Journal of microbiology, epidemiology and immunobiology

Surveillance of human immunodeficiency virus type 1 (HIV-1) infection has a number of limitations related to the long-term asymptomatic course of the disease, a high level of stigmatization of HIV-infected individuals, as well as the difficulty of collecting information on the mechanisms of HIV-1 transmission. In these conditions, genomic surveillance is becoming important, which allows for obtaining objective data on the structure and dynamics of the epidemic process. One of the main tools of genomic surveillance is the analysis of HIV-1 molecular clusters. This review presents the possibilities of using the analysis of HIV-1 molecular clusters to study the features of the epidemic process of HIV infection, as well as describes the methodological and ethical aspects of using this method in the system of surveillance of HIV infection.

Introduction. Hepatitis C virus (HCV) remains a significant public health concern. The application of existing antiviral agents is restricted by their high cost and the development of viral resistance, while vaccine development is impeded by the considerable genetic variability of HCV. The outcome of infection is largely determined by the host's genetic factors, which influence both the viral entry into the cell and the effectiveness of antiviral immunity. Identification of genetic determinants involved in these processes is essential for understanding pathogenesis and discovering novel therapeutic targets.

Objective. A comprehensive assessment of the potential involvement of candidate genes and their products in the pathogenesis of HCV infection at the stages of viral entry into the cell and the formation of the host immune response, based on an integrative analysis of gene expression, subcellular localization of their products, and participation in molecular pathways and biological processes.

Materials and methods. In this study, a comparative analysis of 35 most promising candidate genes was performed against five background genes (CD81, CLDN1, LDLR, OCLN, SCARB1) encoding key HCV entry receptors. To analyze biological mechanisms associated with priority genes, the FUMA GWAS platform was used in the functional mapping mode GENE2FUNC (https://fuma.ctglab.nl/gene2func). Evaluation of candidate genes included analysis of their expression profiles, subcellular localization of protein products, as well as involvement in molecular pathways and biological processes. A ranking scoring system was developed, based on point-based ranking, which allowed determining the significance of each candidate gene in the context of its potential involvement in HCV pathogenesis. The system includes sequential assessment by several independent criteria, the results of which are summed into a single score. The degree of association between candidate genes and background genes was assessed using the phi-correlation coefficient (φ) across categories of subcellular localization, molecular pathways, and biological processes.

Results. Application of the developed scoring system identified 25 significant candidate genes. The highest scores were obtained for genes involved in intercellular junction organization (CLDN3, CLDN5, CLDN12, ESAM, F11R, TJP1, TJP2) and lipid metabolism regulation (APOE, LDLRAP1). Enrichment of several candidate genes in immunological processes was revealed. A stable association of C3 and CD19 genes with immune process regulation was established, which is of particular interest in light of HCV's ability to infect mononuclear cells. The APOE, ITGB1, F11R genes demonstrated involvement in inflammatory and defense responses, while IFITM1 was associated with response to cytokine stimulation.

Conclusion. A group of candidate genes potentially influencing HCV infection pathogenesis both at the viral entry stage and through immune modulation was identified. The obtained data expand understanding of virus-host interactions and justify the need for experimental validation of the identified genes as potential biomarkers and therapeutic targets.

Introduction. Vibrio cholerae motility plays a key role in the pathogenesis of cholera, so finding ways to suppress it is a promising approach to combating this infection.

Objective: to study the effect of Fluorothiazinone on the motility of V. cholerae.

Materials and methods. Flagellar motility was determined in 0.3% agar, with the motility zone measured, in 40 strains V. cholerae El Tor of varying epidemiological significance. The ability of these strains to acquire resistance to Fluorothiazinone was also assessed through repeated subcultures on alkaline agar containing Fluorothiazinone (100 mg/L).

Results. A significant decrease in the motility of all studied cultures was observed in the presence of Fluorothiazinone, without the development of resistance.

Conclusion. The dose-dependent ability of Fluorothiazinone to reduce the motility of V. cholerae was demonstrated for the first time.

Introduction. Ixodid tick–borne borrelioses (ITBB) is a naturally occurring focal vector-borne infection. The most common pathogens in Russia are Borrelia garinii, B. afzelii, and B. bavariensis. One of the key factors in their pathogenicity is the surface protein P66, encoded by p66 gene. The polymorphism of this gene in B. bavariensis has been poorly studied, and the frequency of its genetic variants in the development of ITBB infection in humans remains unclear.

Aim — to present the main results of a complex study of p66 gene polymorphism in B. bavariensis isolates circulating in the natural focus. Objective: to analyze the variability of p66 gene in B. bavariensis isolates from components of pathogen’s parasitic system in comparison with the frequency of nucleotide sequence variants of this gene in isolates from ITBB patients.

Materials and methods. The p66 gene loci were sequenced in 238 B. bavariensis isolates obtained from people with ITBB, as well as from Ixodes ticks (I. persulcatus, I. trianguliceps) and from small mammals of 8 species from a natural focus in the Middle Urals (58°.00′ N, 56°.15′ E; 58°.32′ N, 57°.43′ E).

Results. The generalized scheme of the transmission routes of ITBB pathogens is presented as the basis for their circulation in natural foci and possible polymorphism of p66 gene. Among the studied isolates, 12 variants of the gene locus encoding fragments of P66 protein were found, which bear various amino acid substitutions. The spectrum and ratio of different alleles in isolates from vectors and reservoir hosts were virtually identical - two variants were predominant, as was the case among isolates from sick people with ITBB.

Conclusion. Amino acid substitutions in P66 protein found in the two dominant allelic variants of B. bavariensis affect its conformational structure and presumably enhance the adhesive function of the ITBB pathogen, which allows them to be considered as targets for the development of preventive drugs.

Introduction. Influenza A virus is one of the major global infectious threats. Along with seasonal epidemics, zoonotic influenza viruses (subtypes А(H5Nх), А(H7Nх), А(H9N2)) pose an increased risk, requiring constant monitoring of herd immunity.

The aim of the work was to study human blood sera against influenza viruses, both vaccine strains and virus strains with pandemic potential.

Materials and methods. Blood sera from healthy donors collected in different regions of the Russian Federation were tested in the hemagglutination inhibition (HI) assay with vaccine strains of influenza A and B viruses. Blood sera from individuals involved in poultry farming were tested in the hemagglutination inhibition and virus neutralization assays with avian influenza viruses.

Results. From 2021 to 2025, only a few samples were positivein the HI assay with A(H5Nx) influenza viruses, and approximately 1% of samples were positive in HI assay with A(H9N2) virus. All samples positive in the HI assay with A(H5) viruses were negative in the neutralization assay, and approximately 85% of samples positive in the HI assay with A(H9N2) virus contained virus-neutralizing antibodies.

Conclusion. By 2023–2024, humoral immunity to seasonal influenza, following its decline during the COVID-19 pandemic, was at levels typical of pre-pandemic seasons and generally met the recommendations of Rospotrebnadzor and the World Health Organization. Currently, influenza viruses with pandemic potential, such as subtypes A(H5N1) and A(H9N2), are not circulating in the human population in the Russian Federation. However, insufficient herd immunity to seasonal influenza viruses poses additional risks for the emergence and spread of new virus variants.

Introduction. West Nile fever (WNF) is a widespread zoonotic natural focal arbovirus infection. In Russia, intense WNF epidemics are observed in the south and southeast of the European part of the country. Etiotropic treatment and specific immunoprophylaxis for this disease in humans have not been developed. A promising approach to rapid diagnostics of WNV is the detection of pathogen RNA using reverse transcription loop-mediated isothermal amplification (RT-LAMP).

The objective is to develop a method for detecting RNA of West Nile virus (WNV) genotypes 1 and 2 using RT-LAMP with various detection options and to test it on clinical material and samples collected during epizootological monitoring.

Materials and methods. A comparative in silico analysis of WNV genomes was performed using the NCBI GenBank database. The presence of WNV RNA was confirmed by RT-PCR. Detection of RT-LAMP results was performed by gel electrophoresis, in real time, and by endpoint analysis using intercalating dyes. Analytical specificity was tested on clinical and field specimens, as well as cell cultures infected with WNV and heterologous microorganisms. Analytical sensitivity was assessed using a recombinant plasmid containing the target fragment of the WNV cDNA sequence.

Results. The 5'-UTR fragment and the WNV polyprotein gene locus encoding the capsid protein were selected as the target. Eight unique LAMP primers were designed. The reaction mixture composition and RT-LAMP reaction conditions were optimized. The reverse transcription and amplification time was 45 minutes. The analytical sensitivity of the reaction was 5 × 10³ GE/mL, and the analytical specificity was 100%, comparable to PCR.

Conclusion. The use of the designed primer set enables rapid, highly sensitive, and specific detection of WNV genotypes 1 and 2 RNA in field and clinical samples using RT-LAMP. The proposed method, along with existing developments for the detection of WNV based on PCR, is promising for molecular genetic diagnostics of WNV.