Vadim V. Petrov

Relevance. In 2021, the World Health Assembly called on WHO Member States to strengthen the role of genomic epidemiological surveillance.Objective. To present a revolutionary range of technological tools that determine the success of genomic epidemiological surveillance.Results and discussion. Approaches that can take genomic epidemiological surveillance to a new technological level include rapid nucleic acid amplification methods, including isothermal amplification methods, metagenomic and targeted analysis using high-throughput sequencing technologies, a targeted genome editing system, as well as diagnostic solutions based on it, and the development of genomic sequence databases. In addition, it is necessary to note the importance of developing and implementing a comprehensive approach to the implementation of the genomic epidemiological surveillance system, taking into account the rapid development of a number of fundamental biological sciences related to epidemiology, as well as the wide application of information technologies in the processing of large data sets. Conclusion. Global trends confidently demonstrate a reduction in the time it takes for a technology to transition from scientific development to widespread practical application necessary to protect the population in the context of an epidemic spread of infections caused by previously unknown pathogens. For timely forecasting and prompt response to biological threats and ensuring sanitary and epidemiological well-being, the Russian Federation has successfully applied a triad of technologies: genomic epidemiological surveillance, mobile technologies and big data analytics. The authors consider biotechnological areas and technologies, the improvement of which will ensure the technological leadership of the Russian Federation in the field of genomic epidemiological surveillance.

Introduction. The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) possesses 5'-3' DNA polymerase activity, 5'-3' displacement activity and high processivity. These properties make it possible to use Bst DNA polymerase in loop-mediated isothermal amplification (LAMP), which provides highly specific amplification of the target sequence and is used for rapid detection of agents causing human infectious diseases. The purpose of the study was to produce a recombinant Bst polymerase enzyme in the bacterial expression system and to assess its properties for LAMP-based diagnostics of infectious diseases. Materials and methods. Expression constructs carrying the Bst polymerase gene were obtained using genetic engineering techniques. Different Escherichia coli strains were used for protein expression. Metal-chelate and gel filtration chromatography techniques were used for protein purification. Catalytic characteristics of the enzyme were assessed in loop-mediated isothermal amplification reactions using AmpliSens SARS-CoV-2-IT, AmpliSens IAV-IT and AmpliSens IBV-IT diagnostic systems designed for high-quality detection of SARS-CoV-2, influenza A virus (IAV) and influenza B virus (IBV) RNA, respectively. Results. The offered protocol for production, extraction and purification of recombinant Bst polymerase makes it possible to produce the enzyme in the bacterial expression system using E. coli cells in a soluble form and reaching the yield up to 20% of the total cell mass. In LAMP reactions, the obtained enzyme demonstrates activity comparable with that of the commercial enzyme Bst 2.0 (NEB). Conclusion. Considering the fast purification and production of the enzyme, the obtained recombinant Bst polymerase can be used in LAMP-based diagnostic kits.

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.

Over the two years of the novel coronavirus infection (COVID-19) pandemic, there has been an evolution of views in various fields of medicine, which has led to a powerful development of scientific research in the field of epidemiology, clinic, diagnosis and therapy of COVID-19. This article discusses the evolution of views and approaches to the study of the clinic and therapy of COVID-19. The symptoms and aggravation of the course of cardiovascular diseases with COVID-19 have been established. The main strategy for organizing surgical care for patients with COVID-19 is indicated. The main criteria for the treatment of COVID-19, the need to prescribe SGCS on an individual basis, and the need to search for new methods of anti-inflammatory therapy for COVID-19, one of which may be the use of alkylating drugs in ultra-low doses, are described.

Over the two years of the novel coronavirus infection (COVID-19) pandemic, there has been an evolution of views in various fields of medicine, which has led to a powerful development of scientific research in the field of epidemiology, clinic, diagnosis and therapy of COVID-19. The article highlights the evolution of views and approaches to the study of the epidemiology and radiology of COVID-19. The data of molecular genetic studies are shown, which are the most important component of epidemiological surveillance. The study of the manifestations of the COVID-19 epidemic process made it possible to distinguish two stages in the development of the epidemiological situation in the Russian Federation. At the first stage of the epidemic, two rises in the incidence rate of the population were recorded, regulated by social and natural factors. The second stage of the epidemic was due to a change in the biological properties of the SARS-CoV-2 virus, followed by a change in the prevailing genovariants (Alpha, Delta and Omicron). At the second stage of the epidemic, three rises in the incidence of the population were recorded. The general principles for the use of radiodiagnosis methods, which are used primarily to detect lung damage in COVID-19, are given. With the accumulation of experience, a natural change in ideas about the algorithms for the use of visualization technologies has occurred.

Introduction. Currently, the basis for molecular diagnostics of most infections is the use of reverse transcription polymerase chain reaction (RT-PCR). Technologies based on reverse transcription isothermal loop amplification (RT-LAMP) can be used as an alternative to RT-PCR for diagnostic purposes. In this study, we compared the RTLAMP and RT-PCR methods in order to analyze both the advantages and disadvantages of the two approaches.Material and methods. For the study, we used reagent kits based on RT-PCR and RT-LAMP. The biological material obtained by taking swabs from the mucous membrane of the oropharynx and nasopharynx in patients with symptoms of a new coronavirus infection was used.Results. We tested 381 RNA samples of the SARS-CoV-2 virus (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) from various patients. The obtained values of the threshold cycle (Ct) for RT-PCR averaged 20.0 ± 3.7 s (1530 ± 300 s), and for RT-LAMP 12.8 ± 3.7 s (550 ± 160 s). Proceeding from the theoretical assumptions, a linear relationship between values obtained in two kits was proposed as a hypothesis; the correlation coefficient was approximately 0.827. At the same time, for samples with a low viral load (VL), the higher Ct values in RT-LAMP did not always correlated with those obtained in RT-PCR.Discussion. We noted a significant gain in time for analysis using RT-LAMP compared to RT-PCR, which can be important in the context of testing a large number of samples. Being easy to use and boasting short turnaround time, RT-LAMP-based test systems can be used for mass screening in order to identify persons with medium and high VLs who pose the greatest threat of the spread of SARS-CoV-2, while RT-PCR-based diagnostic methods are also suitable for estimation of VL and its dynamics in patients with COVID-19.

This review presents the basic principles of application of the loop-mediated isothermal amplification (LAMP) reaction for the rapid diagnosis of coronavirus infection caused by SARS-CoV-2. The basic technical details of the method, and the most popular approaches of specific and non-specific detection of amplification products are briefly described. We also discuss the first published works on the use of the method for the detection of the nucleic acid of the SARS-CoV-2 virus, including those being developed in the Russian Federation. For commercially available and published LAMP-based assays, the main analytical characteristics of the tests are listed, which are often comparable to those based on the method of reverse transcription polymerase chain reaction (RT-PCR), and in some cases are even superior. The advantages and limitations of this promising methodology in comparison to other methods of molecular diagnostics, primarily RT-PCR, are discussed, as well as the prospects for the development of technology for the detection of other infectious agents.