Phylogenetic analysis and molecular genetic characteristics of West Nile virus lineage 2 isolates circulating in the Russian Federation.

Since its initial detection in Africa, the West Nile virus has disseminated widely across all continents, becoming endemic in numerous countries, including the Russian Federation. A substantial expansion of the West Nile virus range was observed in the European part of the Russian territory in 1999. In light of this epidemiological trend, research endeavours focusing on monitoring West Nile virus circulation activity in endemic regions of the country have gained paramount significance. A substantial dataset has been accrued from 2007 onwards regarding genomic variability and dissemination dynamics across the country throughout the entire monitoring period for the West Nile fever pathogen. The objective of this study was to characterise West Nile virus isolates that have been circulating in the Russian Federation and identify their molecular and genetic characteristics. A phylogenetic analysis of 55 complete genome sequences revealed that the West Nile virus population within the Russian Federation is genetically heterogeneous and is represented by four major clades. One of these clades is currently exhibiting extensive spread into new regions of the country.

The application of mass spectrometry method for the study and identification of medically important viruses (review of literature).

It is difficult to overestimate the urgency of the problem of well-timed diagnosis of viral infections. According to the WHO, dozens of outbreaks of viral diseases are recorded annually, both in developing and developed countries. Moreover, the seasonal flu virus alone is capable of infecting up to 20% of the population, even in European countries with a high level of medicine. And the annual number of deaths due to viral infections, according to official statistics, exceeds 600 thousand people around the world. That's why the provision of a reliable and fairly rapid diagnosis of viruses, along with subsequent therapy, makes a significant contribution to reducing the incidence of mortality. Despite the fact that PCR-based methods currently remain the most common method for identifying viruses in clinical practice, as recent experience shows, in addition to the already known disadvantages, in the event of large outbreaks, such test systems may simply not be in the required amount. In this regard, it is necessary to supplement and improve the existing tools for identification and research of clinically significant viruses. The MALDI-TOF mass spectrometry method combines a degree of accuracy and versatility, sufficient both for the identification of clinical strains isolated from patients, and for the study of the phenotypic properties of viruses in research laboratories and centers. This article presents and summarizes the main data on the existing or potential application of the method of time-of-flight mass spectrometry with matrix-associated laser desorption / ionization for the identification or study of viruses.

[Assessment of the possibility of application in laboratory practice of reagent kit for diagnosis of glanders and melioidosis by real-time polymerase chain reaction.]

The reagent kit AmpligenBurk-mallei/pseudomallei-RT PCR is designed for detecting in vitro diagnostics and differentiate the DNA of glanders and melioidosis pathogens by real-time multiplex PCR in biological (clinical) material and cultures of microorganisms, as well as environmental objects and solid food products (rice). During clinical testing diagnostic value of reagent kit AmpligenBurk-mallei/pseudomallei-RT PCR has been studied. Based on the results obtained, a high analytical sensitivity (1×103 microbe cells/ml) and specificity (100%) of PCR-RT with the developed reagent kit were established, regardless of the type of material being studied. The diagnostic sensitivity of PCR-RT using a set of reagents was at least 98.0% and specificity at least 99%. The stages of state examination have been completed, a registration certificate has been obtained at Roszdravnadzor, production, sale and use of reagent kit in medical laboratory practice have been permitted.

[Preparation for state registration of the reagent kit for the detection and differentiation of the DNA of burkholderia «pseudomallei¼ group.]

The reagent kit designed to detect and simultaneously differentiate the DNA of three species of Burkholderia pseudomallei - causative agents of melioidosis (B. pseudomallei), glanders (B. mallei) and B. thailandensis by the set of genes of ß-lactamases with B and D molecular classes using a multiplex polymerase chain reaction with electrophoretic detection was developed for clinical laboratory diagnosis. The functional properties of the reagent kit were evaluated, tests were carried out, the stages of examination and registration in the Federal Service for Surveillance on Consumer Rights' Protection and Human Well-being were completed. During clinical testing the effectiveness of the reagent kits in the study of various samples of clinical material and isolated cultures of microorganisms was confirmed. It has been established that the indicator of diagnostic sensitivity of the reagent kit for the detection and differentiation of the glanders, melioidosis and B. thailandensis causative agents was less than 99 %, diagnostic specificity - not less than 99 % with a confidence probability of 90 % in the analysis of each of the indicators.

[Zika fever immunodiagnostics: overview of test systems.]

The threat of rapid spread of Zika virus beyond endemic regions has given rise to more research in field of epidemiology and clinic, as well as to the search for Zika fiver new diagnostic and preventive tools. Between 2013 and 2017 in Russia 18 cases of infection transmission by travellers were reported. Fever Zika reference monitoring center in Volgograd Research AntiPlague Institute (Volgograd, Russian Federation) provides counseling and methodological assistance on laboratory diagnosis and monitoring of Zika fever. In this regard, a literature review of commercial test systems for immunodiagnostics of this infection was performed. Currently, a number of test systems for solid-phase enzyme-linked immunoassay method (ELISA), immunochromatography and indirect immunofluorescent method (IIFT) have been developed for immunodiagnostics of Zika fever. Euroimmun Ltd. remains the only manufacturer that has access to detailed information on validation of the specificity of the produced diagnostic kits. Independent studies confirm that Euroimmun test systems have high specificity and high sensitivity, which is proved by the study of the material from various populations, including Europeans travelling to Zika virus endemic regions and people residing in these regions. A detailed overview of characteristics of Euroimmun test systems for immunodiagnostics of Zika fever allows us to conclude that there is a rationale for the use of these test systems for Russian Federation sanitary protection by identification of antibodies in patients, presumably infected with the Zika virus.

[The problems of identification of various strains of vegetative form of Bacillus anthracis using MALDI-ToF MS technique.]

The article considers experience of application of mass-spectrometry with matrix-activated laser desorption/ionization for fast and reliable identification of Bacillus anthracis and heterologous species of microorganisms. The particular interesting characteristics and difficulties occurred during identification are covered.

[The application of time-of-flight mass spectrometry with matrix activated laser desorption-ionization (MALDI-ToF) for identifying agents of glanders and melioidosis].

The article presents the results of application of developed methodological approach to identifying Burkholderia pseudomallei and Burkholderia mallei using direct mass spectrometry profiling of cellular proteins. The protocol of sampling preparation of cultures of melioidosis and glanders was optimized with taking in account characteristics of observation of requirements of biological safety for operations with pathogenic biological agents of pathogenicity group II. The dependence of quality of mass spectrums (number of individual peaks and their intensity) from medium of fermentation of microorganisms was evaluated. The characteristic mass spectrums of collection strains B.pseudomallei (5) and B.mallei (5) were obtained. The set of reference mass-spectrums was generated for identification data base S.A.R.A.M.I.S.TM (Anagnostec Gmbh.). The mentioned data base was used for identification of 43 strains of pathogenic Burkholderia. The opportunity of reliable identification of taxonomic belonging of examined microorganisms up to species' level. The cluster analysis of obtained mass-spectrums of common cellular proteins of collection strains of pathogenic Burkholderia demonstrated grouping of examined strains according to their species' belonging. The supplemented data base of mass-spectral characteristics hereinafter will permit applying express-identification of isolates suspicious for belonging to agents of melioidosis and glanders. The updated data base will become a basis for developing schemes of hemotyping of strains of Burkholderia using mass spectrometry technique.

[SPREAD OF ESPECIALLY DANGEROUS MYCOSES IN THE WORLD].

Contemporary information on the spread in the world of especially dangerous mycoses - coccidioidomycosis, histoplasmosis, blastomycosis and paracoccidioidomycosis are presented in the review. Sources and infection routes of causative agents of these diseases are examined, clinical forms of mycoses are briefly characterized. An increase of morbidity due to them over the last decade is noted. A necessity of timely diagnostics of imported mycoses outside endemic regions is underscored.

[Topical issues of biological safety under current conditions. Part 3. Scientific provision for the national regulation of the biological safety framework in its broad interpretation].

Consequent of investigation concerned with biological safety (BS) framework development in its broad interpretation, reflected in the Russian Federation State Acts, identified have been conceptual entity parameters of the up-to-date broad interpretation of BS, which have formed a part of the developed by the authors system for surveillance (prophylaxis, localization, indication, identification, and diagnostics) and control (prophylaxis, localization, and response/elimination) over the emergency situations of biological (sanitary-epidemiological) character. The System functionality is activated through supplying the content with information data which are concerned with monitoring and control of specific internal and external threats in the sphere of BS provision fixed in the Supplement 2 of the International Health Regulations (IHR, 2005), and with the previously characterized nomenclature of hazardous biological factors. The system is designed as a network-based research-and-practice tool for evaluation of the situation in the sphere of BS provision, as well as assessment of efficacy of management decision making as regards BS control and proper State policy implementation. Most of the system elements either directly or indirectly relate to the scope of activities conducted by Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, being substantial argument for allocating coordination functions in the sphere of BS provision to this government agency and consistent with its function as the State Coordinator on IHR (2005). The data collected serve as materials to Draft Federal Law "Concerning biological safety provision of the population".

[Topical issues of biological safety under current conditions. Part 2. Conceptual, terminological, and definitive framework of biological safety].

In accordance with the established conceptual base for the up-to-date broad interpretation of biological safety, and IHR (2005), developed is the notional, terminological, and definitive framework, comprising 33 elements. Key item of the nomenclature is the biological safety that is identified as population safety (individual, social, national) from direct and (or) human environment mediated (occupational, socio-economic, geopolitical infrastructures, ecological system) exposures to hazardous biological factors. Ultimate objective of the biological safety provision is to prevent and liquidate aftermaths of emergency situations of biological character either of natural or human origin (anthropogenic) arising from direct and indirect impact of the biological threats to the public health compatible with national and international security hazard. Elaborated terminological framework allows for the construction of self-sufficient semantic content for biological safety provision, subject to formalization in legislative, normative and methodological respects and indicative of improvement as regards organizational and structural-functional groundwork of the Russian Federation National chemical and biological safety system, which is to become topical issue of Part 3.

[Prophage CTXphi genome variability and its role in alteration of Vibrio cholerae El Tor virulence characteristics].

Comparative analysis of CTXphi prophage genome of 366 V. cholerae El Tor strains isolated from infected people and water was carried out using the polymerase chain reaction. Four groups of vibrios, which carry different combinations of ctxA, zot, and ace genes from core region of CTXphi prophage coding key (cholera enterotoxin) and accessory (Zot and Ace toxins) pathogenicity factors, were determined: ctxA(+) zot(-) ace(+), ctxA(-) zot(+) ace(+), ctxA(-) zot(+) ace(-), ctxA(-) zot(-) ace(+). Vibrios that had lost all tested genes were also revealed. Genomic rearrangements occurring in water environment in virulent V. cholerae strains, which acquired foreign pathogenicity genes necessary for their existence in human organism, were proposed as one of the mechanisms of formation of clones with an incomplete or no prophage. Infection process in model animals challenged with wild and isogenic strains of V. cholerae differing in the set of the phage genes (ctxA, zot, and ace) was comparatively analyzed. It was shown that variability of CTXphi prophage genome was an important factor of modification of cholera vibrios virulent characteristics. Obtained data point to usefulness of ctxA, zot, and ace phage genes detection in wild V. cholerae isolates as it could permit evaluation of their virulent potential determining the severity of the infection.

[Effects of the recombinant plasmid carrying the genes of cholera prophages CTX and RS1 on the expression of virulence and immunogenicity genes in the cholera pathogen].

Using toxin-coregulated adhesion pili (TCP), the etiologic agent of cholera is able to colonize human small intestine, where this pathogen proceeds with the production of the secreted cholera toxin (CT), inducing the development of severe diarrhea. At the same time, TCP and CT are not only the major factors of pathogenicity but also form a part of the group of key protective antigens. Immunoenzyme, immunoblotting, self-agglutination investigations, electron-microscopic studies, and electrophoretic assay of the outer membrane proteins showed that the recombinant plasmid carrying a number of cloned genes of two prophages, CTX and RS1, introduced into model Vibrio cholerae strains classical biovariant, resulted in the formation of strains with an enhanced rate of synthesis of three protective antigens: CT, TCP, and an outer membrane protein, OmpU. A simultaneous increase in the level of biosynthesis of the three antigens in V. cholerae was demonstrated to be specified by alterations in the expression of the toxR regulatory gene. Information was obtained suggesting that the transcriptional activity of toxR gene was dependent on the activity of rstC antirepressor gene derived from RS1 pro-phage and localized in the cloned fragment. Strains hyperproducing the three protective antigens can be used to construct more efficient non-living cholera vaccines, and to isolate the indicated proteins applicable to the development of diagnostic test-systems.

[Comparative analysis of the major protective antigens production in Vibrio cholerae recombinant and producer strains of the classical biovar].

The comparative study of 4 constructed protective antigen producing strains of the classical biovar and V. cholerae strains 569 B Inaba and M41 Ogawa, used in manufacturing the cholera chemical vaccine "cholerogen-toxoid", was carried out. The study revealed that V. cholerae plasmid strains 2414 Ogawa, 2415 Inaba and nonplasmid strains 2416 Ogawa, 2417 Inaba had a higher level of production of the main protective antrigens in comparison with producer strains. They also synthesized much more (4-5 fold) cholera toxin, toxin co-regulated adhesion pili, contained protein OmpU in their outer membrane, exceeded 2- to 3-fold in the synthesis of pathogenicity enzymes (proteases, phospholipases) and synthesized the same amounts of 01 antigen, serovars Inaba and Ogawa. The use of the newly created protective-antigen producing strains in vaccine manufacturing could facilitate the preparation of a more effective cholera chemical vaccine "cholerogen-toxoid".

[Phenotypical analysis of heterogenic Vibrio cholerae strain Dacca 35 Ogawa]. / Fenotipicheskii analiz geterogennogo shtamma Vibrio cholerae Dakka35 Ogava.

The comparative analysis of the production of the main pathogenicity factors by toxigenic and non-toxigenic clones of V. cholerae natural classical strain Dacca 35 Ogawa has been carried out. The data obtained in this analysis indicate that the appearance of turbid colonies, not synthesing cholera toxin, is linked with the production of an exopolysaccharide layer on the outer surface of the cells, which determines their morphology. The suggestion has been made that the regulatory gene toxR controls the expression of not only cholera toxin, protein OmpU, but also exopolysaccharide.

[Isolation and phenotyping of Vibrio cholerae strains with the enhanced production of main protective antigens]. / Poluchenie i fenotipicheskii analiz shtammov kholernogo vibriona s povyshennoi produktsiei osnovnykh protektivnykh antigenov.

Two V. cholerae strains of classical biovar, 2414 (serovar Ogawa) and 2415 (serovar Inaba), with of increased production of main protective antigens--cholera toxin, toxin-coregulated pili of adhesion (TCP), outer membrane protein OmpU, as well as phospholipases and proteases, have been detected among natural and recombinant strains under study. A simultaneous increase in the production of the above-mentioned main immunogenicity factors in strains 2414 and 2415 is seemingly linked with the presence of recombinant plasmid pCT105 with cloned genes of cholera toxin in these microbial cells. As the result of plasmid-chromosomal relationships, this plasmid probably ensures the effective expression of global regulating gene toxR. The strains capable of the hyperproduction of cholera toxin, TCP and protein OmpU may be used for the manufacture of more effective chemical vaccine (choleragen-toxoid).