Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

Background. The ongoing pandemic of a new coronavirus infection (COVID-19) determines the relevance of the analysis of epidemiological patterns of SARS-CoV-2 spread among the population of the Russian Federation.Aim — study of the manifestations of the epidemic process of COVID-19 in the Russian Federation in 2020–2022.Materials and methods. A retrospective epidemiological analysis of the incidence of COVID-19 in the Russian Federation was carried out from 03/30/2020 to 04/24/2022. The data from the Rospotrebnadzor report No. 970 “Information on cases of infectious diseases in persons with suspected new coronavirus infection”, information portal Stopcoronavirus.rf, etc. were used. The presence of SARS-CoV-2 RNA was confirmed by real-time RT-PCR.Results and discussion. The analysis of the manifestations of the epidemic process of COVID-19 in the Russian Federation in 2020–2022 showed the presence of two stages which differed depending on the influence of the biological factor and the ongoing anti-epidemic measures. There was a pronounced trend in the development of the epidemic process, starting from megacities (Moscow, Moscow region and St. Petersburg), which are major transport hubs and centers of migration activity of the population, to the regions of the Russian Federation. The SARS-CoV-2 pathogenicity has been shown to decrease with each subsequent cycle of the rise in the incidence of COVID-19 against the background of the increased contagiousness of the virus.Conclusion. As a result of the study, risk areas (megacities) and risk groups were identified.

Background. The ongoing pandemic of the novel coronavirus infection (COVID-19) draws attention to the significance of molecular and genetic monitoring of the SARS-CoV-2 spread among the population of the Russian Federation. The aim of the study was to analyze the dynamics of circulation of SARS-CoV-2 genetic variants in Russia.Materials and methods. The analysis of the circulation dynamics for SARS-CoV-2 genetic variants in Russia was carried out, covering the period from 28/12/2020 to 26/6/2022. The analysis included the data from Rospotrebnadzor Report No. 970 "Information about Infectious Diseases in Individuals with Suspected Novel Coronavirus Infection" and the Virus Genome Aggregator of Russia (VGARus). The presence of SARS-CoV-2 RNA was confirmed by the real-time reverse transcription polymerase chain reaction. The primer panels developed at the Central Research Institute of Epidemiology were used for amplification of genomic fragments and the subsequent sequencing.Results and discussion. Using the Russian VGARus platform developed by the Central Research Institute of Epidemiology, we received the data on mutational variability of SARS-CoV-2. By monitoring the circulation of SARS-CoV-2 genetic variants in Russia from 28/12/2020 to 26/6/2022, we found that Delta and Omicron genetic variants prevailed at different stages of the epidemic.Conclusion. The data of molecular and genetic studies are an essential component of epidemiological surveillance, being critically important for making executive decisions aimed at prevention of further spread of SARS-CoV-2 and laying the groundwork for creating new vaccines.

Introduction. Since the outbreak of the COVID-19 pandemic caused by SARS-CoV-2 novel coronavirus, the international community has been concerned about the emergence of mutations altering some biological properties of the pathogen like increasing its infectivity or virulence. Particularly, since the end of 2020, several variants of concern have been identified around the world, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). However, the existing mechanism of detecting important mutations are not always effective enough, since only a relatively small part of all pathogen samples can be examined by whole genome sequencing due to its high cost.Material and methods. In this study, we have designed special primer panel and used it for targeted highthroughput sequencing of several significant S-gene (spike) regions of SARS-CoV-2. The Illumina platform averaged approximately 50,000 paired-end reads with a length of ≥150 bp per sample. This method was used to examine 579 random samples obtained from COVID-19 patients in Moscow and the Moscow region from February to June 2021.Results. This study demonstrated the dynamics of distribution of several SARS-CoV-2 strains and its some single mutations. It was found that the Delta strain appeared in the region in May 2021, and became prevalent in June, partially displacing other strains.Discussion. The obtained results provide an opportunity to assign the viral samples to one of the strains, including the previously mentioned in time- and cost-effective manner. The approach can be used for standardization of the procedure of searching for mutations in individual regions of the SARS-CoV-2 genome. It allows to get a more detailed data about the epidemiological situation in a region.

Background. The COVID-19 pandemic has exposed health problems, but at the same time has become a powerful impetus for the development of new scientific research in the field of epidemiology, clinic of infectious diseases, diagnostics, bioinformatics and digital methods. On the basis of the Central Research Institute of Epidemiology of Rospotrebnadzor, new unique test systems for the detection of SARS-CoV-2 RNA based on real-time PCR based on loop isothermal amplification (IT) technology have been developed, which allows you to examine samples 34 times faster than those developed previously. The Central Research Institute of Epidemiology of Rospotrebnadzor has developed and put into operation the Russian Platform for Aggregation of Information on Virus Genomes (VGARus). The VGARus database contains information about the nucleotide sequences of the SARS-CoV-2 viruses and their mutations, and the SOLAR Integration Platform has been created to quickly transfer the results of PCR studies to all interested citizens of the Russian Federation. Aims to study the manifestations of the epidemic process of COVID-19 and the prevalence of genovariants of the SARS-CoV-2 virus in the Russian Federation. Methods. A retrospective epidemiological analysis of the incidence of COVID-19 was carried out from March 30, 2020 to May 17, 2022 in the Russian Federation. The database was formed on the basis of the materials of the Rospotrebnadzor report form No. 970 Information on cases of infectious diseases in persons with suspected new coronavirus infection, data from the WHO, the domestic information portal Stopkoronavirus.rf and the Yandex DataLens data visualization and analysis service were used, information on SARS-CoV-2 genovariants in the VGARus database. Results. When analyzing the manifestations of the COVID-19 epidemic process in the Russian Federation for 20202022. Two stages have been identified. The first stage was characterized by the rapid spread of the SARS-CoV-2 virus from megacities to other regions of the country and the use of non-specific prevention measures. The beginning of the second was due to the evolution of the SARS-CoV-2 virus and a change in its biological properties, followed by a change in the prevailing genovariants on the territory of the Russian Federation. Conclusion. As a result of the study, it was found that with each subsequent increase in the incidence of COVID-19, there was a decrease in the severity of the course and the proportion of pneumonia in the structure of the clinical forms of the disease.