Late in December 2019, an outbreak of an unknown coronavirus, later identified as SARS-CoV- 2, emerged in the city of Wuhan, China. It causes a dangerous respiratory coronavirus disease in humans - COVID-19. Objective. To detect cases of the disease and prevent its spread across the Russian Federation it is necessary to create an effective diagnostic test system. Material and methods. Based on the analysis of the alignment of the SARS-CoV-2 nucleotide sequences, primers and a probe for RT-PCR were selected, and the analysis conditions were optimized. Results. The diagnostic system was developed and registered in the shortest possible time in real-time RT-PCR format for detecting SARS-CoV-2 coronavirus RNA in smears from the nasopharynx and oropharynx, sputum and feces. The high specificity of the system was verified on a representative set of viruses and microorganisms, the analytical sensitivity was 1x103 copies / ml in smears from the mucous membrane of the nasopharynx and oropharynx and sputum, 5x104 copies / ml in fecal samples. Diagnostic sensitivity and specificity established during clinical trials on samples from patients with confirmed COVID-19 infection, from patients with a different etiology of a disease and clinically healthy people were to 100% (range 94.2-100% with a confidence level of 95%).

In April 2022, several cases of acute hepatitis of unknown origin were reported in children from 12 countries. In many cases, enteric adenovirus or SARS-CoV-2 and adenovirus coinfection were detected.

The emergence of novel SARS-CoV-2 genetic variants with increased transmissivity and reduced antibody neutralization efficiency is a threat to global public health. Reverse transcription polymerase chain reaction (RT-PCR) with the use of fluorescent probes, which make it possible to detect the single nucleotide substitutions, is a technique suitable for screening the SARS-CoV-2 RNA-containing samples for the already known functionally significant mutations in the S-gene, identification of which allows to define and differentiate the most epidemiologically significant genetic variants. The study was aimed to develop an assay for the large-scale monitoring of the spread of the SARS-CoV-2 top-priority variants. Based on the whole-genome alignment of the SARS-CoV-2 sequences, deposited in the GISAID database, primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Alpha, Beta/Gamma and Delta variants of concern (VOC). The developed reagent kit for detection of the key mutations in the SARS-CoV-2 S gene by the real time RT-PCR has good analytical and diagnostic characteristics and was authorized as a medical device (reagent) for in vitro use. The results of detecting the VOC and the key mutations with the use of the developed reagent kit were consistent with the data of the whole genome sequencing of 1,500 SARS-CoV-2 RNA samples. The developed reagent kit and the subsequent SARS-CoV-2 RNA sequencing assay used to perform the epidemiological monitoring of SARS-CoV-2 variants made it possible to promptly report the emergence of the Delta genetic variant in Russia, and to trace the dynamic changes in the prevalence of Delta in Moscow Region in April–September 2021.

Background: Different species of Campylobacter are the most common causes of bacterial gastroenteritis. There are many methods to detect the presence of Campylobacter, including PCR, but it takes about 5-6 hours. Using loop-mediated amplification assay allowed reducing the time of detection and simplifying the procedure at all. Aims: To develop a loop-mediated isothermal amplification assay (LAMP) with fluorescent probe for the diagnosis of campylobacteriosis. Methods: Stool suspensions were prepared and bacterial fractions were separated as in methodological recommendation of Central Research Institute of Epidemiology described. DNA was extracted using AmpliTest RIBO-prep (FSBI SPC FMBA, Russian Federation) according to the manufacturers instruction and detected with AmpliSens OKI-screen-FL" (FBIS CRIE, Russian Federation). Primers and probes were selected in 16S rDNA gene region. Analytical specificity was confirmed on bacterial cultures, analytical sensitivity was assessed using a recombinant plasmid containing the target Campylobacter DNA sequence fragment. LAMP amplification was performed at 65 C for 30 min. Results: An assay for the detection of Campylobacter spp. based on loop-mediated isothermal amplification is developed, the reaction time does not exceed 30 minutes. The analytical sensitivity of the developed technique is comparable to the real-time PCR and is equal to 103 copies / ml, the analytical specificity is 100%. The evaluation of 127 clinical samples, previously characterized by the commercial kit "AmpliSens OKI-screen-FL" (FBIS CRIE, Russian Federation), showed high diagnostic specificity and sensitivity of the developed LAMP-method. No false positive results were found, 108 samples were negative by LAMP and PCR. Campylobacter spp. DNA was detected by the LAMP method in 18 out of 19 PCR-positive samples. One discordant LAMP negative sample can be attributed to the low bacterial load of Campylobacter spp. for a given sample. Conclusions: A method for the rapid detection of Campylobacter spp. loop-mediated isothermal amplification is developed, and its high analytical and diagnostic characteristics have been shown experimentally. Keywords: Gastrointestinal infections, molecular diagnostics, rapid diagnostics, Loop-Mediated Isothermal Amplification (LAMP), Campylobacter spp.