Agent-Based Simulation of the COVID-19 Epidemic in Russia.

The COVID-19 pandemic has created a public health emergency in Russia and across the world. The wavelike spread of the new coronavirus infection, caused by newly emerging variants of the coronavirus, has led to a high incidence rate in all subjects of the Russian Federation. It is becoming extremely topical to get the opportunity to manage the development of the epidemic and assess the impact of certain regulatory measures on this process. This will help government agencies make informed decisions to control the burden on healthcare organizations. It is often impossible to obtain such assessments without using modern mathematical models.

[The use of non-Euclidean metrics in epidemiological classifications]. / Ispol'zovanie neevklidovykh metrik v épidemiologicheskikh klassifikatsiiakh.

A non-Euclidean metric, stable to pollutions in sample data, for hierarchical cluster analysis in epidemiology is proposed. The simplicity of calculations permits its easy use in practice. On the basis of this metric the towns of Tula Province have been grouped according to morbidity rates in the shigellosis of Flexner and Sonne with the conjugated value of parameters.

[Validity of epidemiological classification: construction of a discriminant criterion]. / Dostovernost' épidemiologicheskikh klassifikatsii: postroenie diskriminantnogo kriteriia.

A new criterion has been proposed to assess the validity of group division differences obtained by preliminary cluster analysis. The method was used to provide evidence for the validity of differences between the groups as to epidemiological classifications. The paper shows it expedient to use the method in the epidemiological analysis.

[The structure of populations of the causative agents of infectious diseases and the mechanism of the development of the epidemic process]. / Struktura populiatsii vozbuditelei infektsionnykh boleznei i mekhanizm razvitiia épidemicheskogo protsessa.

The parameters of clonality and preservation capacity, characterizing the population structure of the causative agents of infectious diseases, have been worked out on the basis of the clonal concept and the concept of self-restructuring of microbial populations. Different correlations between these parameters determine the existence of 9 independent groups of infections. The mechanisms and manifestations of the epidemic process of these infections have been described and the priority directions of anti-epidemic measures formulated.

[The plasmid heterogeneity of Shigella sonnei phase-I and -II strains]. / Geterogennost' plazmid shtammov Shigella sonnei I i II faz.

The plasmid composition of S. sonnei standard strains has been studied by the method of electron microscopy of the preparations of plasmid DNA. In S. sonnei cells I-941-HP, phase I, plasmids of 2,500; 5,000; 5,600; 6,100 and 6,800 base pairs, as well as plasmids of 85,000-117,000 and 170,000-235,000 base pairs have been detected. In S. sonnei cells, phase II, plasmids of 2,500; 4,900 and 6,100 base pairs, as well as plasmids of 85,000-109,000 base pairs, have been found. Thus, virulent S. sonnei in phase I contain additional plasmids of 5,600; 6,800; 110,000-117,000 and 170,000-237,000 base pairs. The range of plasmid lengths between 85,000-117,000 and 170,000-237,000 base pairs exceeds the usual background of electron-microscopic studies, which makes it possible to come to the conclusion on the intrastrain heterogeneity of these classes of plasmids. The suggestion has been made that the transition of S. sonnei from phase I to phase II is linked with the loss of fragments of the genetic material, limited by inverted DNA repetitions.

[Dissociation and ultrastructure of the cells of Shigella sonnei isolated from gnotobiotes and obtained in vitro]. / Dissotsiatsiia i ul'trastruktura kletok Shigella sonnei, vydelennykh ot gnotobiontov i poluchennykh in vitro.

The dissociation variants of S. sonnei in phase I, isolated from germ-free rats and obtained in vitro, have been studied. Such dissociation variants have been found to form colonies with classical and atypical morphology. The electronmicroscopic study has revealed that different dissociation variants include small dense cells with the markedly thickened cell wall and pronounced microcapsule and spheroplasts with the damaged cell wall and less pronounced microcapsule. The formation of these cells is supposed to be the way of the adaptation of S. sonnei in the course of the infectious process and linked with changes in their virulence in the population cycle.

[Fast and slow genome rearrangements: molecular and genetic mechanisms of changes in virulence]. / Bystrye i medlennye perestroiki genoma: molekuliarno-geneticheskie mekhanizmy izmenenii virulentnosti.

Different mechanisms of virulence changes at the molecular and populational levels are discussed. The methodology and mechanisms of Streptococcus pyogenes variability are analysed. The views of the adaptive role played by insertion sequences are developed, and the design of an epidemiologico-genetic experiment is proposed, which consists in obtaining highly virulent insertion mutants and testing their properties.

[Phenomenology and molecular mechanisms of Shigella sonnei dissociation: its variability in model in vivo and in vitro systems]. / Fenomenologiia i molekuliarnye mekhanizmy dissotsiatsii Shigella sonnei: izmenchivost' v model'nykh sistemakh in vivo i in vitro.

The dynamics of the accumulation of phase II S. sonnei in the infectious process in germ-free rats, during cultivation and in subcultures was studied. The in vivo variability of S. sonnei showed a sharply defined phasic character of the process with the periods of the apparent absence of phase II, the increase of its occurrence and stabilization with the preservation of S-forms in minor amounts. Kanamycin-resistant phase II accumulated in vivo more rapidly than in vitro. Cultivation with sodium desoxycholate was found to accelerate the process of disassociation. The characteristic feature of all dissociants detected in all systems was their plasmid profile: in phase I, plasmids of 120 and 60 Md, as well as small plasmids, were detected; in phase II disassociants, plasmid with a molecular weight of 120 Md was absent. The restriction analysis of total plasmid DNA by means of restrictase EcoR1 showed the absence of 3 fragments in phase II while other 13 fragments were retained. These results open prospects for the molecular cloning of the gene antigen of phase II.