Russian Journal of Infection and Immunity

Mycobacteriophages are viruses that selectively infect mycobacteria. Due to their specificity and lytic activity, they are considered a promising tool for controlling mycobacterial infections, especially amid rising antibiotic resistance. Their significant genetic diversity and unique biological properties have generated sustained global research interest, supported by successes in treating complex infections caused by non-tuberculous mycobacteria. However, data on phage populations and applied research results in the Russian Federation remain fragmented, necessitating systematization to assess the genuine potential. This review is based on literature data and the authors’ personal results, summarizing current knowledge on mycobacteriophage biology and analyzing the prospects for their therapeutic and diagnostic application. It examines data on mycobacteriophage taxonomic and genomic diversity in a global context, describes the first characterized Russian isolates, including phages Vic9 and Yasnaya_Polyana, and details a domestic collection of 15 phages. The collection aligns with global trends and includes unique findings, such as the phage Arbat with an anomalously large genome and extremely low similarity to known phages. In the therapy context, the review explores strategies for creating effective therapeutic agents, including the design of phage cocktails and genetic modification to switch them to a lytic state. It presents a critical analysis of international clinical experience using phages in parallel with mycobacterioses and highlights fundamental barriers to phage therapy for tuberculosis. Special attention is paid to domestic delivery systems, particularly liposomal formulations of phage D29, which have demonstrated high efficacy against M. tuberculosis, including multidrug-resistant strains, and a favorable safety profile in preclinical studies. In the diagnostics section, the evolution of phage-based methods is traced — from biological amplification tests to reporter systems — and the Russian-developed test system “TB-Phage-LCh” for phenotypic tuberculosis drug susceptibility testing is presented. Despite regulatory complexities and the need to study immunogenicity, this work demonstrates that Russian Federation possesses a solid scientific foundation for developing this field. Further research focused on in-depth characterization of domestic isolates, optimization of therapeutic platforms, and conducting controlled clinical trials could lead to creating effective phage-based drugs and diagnostic tools capable of holding an important place in the arsenal against drug-resistant mycobacterial infections.

Despite the substantial significance of yeasts in biotechnology and medicine, the number of well-described fungal species remains limited, with their ecological and pathogenic roles still being uncovered. Halotolerance, a key aspect of osmotolerance, is considered a potential virulence factor that promotes microbial survival in the environment and within the host, particularly by resisting phagocytic oxidative and ionic stress. This study aimed to investigate and quantitatively compare the halotolerance of the most common gut-associated yeasts. There were analyzed 78 clinical strains of six species: Candida albicans, Pichia kudriavzevii, Geotrichum candidum, Trichosporon asahii, Trichosporon ovoides, and Rhodotorula mucilaginosa. Strains were cultivated in Sabouraud broth with NaCl concentrations ranging from 0.5% to 20% at two temperatures, 25°C and 35°C. Growth was measured spectrophotometrically at 450 nm after 96 hours of incubation. A second-degree polynomial regression model, implemented using Python programming language, was applied to analyze the non-linear growth response to salinity and to identify precise inflection points, indicating critical tolerance thresholds where growth inhibition dynamics shifted. The results revealed significant species-specific differences. G. candidum and P. kudriavzevii were the least tolerant (inflection points ~6.2% and ~8.5% NaCl at 25°C, respectively). C. albicans and R. mucilaginosa exhibited moderate tolerance, while Trichosporon spp. demonstrated exceptional halotolerance, maintaining growth potential at concentrations exceeding 15% NaCl. A notable synergistic effect of combined osmotic and temperature stress was observed for most species, with reduced tolerance at physiological temperature. These findings indicate that pronounced halotolerance may serve as an important virulence factor for opportunistic pathogens, likely enhancing their persistence in the host environment and potentially contributing to cross-resistance mechanisms against antifungal agents through shared adaptive responses to cellular stress.

Despite the continuing interest in influenza infection and relevant pathogens, a significant number of publications in this field are devoted to influenza A viruses, while influenza B viruses receive less attention. In PubMed database, there are 10 times fewer articles on influenza B vs. influenza A viruses. However, despite the complete disappearance of influenza B/Yamagata lineage viruses in the post-COVID-19 pandemic period, B/Victoria lineage viruses continue to circulate, posing a problem for national health. The fact that only B/Victoria lineage circulate currently in human population gives a reason to believe that it should be closely investigated. An important place among the major properties of influenza virus hemagglutinin (HA) is referred to its potential to shape antigenic diversity of influenza viruses. It has been reliably proven that mutations in specific positions of HA1 receptor-binding site affect antigenic specificity. Therefore, assessing key amino acid positions located in this area is of substantial scientific and practical interest. This is especially important in practice, e.g., in influenza vaccine production that includes passaging in a sensitive substrate (usually in developing chicken embryos) within manufacturing technology. During passaging, substrate-adapting substitutions may occur in the region of the receptor-binding pocket, which may lead to undesirable changes in antigenic and biological properties of vaccine preparation. Our study is aimed at assessing a role of one of such egg-adapting substitutions (G141R). It was found that passaging of two currently circulating influenza B/Victoria viruses, B/Austria/1359417/2021 and B/Catalonia/2279261NS/2023, and LAIV vaccine strains prepared on their platform in developing chicken embryos resulted in HA1 G141R substitution that increased cold-adaptation of LAIV candidates, but not affecting their antigenic properties, temperature-sensitive phenotype, or degree of HA thermostability. The data presented in the article indicate that it is necessary to pay close attention to the emergence of mutations in the genome of influenza vaccine strains during their preparation, monitoring their possible impact on the key properties of such strains.

Among the highly oncogenic human papillomavirus (HPV) types, HPV 16 is of paramount importance in the pathogenesis of cervical cancer. Viral oncogenes E6 and E7, expressed by the HPV genome, play a key role in developing neoplasia. The aim was to study the prevalence, mutations in the E6–E7 genes, HPV 16 lineages and sublineages in underlying, precancerous lesions, and cervical cancer.

Materials and methods. Cervical samples from 223 patients with morphologically confirmed background, precancerous diseases and cervical cancer in St. Petersburg were examined. HPV detection and genotyping were performed using real-time PCR. Sequencing of the E6–E7 genes of HPV 16 was performed using the Sanger method. Single-nucleotide polymorphisms were identified against the European lineage HPV 16 K02718 reference sequence.

Results. In patients with underlying conditions, the proportion of HPV-positive samples was 55.0%. As the severity of tumor lesions progressed, the frequency of viral detection increased: from 65.0% in low-grade dysplasia to 95.1% in squamous cell carcinoma (p = 0.002). Monoinfection with HPV 16 was identified in 68.3% of patients with precancerous and malignant cervical lesions. The proportion of HPV 16 increased with the progression of neoplasia: from 38.4% in low-grade dysplasia to 77.6% in cervical cancer (p = 0.008). Sequencing of HPV 16 E6–E7 genes revealed nucleotide variations characteristic of phylogenetic lineage A. The most prevalent variant was 350G (56.3%), whose detection rate in cervical cancer exceeded that in the group without pathology — 69.8% vs 44.2% (p = 0.019). The frequency of the European variant 350T ranged from 9.7% to 35.5% depending on the degree of cervical lesion. Phylogenetic analysis revealed that 98.6% of clinical isolates belonged to lineage A, of which 74.8% were assigned to sublineage A2 of HPV 16. Sublineages A1, A2, A3, and D1 were detected in background cervical diseases, with a predominance of sublineage A2 (p = 0.001). Multiple mutations in the E6–E7 genes were detected in two isolates from imported cases, and they were assigned to sublineage D1. Only sublineages A1 and A2 of HPV 16 were detected in cervical intraepithelial neoplasia and cervical cancer. Conclusion. The study results showed that in a megacity in northwestern Russia, HPV 16 sublineage A2 plays a leading role in the etiopathogenesis of precancerous lesions and cervical cancer, with sublineage A1 also making a substantial contribution.

The aim of the present study was to perform genotyping of the three most polymorphic regions in the cytomegalovirus (CMV) genome, i.e., UL55 (gB), UL73 (gN), UL75 (gH) in newborns with congenital cytomegalovirus infection (CMVI), to determine distribution of genotypes circulating in the current cohort of patients in St. Petersburg and to compare them with those of CMV circulating in the Russian Federation and worldwide. The study was performed at the Pediatric Research and Clinical Center for Infectious Diseases at the Federal Medical Biological Agency. The study included 61 blood, saliva, urine DNA samples isolated from 26 infants with clinical manifestations of congenital CMV. Molecular genetic methods were used as follows: DNA isolation from biological samples; qualitative detection of CMV DNA by amplification of specific viral DNA fragment using real-time PCR detection of amplicons, preparation of sequencing libraries enriched by hybridization with labeled oligonucleotides. The obtained results of DNA sequencing were processed using bioinformatics methods. According to the results of our study, it was shown that the sequencing of viral DNA segments from various biological samples has yielded different results on CMV genetic polymorphisms. For instance, the genotypes of all three studied regions with satisfactory coverage (according to sequencing data) were obtained more often in urine and saliva than in peripheral blood samples. When analyzing the distribution of genotypes in the UL55 region, the genotype gB7 prevailed being determined in 50% of newborn patients. Analysis of the obtained UL73 region sequencing data allowed to identify the dominant gN4c genotype (37.5%). According to the sequencing results for UL75 region of CMV encoding glycoprotein H, the genotypes gH1 and gH2 showed equal distribution (by 50%). When comparing the genotypes observed in this study with those obtained in Russia and worldwide, some differences in the nucleotide sequence were revealed for the specified regions of CMV genome. Phylogenetic analysis of CMV made it possible to illustrate heterogeneity of gene variant distribution among newborn children in St. Petersburg.

Mild cognitive impairment (MCI) in a number of cases precedes the development of dementia. Neuroinflammation is one of the key factors in neurodegeneration pathogenesis. Chronic infections and parasitic infestations contribute significantly to neuroinflammation. It has been evident about a link between systemic inflammation, disorders of cellular and humoral immunity and MCI progression. In this context, of particular interest is a role for a common intracellular pathogen Toxoplasma gondii may be involved in MCI pathogenesis and clinical dynamics. Currently, the frequency and clinical significance of toxoplasmosis reactivation in MCI remain unknown. Given Toxoplasma gondii-related immunotropic effects, it is also relevant to investigate an association between latent toxoplasmosis reactivation, immune parameters and inflammatory mediators in MCI. The study was aimed at assessing the frequency of chronic toxoplasmosis reactivation and its associations with cell immunity, levels of main cytokines and chemokines along with clinical dynamics in MCI. For this, individuals were divided into the following groups: main group included 130 patients with MCI, and comparison group — 81 patients with subjective cognitive impairment (preMCI). The serum was tested for anti-Toxoplasma gondii IgG, IgM, and IgA antibodies using enzyme-linked immunosorbent assay, the concentration of cytokines and chemokines was determined by multiplex assay. Cell immunity was assessed using flow cytometry. The Kruskal–Wallis test was used to assess the significance of differences, followed by pairwise comparisons with Mann–Whitney test. An increased frequency of latent toxoplasmosis reactivation (positive for anti-Toxoplasma gondii IgA in combination with IgG > 50 IU/mL) was observed in MCI. In MCI patients, reactivation of toxoplasmosis was associated with impaired activation of Th1-cell immunity (lower total and subset T-cell counts including CD4⁺CD57⁺ T-cells and CD8⁺CD57⁺ T-cells), as well as increased levels and activation of NK-cells. Higher anti-Toxoplasma gondii IgG level in patients was associated with elevated neuroinflammatory markers CCL4 and CCL20, and with less favorable one-year-follow-up clinical dynamics. The results suggest that reactivation of latent toxoplasmosis in MCI may be clinically relevant, and it is important to determine not only anti-Toxoplasma gondii IgG and IgM, but also IgA to detect it.

Introduction. Despite successes in hepatitis B virus (HBV) molecular virology, prevention, and treatment, HBV infection remains relevant. The study aimed to analyze serological and molecular genetic markers among older individuals in Novosibirsk, and characterize identified HBV variants.

Materials and methods. The study included 630 conditionally healthy individuals undergoing routine medical examination. Serological markers (HBsAg, AntiHBs, AntiHBc, HBeAg, AntiHBe) were determined by ELISA, and HBV DNA — by real-time PCR. Full-length genomic sequences of identified HBV isolates were obtained using next-generation sequencing (NGS). Results. HBV genetic material was detected in 6 patients, and their full genome sequences were obtained. The genotype and subgenotype of identified HBV variants were determined, and clinically significant mutations were analyzed. Only 29% of patients had protective antiHBs levels (> 10 IU/mL), with 38% also having antiHBc antibodies. Low-titer protective antibodies (10–100 IU/mL) were most common in both АntiНВs+/AntiНВс– and AntiНВs+/AntiНВс+ groups. Low titers were more frequent in the AntiНВs+/AntiНВс– group, while high titers (> 400 IU/mL) were more common in the AntiНВs+/AntiНВс+ group.

Conclusions. It has been shown that among the older age groups, there is a low intensity of humoral immunity to HBV, which may indicate a widespread problem of reducing the level of protective antibodies over time post-vaccination, or insufficient vaccination coverage in this population group. A decrease in HBV antibody titer below the protective level in the elderly significantly increases the a of primary infection or reinfection with HBV in this population group. As a recommendation, the inclusion of AntiHBs serological monitoring in the medical examination program for the elderly can be considered. The data obtained also actualize the problem of booster vaccination in this age group. The total presence of mutations potentially associated with disease progression in the identified HBV variants and the widespread prevalence of mutations that can alter HBsAg antigenicity require attention to these patients.

The article is aimed at conducting post-analysis of COVID-19 epidemiological data in Novosibirsk for the period from 2020 to 2023. The study emphasizes the importance of data post-analysis for understanding the dynamics of SARS-CoV-2 spread and the characteristics of its impact on public health. The study results make possible to assess of how population susceptibility to different virus strains has changed, what is the difference between an outbreak of diseases associated with the emergence of a new virus strain and its seasonal infection spread. There was applied the SSA method for analyzing time series to separate them into components as well as studying key indicators such as the number of new infections, deaths, critical cases, hospitalizations, and ventilator-dependent patients in the Novosibirsk region. Three main components have been identified for the described data sets: a general trend that reflects changes in the rate of virus spread related to spread of new strains, as well as periodic phenomena associated with virus strains and seasonality. The results show that a significant part of the changes in disease dynamics is accounted for by the emergence of new strains, but also due to «chronicity» epidemic with seasonal fluctuations. The observed relationships and time lags between the number of critically-ill patients and the number of recorded deaths due to COVID-19, as well as between the number of hospitalized patients and ventilator-dependent patients are shown. Thus, it is concluded that the identified trend depicting a change between the number of infected people and development of virus strains can be useful for refining the parameters of mathematical models for COVID-19 spread. The SEIR-HCD differential model, which was previously used to simulate the disease spread in the Novosibirsk region, was chosen as an illustrative example. It is shown that the parameter of the virus spread rate, restored through the selected trend, when introduced into the model, provides a smaller modeling error than the if it was generated using the solution of the inverse issue.

Background. Toxoplasmosis is a zoonotic disease which takes humans and a wide-range of animals as intermediate hosts and can be transmitted sexually, potentially leading to serious outcomes like congenital toxoplasmosis in a pregnant woman’s foetus. However, sexual transmission is not the most common route, which includes ingesting contaminated undercooked meat, organ transplantation, blood transfusion, unwashed vegetables, or contact with the feces of infected cats. Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation, causing pain and disability with a prevalence of about 1% globally. Emerging evidence suggests a link between toxoplasmosis and autoimmune disorders. The present study aimed to evaluate the seroprevalence of toxoplasmosis in Iraqi RA subjects in comparison with apparently healthy controls living in Diyala Province, middle of Iraq.

Materials and methods. Blood from RA subjects diagnosed at the Rheumatology Clinic at Baquba Teaching Hospital was collected, alongside samples from age- and sex-matched healthy controls. The sera from both groups screened for anti-Toxoplasma gondii antibodies using the enzyme-linked immunosorbent assay (ELISA), while arthritis was clinically diagnosed by specialist physicians.

Results. The results showed a significant difference (p = 0.0363) in T. gondii IgG seropositivity between RA subjects (40.0%) in comparison with healthy individuals (26.0%) in Diyala Province. No participant in either group tested positive for IgM antibodies, indicating the presence of chronic rather than recent infections. The present study found an odds ratio of 1.9 for toxoplasmosis in Iraqi RA patients in comparison with control subjects, which means RA patients are nearly 2 times more likely to have toxoplasmosis in comparison with healthy subjects. Gender and age were not found to significantly influence the seropositivity rate in either group.

Conclusion. The findings indicate that Iraqi RA patients living in Diyala Province have a higher IgG seropositivity than apparently healthy individuals, suggesting a potential association between toxoplasmosis and RA.