[Molecular epidemiological analysis of SARS-CoV-2 genovariants in Moscow and Moscow region].

INTRODUCTION: SARS-CoV-2, a severe acute respiratory illness virus that emerged in China in late 2019, continues to spread rapidly around the world, accumulating mutations and thus causing serious concern. Five virus variants of concern are currently known: Alpha (lineage B.1.1.7), Beta (lineage B.1.351), Gamma (lineage P.1), Delta (lineage B.1.617.2), and Omicron (lineage B.1.1.529). In this study, we conducted a molecular epidemiological analysis of the most prevalent genovariants in Moscow and the region. The aim of the study is to estimate the distribution of various variants of SARS-CoV-2 in Moscow city and the Moscow Region. MATERIALS AND METHODS: 227 SARS-CoV-2 sequences were used for analysis. Isolation of the SARS-CoV-2 virus was performed on Vero E6 cell culture. Sequencing was performed by the Sanger method. Bioinformatic analysis was carried out using software packages: MAFFT, IQ-TREE v1.6.12, jModelTest 2.1.7, Nextstrain, Auspice v2.34. RESULTS: As a result of phylogenetic analysis, we have identified the main variants of the virus circulating in Russia that have been of concern throughout the existence of the pandemic, namely: variant B.1.1.7, which accounted for 30% (9/30), AY.122, which accounted for 16.7% (5/30), BA.1.1 with 20% (6/30) and B.1.1 with 33.3% (10/30). When examining Moscow samples for the presence of mutations in SARS-CoV-2 structural proteins of different genovariants, a significant percentage of the most common substitutions was recorded: S protein D614G (86.7%), P681H/R (63.3%), E protein T9I (20.0%); M protein I82T (30.0%), D3G (20.0%), Q19E (20.0%) and finally N protein R203K/M (90.0%), G204R/P (73.3 %). CONCLUSION: The study of the frequency and impact of mutations, as well as the analysis of the predominant variants of the virus are important for the development and improvement of vaccines for the prevention of COVID-19. Therefore, ongoing molecular epidemiological studies are needed, as these data provide important information about changes in the genome of circulating SARS-CoV-2 variants.

Flow cytometric assay for the detection of anti-SARS-CoV-2 Spike protein antibodies in serum of vaccinated volunteers

Introduction. The determination of antibodies against the Spike (S) protein of the novel coronavirus is widely used to confirm current or past infection with SARS-CoV-2, and as an indicator of the effectiveness of vaccination against COVID-19. The most common method for detecting anti-S-antibodies is enzyme-linked immunosorbent assay (ELISA), which uses a recombinant S-protein. Immunofluorescence followed by flow cytometry provides an alternative approach to detect anti-S-antibodies, where a protein in the native transmembrane conformation is used as the S-antigen. The aim of the study was to develop a method for determining anti-S-antibodies using flow cytometry, and to select the most appropriate method for processing experimental data. Material and methods. The study involved 22 volunteers (7 men and 15 women aged 25 to 70 years, median 48). All volunteers were vaccinated with two doses of the <<Sputnik V>> vaccine between January and February 2021. Donor sera samples were collected before vaccination with <<Sputnik V>> and 3 months after vaccination. 5 volunteers had already had a mild form of COVID-19 before the time of vaccination. The remaining 17 volunteers did not encounter the SARS-CoV-2. Antibodies against S-protein were determined by immunofluorescence with registration on a flow cytometer. HEK293 cells were transiently transfected with a plasmid encoding the wild type S-protein which was used as target. Transfection was performed by the calcium phosphate method. Cells were incubated with serially diluted sera and then stained with anti-IgG-PE and anti-IgM-FITC secondary antibodies. The fluorescence level was measured using a flow cytometer. As a measurement result, the mean fluorescence intensity (MFI) obtained at 1:18 serum dilution, or the area under the titration curve (area under curve, AUC) was used. Anti-RBD-antibodies were determined using enzyme immunoassay, and virus-neutralizing activity using pseudotyped or surrogate virus-neutralization analysis (pVNA and sVNA). Results. Using the developed method, the formation of anti-S antibodies of the IgG and IgM isotypes was shown 3 months after immunization with the <<Sputnik V>> vaccine. In a simplified version of the method, the relative concentration of antibodies was determined at a single dilution of the test serum by measuring the mean fluorescence intensity (MFI) of the target cells. More reliable results were obtained by construction the titration curve and calculating the area under the curve (AUC). The results thus obtained correlated well with the detection of anti-RBD antibodies by ELISA, as well as with virus neutralization data in pseudotyped and surrogate assays. Conclusion. Flow cytometry is a convenient method for the simultaneous determination of anti-S antibodies of IgG and IgM isotypes in human serum. The advantages of the method include the fact that the S-protein is presented in a native transmembrane conformation. After minor modification, the established method can be used to determine the level of anti-S-antibodies against mutant variants of SARS-CoV-2. Copyright © 2022 Meditsina Publishers. All rights reserved.