methods. In the period from June 23 to July 26, 2020, a serological study of blood samples from 3372 volunteers of different age groups was conducted. The content of antibodies to SARS-CoV-2 was determined by ELISA using a set of reagents “ELISA anti-SARS-CoV-2 IgG” produced by the State Scientific Center of Applied Microbiology and Biotechnology of the Rospotrebnadzor (Russia).Results and discussion. In general, the incidence of COVID-19 in the Saratov Region is taking place against the background of moderate seroprevalence to the SARS-CoV-2 virus, accompanied by a high incidence of non-apparent (asymptomatic) forms of the infectious process. The absence of clinical symptoms of the disease, in the context of the limited use of methods for determining the RNA of the SARS-CoV-2 virus in PCR (11 % of the region’s population) makes it difficult to assess the real spread of the virus in the population and to establish the timing of the formation of persistent herd immunity. A low rate of antibody response among individuals with a positive result of PCR analysis, as well as among volunteers who had an infection in May, June 2020, indicates a weak formation of the immune response, or the prevalence of individuals reacting mainly by activating the cellular link of the immune system in the population. The obtained results, although they need to be explained in a number of respects, can be applied to the organization of preventive measures, including vaccination, in the region.

The review presents the materials on the use of mobile laboratories, developed in the Russian Federation, in the framework of four main areas: monitoring of territories to identify the circulation of pathogens of natural-focal infectious diseases; monitoring of territories during the exacerbation of the epizootic situation; participation in the elimination of outbreaks of infectious diseases; monitoring of territories to control and predict the epidemiological and epizootiologic situation in preparation for mass events. The tactical and technical characteristics and the procedure for organizing the operation of the mobile laboratory for monitoring and diagnostics mounted on the platform of the KamAZ chassis are considered. A distinctive feature of the laboratory from the existing Russian and foreign counterparts is the availability of the necessary conditions for conducting research using bacteriological analysis, rapid and accelerated diagnostic methods, and performing a full cycle of works – from the preparatory stage to the destruction of infected material. Hightech equipment allows the realization of two research schemes: the first – bacteriological analysis alongside the PCR, which ensures high reliability of the results; the second – conducting the PCR at the first stage, and when identifying genetic markers of the pathogen – performing bacteriological analysis of positive samples in order to isolate the culture of the pathogen and identify it subsequently. The second scheme will reduce the volume of bacteriological studies; make changes in the tactics of epizootiological survey. Tests of the mobile laboratory have demonstrated the effectiveness of its use in the epizootiological examination of natural plague foci, including cross-border ones. Owing to the use of a mobile laboratory in the Gorno-Altaisk high-mountain natural focus of plague, a new epizootic site was identified, located in a remote area, used by the population as a summer pasture for grazing domestic animals. The use of mobile laboratories will strengthen the laboratory base of institutions that monitor particularly dangerous, natural-focal and other dangerous infectious diseases; will help to bring the advanced diagnostic technologies directly to the natural focus, reduce the risk of epidemic complications due to plague and other particularly dangerous infections in cross-border natural foci.

Objective: to study the evolution of SARS-CoV-2 virus in the process of adapting to human organism duringthe current pandemic.Materials and methods. Database (GISAID) on nucleotide sequences of SARS-CoV-2 virus genome, obtained from clinical samples during the period of late December, 2019–July, 2020. Phylogenetic tree diagram construction was carried out applying BioNumerics v.7.6 software using Maximum parsimony algorithm.Results and discussion.The most substantial change in the genomes of SARS-CoV-2 virus are associated one-time mutations in ORF1b (P314L) and S (D614G) genes, as a result of which the overwhelming majority of identified isolates of this virus have the stated pair of substitutions to date. Many researches link the substitution in S (D614G) gene to the decreased pathogenicity in the strains that contain it, which may be also explained by enhanced methodology of patient treatment in the course of pandemic. The effect of the mutation in ORF1b (P314L) gene has not yet been investigated. P314L and D614G mutations are closely related and only their combined presence in the genome favored the dissemination of the genovariants of SARS-CoV-2 virus. Analysis of congregated epidemiological data testifies to the fact that the spread of new genovariants may be associated with biological properties facilitating human-to-human transmission. Thereat, associated decrease in lethality may reflect not only advancements in methods of treatment, but possible attenuation of virulent properties. Thus, observed growth in dissemination potential against the background of decrease in virulence is, probably, one of the forms of adaptation of new coronavirus to human population and, apparently, will remain in the future as the integration of SARS-CoV-2 virus into the structure of seasonal ARVI agents.

Objectiveof the study was to identify epidemiological peculiarities of HFRS outbreak in the territory of the Saratov Region in 2019 and to determine the key factors contributing to the intensity of epidemic process.Materials and methods.Analyzed are the data on 2702 cases of HFRS registered in the territory of the Saratov Region in 2019, obtained from the Rospotrebnadzor Administration in the Saratov Region and Center of Hygiene and Epidemiology in the Saratov Region. The basic method of investigation was epidemiological one with application of advanced information technologies.Results and discussion.Retrospective analysis of epidemic HFRS manifestations in the Saratov Region showed that HFRS outbreak of 2019 was the largest over the period of disease reporting, both by the number of cases (2702) and by the duration. Early onset of increase in the incidence (may) and allocation of the majority of cases to the territory of the natural park “Kumysnaya Polyana”(75 %) should be considered as characteristic features of the outbreak. We have conducted epidemiological zoning of the Saratov Region allowing for dividing the Region into four types of territories which differ by the level of risk of HFRS exposure (very high, high, medium, and low), as well as distinguishing the most hazardous in terms of HFRS infection territories of Saratov. The key factors affecting the surge in HFRS cases were high numbers of infected rodents during spring months of 2019 due to mild and extremely snowy winter of 2018–2019; reduction in forest engineering works aimed at turning the focal territory into aesthetic forestry. The change in the character of exploitation of 9 % of the natural park “Kumysnaya Polyana” resulted in the increase of population contacts with natural-focal complexes. Mass visits to natural focus during early spring period against the background of low alertness to risks of HFRS infection led to explosive growth of HFRS incidence.

The review analyses the information on the epidemiological situation on COVID-19 around the world. Presented is the assessment of the major epidemiological parameters (basic reproductive rate, lethality, incubation period, and serial interval). Demonstrated is the share of severe cases among different age groups and the general structure of incidence by the severity of clinical course. The paper provides the classification of response models internationally depending upon the complex of measures undertaken at different stages of epidemic process. Reviewed are the key response actions to control the COVID-19 transmission in different countries of the world and the Russian Federation and given is the assessment of their effectiveness.

Objective of the study was to conduct phylogenetic analysis of Yersinia pestis strains of the main subspecies, belonging to antique biovar, phylogenetic branch 0.ANT, isolated in XX – early XXI centuries in the foci of Tien-Shan and Pamir-Alay to identify the regularities of spatial-temporal circulation of plague agent in the territory of the foci. Materials and methods. We have carried out whole genome SNP-analysis of Y. pestis strains of antique biovar, isolated in natural foci of Kyrgyz Republic in 1928–2016. Phylogenetic investigation is based on 1646 identified core SNPs in 51 included in the analysis strains of different phylogenetic lines. Phylogenetic tree was constructed using Maximum Likelihood algorithm, PHYML software package, and HKY85 model. Results and discussion. All 29 studied Y. pestis strains isolated between 1928 and 2016 in the foci of Tien-Shan and Pamir-Alay fall under the phylogenetic branches 0.ANT3 and 0.ANT5 of antique biovar of the main subspecies. Strains of 0.ANT3 branch were collected predominantly in Aksay and Alay foci, while strains of 0. ANT5 – in Upper-Naryn and Sarydzhas foci of Tien-Shan. Strains of phylogenetic lines 0.ANT1 and 0.ANT2 were not found in the foci of Kyrgyz Republic. According to the results of whole genome SNP-analysis, Y. pestis strains isolated in the XXI century belong to phylogenetic branch 0.ANT5. This branch also comprises a strain obtained from a patient (lethal case) in Sarydzhas plague focus in 2013. Genetic homogeneity of the modern strains of 0.ANT5 branch and their wide dissemination testify to the extension of the areal of this population and activation of Tien-Shan foci, caused by climate warming. For the first time ever, genomes of Y. pestis 0.ANT5 branch, isolated in XXI century, including clinical strain dated 2013, have been sequenced. We have obtained the whole-genome sequence of Y. pestis strain, 0.ANT3 branch, which caused pneumonic plague outbreak in Tien-Shan in 1928.

Objective of the investigation was to assess epidemiological and epizootiological conditions in natural plague foci of the Russian Federation, neighboring states and foreign countries in 2019. Negative effect of the current climate warming on the state of parasitic systems of natural foci with circulation of plague microbe of the main subspecies, medieval biovar, phylogenetic branch 2.MED1 is emphasized. In 2019, local plague epizooties were registered in the territory of two (Gorno-Altai high-mountain and Tuva mountain) out of 11 natural plague foci of the Russian Federation. The total area of epizooty covered 2248.5 km2 . All in all, 31 cultures of Y. pestis of the main subspecies, antique biovar, phylogenetic branch 4.ANT and 5 cultures of Altai biovar, central-asian subspecies, phylogenetic branch 0.PE4a were isolated. The forecast for continuing tense epidemiological situation, both for 2020 and for 2021–2025, has been substantiated for natural foci with circulation of the main subspecies of antique biovar, phyologenetic branch 4.ANT: Gorno-Altai high-mountain and Tuva mountain ones. In the remaining nine natural foci in the territory of the Russian Federation epizootic manifestations of plague in 2020 are highly improbable. This prognosis is an indication to optimize the deployment of human and logistical resources of plague control institutions through concentrated preventive activities in the territories of epizootically active natural plague foci. Otlined is the necessity to put a new enhanced classification of Y. pestis into practice.

Aim – to determine the intensity of West Nile virus circulation in anthropogenic biotopes in the territory of the Saratov Region between 2012 and 2017. Materials and methods. 1454 blood serum samples from animals of private households and agricultural cooperatives in 14 districts of the Region were investigated: 1111 samples from horses and 343 samples from the cattle. Sera were examined for the presence of total antibodies to WNV using a test system registered in the Russian Federation to detect antibodies to this virus by a competitive enzyme immunoassay «ID Screen West Nile Competition Multi-species» («ID. Vet», France). Results and discussion. The share of resistant to WNV cohort of live-stock animals in the territory of the Saratov Region over the whole period of study was (14.0±0.9) %, particularly in horses – (15.9±1.1) %, and in the cattle – (7.9±1.5) %. The highest values were observed for horses. High level of resistance in live-stock animals was registered in the districts located on the left bank of the river Volga: central ones – Engels (36.4±5.5), Fedorovsky (29.0±4.6), and Sovetsky (20.0±3.7); southern districts – Rovensky (74.3±5.3 %) and Krasnokutsky (15.7±4.4), which confirms the assumption about the initial introduction of the virus from neighboring territories of the Volgograd Region into the territory of the Left Bank where there are characteristic near-water biotopes and active circulation of the agent takes place. The data obtained on the detection of the resistant live-stock animal cohort testify to the spread of West Nile virus in the territory of the surveyed districts of the Saratov Region and, in particular, anthropogenic biotopes which further points to the formation of persistent natural and natural-anthropourgic foci of West Nile fever.

Objective of the work was to conduct an extended study of Legionella strains isolated from epidemiologically significant environmental objects during the preparation and conduct of mass events in the territory of the Russian Federation in 2013-2014 . Materials and methods . Studied were 53 strains of Legionella pneumophila, isolated from epidemiologically significant objects during the preparation and conduct of a number of mass events (ME): XXVII World Summer Universiade, XXII Olympic Winter Games and XI Paralympic Winter Games, Sochi; Summer Health Promotion Campaign in 2014, Republic of Crimea; IV Caspian Summit, Astrakhan, 2014. Strains were analyzed using multilocus sequencing, time-of-flight mass spectrometry (MALDI-ToF-MS) and atomic force microscopy. Legionella strains were typed by multilocus sequencing in accordance with the algorithm of the European Legionellosis Research Group “Sequence-Based Typing protocol for epidemiological typing of L. pneumophila ". Results and discussion . Strains of L. pneumophila , legionellosis agent, were isolated in the territory of the Republic of Crimea, Moscow, Kazan, Sochi, Astrakhan and characterized. According to the results of slide agglutination, 17 L. pneumophila strains were assigned to 1 serogroup , 37 - to 2-14 serogroups. Based on the data obtained by multilocus sequencing, in accordance with the algorithm of the European Working Group on Legionellosis Surveillance, allelic profiles of all the studied L. pneumophila strains were identified; their belonging to 7 sequence types was established. Using the method of time-of-flight mass spectrometry, legionella strains were characterized, their protein profiles were studied, and a database was formed. Using the method of scanning probe microscopy, information was obtained on the morphology of the cells of 18 legionella strains and the features of their surface structures. Using the methods of multilocus sequencing, time-of-flight mass spectrometry, and atomic force microscopy, molecular-genetic, proteomic, and morphometric features of Legionellosis pathogen strains that circulate in epidemiologically significant sites in the Russian Federation were determined.

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 recolonised by closely related strains from the North Aral region.

The review summarizes the main results of a five-year cooperation activities of the specialists from the Russian Federation and the Republic of Guinea in the fight against dangerous infectious diseases. From the very beginning of the Ebola virus disease epidemic in West Africa, Russia has been actively involved in international efforts to control it. The scientific and technical interaction of the Russian Federation and the Republic of Guinea, the main components of which are strengthening of the laboratory and hospital facilities, training of specialists, can be divided into two stages. The first one (during the period of the epidemic) is sending to Guinea a group of Russian specialists and mobile laboratories from the mobile complex of the specialized anti-epidemic team of the Rospotrebnadzor and opening of the first in the Republic of Guinea inpatient infectious disease hospital for Ebola patients. The second one (after the end of the epidemic) is the creation of a high-tech Center, which allows performing both diagnostic and scientific researches of a wide range. In the course of implementation of the programs on assistance to the Republic of Guinea on combating infectious diseases, public-private partnership mechanisms with UC RUSAL were involved, which made it possible for Russia to participate in the eradication of the Ebola epidemic and the subsequent strengthening of Guinea’s national potential in combating biological threats as efficiently as possible. The five-year interaction between the Russian Federation and the Republic of Guinea resulted in the build-up of Guinea’s national potential to counter biological threats, the creation of laboratory and hospital resources that meet the needs for the elimination of epidemiological threats caused by particularly dangerous infectious diseases, not only in the Republic of Guinea, but also in neighboring countries of West Africa, development of scientific and technical cooperation aimed at improving the system of epidemiological surveillance of communicable diseases in the Republic of Guinea.

Objectiveof the study. This work was carried out to identify markers (antigen and RNA) of CrimeanCongo hemorrhagic fever (CCHF) virus in samples from ticks, collected in all landscape-geographical areas of Guinea: Lower, Middle, Upper and Forest, to obtain up-to-date data on the distribution of the pathogen in the country.Materials and methods. Total of 4276 specimens of 8 species of ticks collected in 2016–2019 in the territory of the Republic of Guinea were studied, which were compiled into 1406 samples. Ectoparasites were collected from livestock animals, dogs, and small mammals. Viral antigen was detected using enzyme immunoassay (ELISA). The presence of RNA of the CCHF virus was determined by reverse transcription polymerase chain reaction (RT-PCR).Results and discussion. As a result of the studies, the antigen of the CCHF virus was detected in 21 samples (1.5 %), and RNA – in 37 (2.6 %). All samples, in which the viral antigen was detected, contained RNA of the CCHF virus. Positive results were obtained in samples from all geographical areas of the country. The main vectors and reservoirs of the pathogen in Guinea are ticks of the species Rh. sanguineus, Rh. geigyi, Rh. annulatus and Am. variegatum. The data obtained confirm the previously available information on the possibility of the pathogen circulation in this region and determine the need for further study of the spread of the CCHF virus in the territory of the Republic of Guinea.

The paper presents the analysis of epidemic activity of natural plague foci around the world, including in CIS and the Russian Federation, over the period of 2000–2018. It was established that in 2010–2018, epidemic manifestations took place in natural plague foci where the main carriers are synanthropic (black, multinippled rats) and commercial (marmots, souslik, ground squirrels) species of rodents. Retaining of low epizootic activity of lowland natural plague foci in the territory of the Russian Federation is observed. In 2018, plague epizooties were detected in the territory of the Gorno-Altai high-mountain and Tuva mountain natural foci, the total coverage area being 2641 km2. 13 strains of the main subspecies and 6 strains of Altaic subspecies of plague microbe were isolated. Demonstrated were the prospects of GIS-technology usage for the enhancement of epidemiological surveillance over plague in Russia. Epizootiological forecast for persisting challenging epidemiological situation in Kosh-Agach district of the Republic of Altai and Mongun-Taiginsky, Ovyursky and Tes-Khemsky Kozhuuns of the Republic of Tuva was substantiated. Recorded was high probability of retention of strained epizootic and epidemiological situation in the south and central parts of the desert zone in the Republic of Kazakhstan, high-mountain areas of the Republic of Kyrgyzstan. Also conservation of epidemic risks for the territories of the countries in Africa (Republic of Madagascar), South (Peru, Bolivia), and North (USA) America, China, and Mongolia was noted.

In 2018, between June14 and July 15, final matches of the FIFA World Cup-2018 were held in 11 cities of the Russian Federation. That event was the biggest mass event with international participation in the history of Russia. During the period, in the process of sanitary-epidemiological welfare provision, developed earlier scintific-and-practical achievementds for prevention of emergency situations of sanitary-epidemiologoical character were implemented to the fullest extent. Objective of the study – analysis of evolution of the developed in Russia scientifically-substantiated approaches in the sphere of sanitary-epidemiological welfare provision of mass events and aggregation of the results of their implementation during preparation and holding of FIFA World-Cup-2018. Utilized were information-analytical materials from the Rospotrebnadzor Administrations by the constituent entities of the Russian Federatuion, Centers of Hygiene and Epidemiology in the entities of the Russian Federation, RusRAPI “Microbe” of the Rospotrebnadzor, data from Organizing Committee “Russia-2018”, Federal Turism Agency, information published in periodical press. Scientifically substantiated model of sanitary-epidemiological welfare provision during mass events was developed in the Russian Federation. It includes expert evaluation and quantification of potential epidemic hazard of mass event which allows for targeted prophylactic and anti-epidemic measures with rationalized loads and adequate frequency of repeat. The paper discusses the complex of measures carried out during preparation and holding of FIFA World Cup-2018 by the functional areas: sanitary protection of the territory; epidemiological surveillnace over relevant anthropozoonotic, natural-focal zoonotic, sapronotic infectious diseaseas; sanitary surveillance over communal facilities, catering facilities, sites of accomodation of the participants and guests; sanitary-hygienic monitoring of ambient environment objects; provision of anti-epidemic preparadeness and readiness of the Rospotrebnadzor authorities and institutions and medical organizations; provision of readiness of laboratory facilities; involvement of additional forces and capacities and interagency cooperation in response to emergency situations of sanitary-epidemiological character.

Emergence of large-scale plague outbreaks in Africa and South America countries in the modern period, characterized by high frequency of pneumonic plague development (including with lethal outcome) keeps up the interest of scientists to the matters of development and testing of means for specific prophylaxis of this particularly dangerous infectious disease. WHO workshop that was held in 2018 identified the general principles of optimization of design and testing of new-generation vaccines effectively protecting the population from plague infection. Application of the achievements of biological and medical sciences for outlining rational strategy for construction of immunobiological preparations led to a certain progress in the creation of not only sub-unit vaccines based on recombinant antigens, but also live and vector preparations on the platform of safe bacterial strains and replicating and non-replicating viruses in recent years. The review comprehensively considers the relevant trends in vaccine construction for plague prevention, describes advantages of the state-of-the art methodologies for their safety and efficiency enhancement.

Epidemic complications in the territory of Gorno-Altai high-mountain natural plague focus, associated with increase in numbers of carriers and vectors of the dangerous diseases, entailed strengthening of preventive element in the system of epidemiological surveillance.Objectiveof the study was to assess the efficiency of disinsection and deratization during anti-epidemic campaign.Materials and methods.Investigations were performed in 2014-2017 in the territory of Kosh-Agach district of the Republic of Altai, based on the archival and operational records from Altai Plague Control Station, Rospotrebnadzor Administration in the Republic of Altai, and our own data. “Interactive Map on Management of Health Promotion Measures in Gorno-Altai high-mountain natural plague focus” was used as an assessment tool.Results and conclusions.The most hard-hitting sections of preventive complex as regards plague are still disinsection and deratization. Application of advanced methods and means of control over numbers of carriers and vectors of the infection testify to their high anti-epidemic effectiveness. Insecticide and rodenticide treatments of encampments situated in epizootic areas, disinsection and deratization in major population centers in the territory of the focus allowed for the reduction in risk of population infection. Technical efficiency of the field disinsection amounted to 96.7 %, community deratization and disinsection varied from 91.6 to 100 %. Emergency insecticide and rodent treatments in epizootic areas alongside other measures provided for epidemiological welfare on plague.

We analyzed the data on availability and usage of mobile laboratories of biological expertise for indication and identification of pathogenic biological agents in foreign countries and in the Russian Federation. We outlined the major types of mobile units that exist abroad and in Russia. Key stages of evolution in design and deployment of mobile laboratories in the network of plague control institutions of the Rospotrebnadzor were described, as well as the broadening of the range of their use in Russia. We assessed operational use of the Russian mobile laboratories, both in Russia and abroad, in the provision of sanitary-epidemiological welfare during mass events, disaster management, and response to epidemic manifestations of particularly dangerous infectious diseases. Major trends in implementation of mobile units of biological expertise in Russia were identified. We addressed their usage in various State Programs on assistance to partner-countries in the matters of International Health Regulations (2005) implementation, control over dangerous infectious diseases. Advanced inventions – Second generation modernized mobile complex of the specialized anti-epidemic teams, mobile laboratory for monitoring and diagnostics, and airmobile anti-epidemic complex – were discussed.

Objective of this study was to investigate the areal of Yersinia pestis strains of antique biovar, main subspecies, phylogenetic line 4.ANT, as well as to establish the borders and spatial structure of mega-focus in the territory of Gorny Altai. Materials and methods. Complex comprehensive analysis of the properties in Yersinia pestis strains of the main subspecies, circulating in Gorny Altai has been conducted. 33 out of them, isolated predominantly in 2012–2017 have been sequenced. Whole genome SNP analysis and search of marker SNPs was performed using Wombac 2.0 software package. Tree diagram was built applying Maximum Likelihood algorithm, using PhyML 3.1 software on the basis of HKY85 model. Results and conclusions. Based on the results of whole genome SNPs analysis of 33 endemic strains and creation of the tree diagram of Y. pestis strains, the presence of natural mega-focus of Y. pestis belonging to the main subspecies, antique biovar, phylogenetic line 4.ANT has been substantiated. Epizootic manifestations on multiple local areas, characterized by persistent autonomous nature of plague manifestations, are registered on an annual basis. Within the boundaries of the areal of Yersinia pestis main subspecies, antique biovar, phylogenetic line 4.ANT, existence of joint natural foci of Yersinia pestis belonging to non-main subspecies ssp. altaica and ulegeica is established. Location of natural foci of the main and non-main subspecies of Yersinia pestis in different altitudinal belts of the Altai Mountains Range on the whole provides for observed multi-host and multi-vector feature of epizootic manifestations. For the first time ever, the data on the areal of the main subspecies of plague microbe are used for setting the boundaries of its natural focus.

The article covers the issues related to the scientific substantiation and methodological support of immunological monitoring of persons vaccinated against plague upon epidemic indications. The problematic issues of the methodology for the assessment of immunological efficiency (efficacy) of plague live vaccine (PLV) are noted. The current tasks and possible prospects for the introduction of immunological monitoring of persons vaccinated against plague upon epidemic indications have been defined. The algorithm of efficacy estimation of plague live vaccine in vaccinated (revaccinated) persons has been tested under real conditions. Analysis of the results of efficacy evaluation of plague live vaccine among vaccinated (revaccinated) people against plague living in the territories of natural foci of this infection has been performed. Demonstrated is the possibility of using immunological monitoring results in creating an objective basis for improving the strategy of specific plague prevention in natural foci of this infection. The priority areas for further optimization of the specific plague prevention in the territories of natural foci of the infection, including those related to the formation of individual regimen revaccination tactics, taking into account the possibilities of creating modern and effective vaccines, are outlined.

Objective of the study was to assess the condition of parasitic systems and activity of natural plague foci of the Russian Federation in 2008–2017. Epizooties of varying intensity were registered in East-Caucasian high-mountain, Gorno-Altai high-mountain, Tuva mountain, and Precaspian sandy natural foci. In 2017, plague epizooties were detected in the territory of Kosh-Agach District of the Republic of Altai and Mongun-Taiginsk, Ovyursk and Tes-Khemsky Kozhuuns in the Republic of Tyva, covering the area of 1921 km2. In order to decrease the risk of infection in the territory of Gorno-Altai high-mountain and Tuva mountain natural plague foci in 2017, a set of survey and preventive measures was carried out, providing for epidemiological welfare of the population. Substantiated has been epizootiological forecast for the retention of an adverse epidemiological situation in Gorno-Altai high-mountain and Tuva mountain plague foci in 2018. Increase in the likelihood of finding individually infected animals in Central-Caucasian high-mountain and Precaspian sandy natural plague foci is expected.

The causes of emergence and development of pneumonic plague outbreak in 2017 on Madagascar were analyzed. Summarized were the literature data, characterizing the spatial and biocoenotic structure of natural plague focus on Madagascar, assessed were the risk factors of plague infection among rural and urban population of the island, as well as the properties of Yersinia pestis strains isolated there in the XX century. It is substantiated that the distinctive type of plague outbreaks on Madagascar is a rural one. It is demonstrated that one of the main causes of wide spread of plague in 2017 is importation of the infection from central regions of the Republic of Madagascar into big cities with further formation of multiple epidemic foci. Confirmed was the circulation of Y. pestis strains that belong to the third branch of irradiation of oriental biovar (1.ORI3). Discussed are the issues of diagnostics and treatment of plague in epidemic foci in the territory of the Republic of Madagascar. The evidence is provided to the fact that the plague outbreak in 2017 on Madagascar is the consequence of a lower surveillance level, first and foremost undervaluation of specific and non-specific prophylaxis capacities regarding this infection.

Objective of the study is to analyze the appurtenance, numbers, and dynamics of interaction of acanthamoeba from soils of GornoAltai plague focus with Yersinia pestis 367 strain, isolated in 2016 in enzootic territory of this focus. Materials and methods. Utilized were soil amoeba from Gorno-Altai high-mountain focus and the strain Y. pestis 367 of the main subspecies of antique biovar, isolated there in 2016. Determination of systematic relation of the isolated amoeba was carried out using PCR with genus specific primers and sequencing of the obtained PCR fragments followed by identification of nucleotide sequences against GenBank database. Localization of Y. pestis cells in acanthamoeba was performed using fluorescent antibody technique by means of Axio Imager Z2 (Carl Zeiss, Germany). Results and conclusions. For the first time ever established has been the presence of Acanthamoeba castellanii in soils of burrows of Marmota altaica in the numbers of up to 300000 cells/gr in Gorno-Altai high-mountain focus. Investigated has been the dynamics of interaction of these microorganisms. Preservation of the agent in vacuoles of endoplasmatic reticulum within 14 days has been revealed. It is an indicative of the possibility of Y. pestis persistence in amoeba of Acanthamoeba subspecies in soil biocoenosis of Gorno-Altai high-mountain plague focus.

The paper presents the analysis of the current epidemiological situation from the viewpoint of identification of risks of emergency situation onset in the sphere of biological safety, which differs from the emergency situation of sanitary-epidemiological welfare in the character of after-effects that are comparable in the quality and the scale to the threats to national and international security. In reference to the parameters of emergency situation in the sphere of biological safety, epidemic of Ebola fever in West Africa countries (2013-2016) has been described. Biosafety emergency situation is most likely to be predicted in the following cases: occurrence of the flu pandemic of the novel subtype (International Health Regulations, 2005); intensification of unfavorable for public health tendencies against the background of Zika fever transmission; larde-scale failures in the provision of biological safety when working with pathogenic biological agents; foreseeable, hard to control consequences of onset and transmission of infectious diseases caused by microorganisms with synthetic genome; occurrence of epidemic events during international mass meetings; justified interpretation of emergency situation, applying IHR (2005), as an after-effect of violation of the Convention on the Prohibition of Biological and Toxin Weapons (CBTW) and the grounds for intervention into the internal affairs of offending countries with social-economic, geo-political aftermaths and damage to the national security.

Alveolar echinococcosis caused by Echinococcus multilocularis is an important zoonotic disease. In the infected mice, emu-miR-4989-3p is present in sera, but its role remains unknown. Using high-throughput sequencing and qPCR, emu-miR-4989-3p was herein confirmed to be encapsulated into E. multilocularis extracellular vesicles. In the transfected macrophages, emu-miR-4989-3p was demonstrated to significantly inhibit NO production compared to the control (p < 0.05). Moreover, transfection of emu-miR-4989-3p also gave rise to the increased expression of TNF-α (p < 0.01). Furthermore, emu-miR-4989-3p induced the dysregulation of several key components in the LPS/TLR4 signaling pathway compared with the control, especially TLR4 and NF-κB that both were upregulated. Conversely, the NO production and the expression of TNF-α, TLR4 and NF-κB tended to be increased and decreased in the mimics-transfected cells upon emu-miR-4989-3p low expression, respectively. These results suggest that emu-miR-4989-3p is one of ‘virulence’ factors encapsulated into the extracellular vesicles, potentially playing a role in the pathogenesis of E. multilocularis.

The paper describes the International Health Regulations (2005), hereinafter referred as IHR (2005), by the example of SARS, A/H5N1/, A/H1N1/09, Zika fever, and MERS-CoV control as an effective tool for prevention and control of public health emergences (ES of sanitary-epidemiological character) of international concern. Late detection of Ebola fever epidemic in West Africa (2013–2016) and announcement of public health emergency of international concern at the time when epidemic up-scaled to a threat to national security of the affected countries and high-priority threat to global community (ES of biological character) is attributed to non-use of methodological capacities of IHR (2005) on verification of ES at an early stage of epidemic development because of unpreparedness of local, regional, national and international public health services to such an epidemic situation. WHO plans to achieve scientifically-based reduction of the time from the onset of epidemic events to the effective response measures. Russian Federation, scientifically implementing IHR (2005) from the very beginning and having devised methodology of IHR implementation on the national level, has a strong premise for scientific provision of this process.

Objective of the study was to evaluate the state of parasitic systems and activity of the natural plague foci of the Russian Federation in 2016 and to develop epizootiological forecasting for 2017. In 2016 epizooties of plague were registered in the territory of the KoshAgach District of the Altai Republic and Mongun-Taiginsky, Ovyursky, and Tes-Khemsky Kozhuuns of the Republic of Tyva. The total area coverage was 1692.6 km2. Isolated were 87 strains of plague microbe, including the isolates from rodents and lagomorphs – 31, from fleas – 47, lice – 7, and Ixodidae ticks – 2. Verified has been epizootiological forecast for the year 2017, which shows that epidemiological situation will remain tense. In order to reduce the epidemic risks, comprehensive plans of preventive activities have been developed. In the territory of the other natural foci epizootic manifestations of plague are not expected to occur. Only in PreCaspian sandy focus, situated in the territory of Lagan and Chernozemelsky Regions of the Kalmyk Republic, probability of the singly infected animal findings during the autumn season, 2017 is retained.