[This corrects the article DOI: 10.1371/journal.pone.0257731.].

Background. The increased antiretroviral therapy (ART) coverage of patients in the absence of routine drug resistance (DR) tests highlight the importance of HIV-1 drug resistance surveillance in Armenia. Aim. The aim of this study was a determination of the prevalence of HIV-1 DR on a large-scale cohort of HIV-infected citizens of the Republic of Armenia who had no experience of taking antiretroviral drugs. Materials and methods. The study was carried out on a cohort of more than 20% of PLHIV in the Republic of Armenia. The resulting 982 nucleotide sequences of the HIV-1 pol gene fragment, encoding the protease and reverse transcriptase region, as well as 367 sequences of the integrase gene, were analyzed using the Stanford University database and the CPR tool for the presence of drug resistance mutations and determination of the resistance level to ARV drugs. The HIV-1 subtype was determined using the Stanford University database and confirmed by phylogenetic analysis. Results. The overall prevalence of HIV DR to ARV drugs in naïve patients was 13.8%. Resistance to non-nucleoside reverse transcriptase inhibitors was 11.2%, nucleotide reverse transcriptase inhibitors — 1.4%, protease inhibitors — 2.0% and integrase inhibitors — 0.5%. The predominant genetic variant among viruses containing DR mutations was subtype B. Resistance was most often recorded among men who have sex with men living in Yerevan. Conclusion. In our study, prevalence of DR was high only for the NNRTI drugs. The results show that the first-line ARV drugs recommended in current national guidelines are highly likely to be effective. The analysis was carried out on a significant proportion of HIV-infected citizens of the Republic of Armenia, which increases the reliability and accuracy of the data obtained.

MicroRNAs are small, highly conserved noncoding RNAs (containing about 20 nucleotides), involved in the regulation of gene activity on the post-transcriptional level and can change the translation process. This review presents a summary of the literature data based on radiation-induced changes of the microRNA expression profiles in the blood. The involvement of miRNAs in human diseases such as cancer has also been demonstrated. Evaluation of changes in microRNA expression confer the possibility to make a diagnosis and determine the stage and prognosis of the disease, as well as the effectiveness of radiotherapy. The involvement of microRNAs in pathological processes affects the radiosensitivity of tumors. The data of the authors demonstrate differences in the activity of the studied microRNAs under the action of ionizing radiation at high and low doses, in normal and malignant human cells, and in oncological diseases of various sites. The study of microRNAs as early biomarkers of pathological processes is shown. The perspectives of microRNA participation in the application of low-dose ionizing radiation before radiotherapy of neoplasms to preserve healthy tissues surrounding the tumor from the damaging effects of high doses are discussed. MicroRNAs can serve as indicators of radiation levels in professional settings, as well as in emergency situations.

The effect of low-dose radiation was studied on the growth dynamics of transfused Lewis carcinoma cells in female C57Bl/6 mice. Fourfold total fractionated irradiation was conducted at a dose of 75 mGy (at a dose rate of 0.154 Gy/min and a voltage of 200 kV), starting from day 10 after the transplantation with a four-day interval. On days 14 and 22, a group of mice was euthanized to study the expression levels of genes and noncoding RNAs (microRNAs and long noncoding RNAs) in tumor cells, as well as in normal tissues (bone marrow, liver, spleen, thymus). The total RNA was obtained, and complementary DNA was synthesized according to the manufacturer's protocol. After that, a real-time PCR reaction was performed using the SYBR Green I dye (Thermo Scientific, United States) or a TaqMan probe and specific primers. Genes and noncoding RNAs were divided into groups of oncogenes and oncosuppressors according to scientific research. In the group of irradiated mice, a decrease in the tumor growth rate was observed, mainly from day 20, accompanied by a change in the activity of the studied genes. The ratio of the activity of oncosuppressors to oncogenes was calculated for the obtained tissues. These fractions were 0.5 for the tumor, 10.7 for the bone marrow, and 2.4 for the spleen and thymus. Thus, it can be stated that in the tumor there was a particularly pronounced activation of oncogenes compared to the activity of oncosuppressors, while the opposite effect was observed in normal tissues.

Purpose: To study the effect of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) on the survival rate of mice and proportion of polychromatophilic erythrocytes (PCE) in the bone marrow cells with micronuclei (MN), as well as post-irradiation urinary excretion of cell-free nuclear DNA (cf-nDNA) and mitochondrial DNA (cf-mtDNA) in rats. Material and methods: Male Balb/c mice aged 2 months and Fisher-344 male rats aged 3 months were used. To determine the survival rate of mice, X-irradiation was performed at a dose of 8 Gy, and to analysis the proportion of PCE in the bone marrow cells with MN, at a dose of 2 Gy. Rats were X-irradiated at a dose of 5 Gy. AICAR was administered to animals intraperitoneally at a dose of 400 mg/kg. The drug was administered 30 min before and 20 min after irradiation of the animals. The DNA content was measured by real-time PCR. Results: The results of the study showed that the introduction of AICAR causes a statistically significant increase in the survival rate of irradiated animals. The greatest effect was shown in the group of mice treated with AICAR 20 min after their irradiation at a lethal dose. The introduction of AICAR before irradiation reduces the proportion of PCE with MN by 30 %, and after irradiation ‒ by 70 %, in comparison to the control. AICAR promoted enhanced urinary excretion of cf-nDNA and cf-mtDNA fragments in rats after irradiation. Conclusion: The results show that AICAR acts as a radiomitigation effector and promotes active DNA excretion of damaged cell from animal tissues in the post-radiation period.

BACKGROUND:Eastern Europe and Central Asia (EECA) is one of the regions where the HIV epidemic continues to grow at a concerning rate. Antiretroviral therapy (ART) coverage in EECA countries has significantly increased during the last decade, which can lead to an increase in the risk of emergence, transmission, and spread of HIV variants with drug resistance (DR) that cannot be controlled. Because HIV genotyping cannot be performed in these countries, data about HIV DR are limited or unavailable. OBJECTIVES:To monitor circulating HIV-1 genetic variants, assess the prevalence of HIV DR among patients starting antiretroviral therapy, and reveal potential transmission clusters among patients in six EECA countries: Armenia, Azerbaijan, Belarus, Russia, Tajikistan, and Uzbekistan. MATERIALS AND METHODS:We analyzed 1071 HIV-1 pol-gene fragment sequences (2253-3369 bp) from patients who were initiating or reinitiating first-line ART in six EECA counties, i.e., Armenia (n = 120), Azerbaijan (n = 96), Belarus (n = 158), Russia (n = 465), Tajikistan (n = 54), and Uzbekistan (n = 178), between 2017 and 2019. HIV Pretreatment DR (PDR) and drug resistance mutation (DRM) prevalence was estimated using the Stanford HIV Resistance Database. The PDR level was interpreted according to the WHO standard PDR survey protocols. HIV-1 subtypes were determined using the Stanford HIV Resistance Database and subsequently confirmed by phylogenetic analysis. Transmission clusters were determined using Cluster Picker. RESULTS:Analyses of HIV subtypes showed that EECA, in general, has the same HIV genetic variants of sub-subtype A6, CRF63_02A1, and subtype B, with different frequencies and representation for each country. The prevalence of PDR to any drug class was 2.8% in Uzbekistan, 4.2% in Azerbaijan, 4.5% in Russia, 9.2% in Armenia, 13.9% in Belarus, and 16.7% in Tajikistan. PDR to protease inhibitors (PIs) was not detected in any country. PDR to nucleoside reverse-transcriptase inhibitors (NRTIs) was not detected among patients in Azerbaijan, and was relatively low in other countries, with the highest prevalence in Tajikistan (5.6%). The prevalence of PDR to nonnucleoside reverse-transcriptase inhibitors (NNRTIs) was the lowest in Uzbekistan (2.8%) and reached 11.1% and 11.4% in Tajikistan and Belarus, respectively. Genetic transmission network analyses identified 226/1071 (21.1%) linked individuals, forming 93 transmission clusters mainly containing two or three sequences. We found that the time since HIV diagnosis in clustered patients was significantly shorter than that in unclustered patients (1.26 years vs 2.74 years). Additionally, the K103N/S mutation was mainly observed in clustered sequences (6.2% vs 2.8%). CONCLUSIONS:Our study demonstrated different PDR prevalence rates and DR dynamics in six EECA countries, with worrying levels of PDR in Tajikistan and Belarus, where prevalence exceeded the 10% threshold recommended by the WHO for immediate public health action. Because DR testing for clinical purposes is not common in EECA, it is currently extremely important to conduct surveillance of HIV DR in EECA due to the increased ART coverage in this region.

Introduction. The aim of the study was to use comparative analysis for assessing efficiency of detection and confirmation of dual HIV infection, using conventional population sequencing (PS) and next generation sequencing (NGS) for an HIV-1 pol gene fragment, which encompasses protease and partially reverse transcriptase (positions 2253–3368).Materials and methods. The study was performed on intersubtype dual HIV infection model samples containing viruses of HIV-1 subtype B, sub-subtype A6 and recombinant form CRF63_02A1. Viruses were mixed pairwise in proportions from 10 to 90% to obtain 3 groups of model samples: CRF63vsB, CRF63vsA6, and A6vsB. The nucleotide sequences obtained by using PS and NGS technologies having 5, 10, 15, and 20% sensitivity thresholds for minor virus variants (NGS5–NGS20, respectively) were used to estimate the number of degenerate nucleotides or the degenerate base (DB) count and the number of synonymous mutations (SM) or the SM count. The fragment of the studied region (positions 2725–2981) was used for the analysis of operational taxonomic units.Results. The application of NGS5 proved highly efficient for detection of dual HIV infection in the model samples. The statistically significant (p < 0.01) increase in DB and SM counts was demonstrated by NGS5 compared to PS. As a result, NGS5 helped detect dual HIV infection in 25 out of 27 model samples, while with PS it was detected only in 15 samples. The analysis of operational taxonomic units confirmed dual HIV infection in all the groups of model samples.Discussion. The efficiency of detection and confirmation of dual HIV infection depends both on the content of each virus in the sample and on genetic characteristics of these viruses. Conclusion. Using NGS genetic testing in routine practice will be instrumental for efficient identification of genetic characteristics of infectious agents and for thorough analysis of the epidemiological situation.

This review presents the literature data of new approaches for the treatment of COVID-19 with low doses of radiation (LDR). In addition, data on the use of LDR for the treatment of various disorders, in particular pneumonia, a number of inflammatory processes of various etiology, as well as Alzheimer’s disease are discussed. The mechanisms of LDR action are briefly described, associated with the activation of the immune system and antiinflammatory response due to the effect on the processes of oxidative stress, which is reflected in an increase in the activity of cytokines (interleukin- (IL-) 6), changes in the expression of a number of genes (such as P53 and NF-κB (p65)) and long non-coding RNAs (ncRNAs) (the authors’ own data are presented). Based on the analysis of the material presented, it can be assumed that further clinical trials of the effect of MDR (5–10 cGy) on patients with COVID-19, who are at different stages of the disease, will reveal the optimal conditions for the development and use of an effective treatment regimen.

Objective. Accurate identification of recent HIV-1 infection cases will ensure a more effective and precise assessment of the dynamics of virus transmission, the time between infection and diagnosis, and the quality of screening and prevention programs. This study was undertaken to adjust the recent HIV-1 infection testing algorithm using a cohort of patients, in whom the time since infection was known. Materials and methods. We used blood plasma samples obtained from 264 HIV-infected patients with a known date of infection. All samples were analyzed using two serological assays aimed to differentiate between cases of recent and established HIV infection. Using the results of sequencing of the pol region, we calculated the proportion of variable positions in order to determine the duration of infection. To identify the cases of recent HIV infection, we evaluated different variants of a diagnostic algorithm that included a combination of serological tests, molecular genetic analysis of the viral genome, and other clinical and laboratory parameters. Results. The effectiveness of the DS-ELISA-HIV-AB-TERM (DS) assay for the detection of recent infection was higher than that of the Architect HIV Ag/Ab Combo assay (Abbott). The sensitivity and specificity of the DS assay were 94.4% and 96.7%, respectively. The sensitivity and specificity of the Abbott assay were 86.4% and 77,4%, respectively. The HIV-1 genome variability threshold of 0.33% allowed the differentiation between samples depending on the time since infection with a cut-off of 12 months: 82.1% of recent samples and 62.7% of established samples were correctly identified using this method. We analyzed the effectiveness of schemes of the algorithm for the detection of recent infection lasting no longer than 9 months. Conclusion. Our findings allow us to recommend the algorithm based on the Russian DS assay for the detection of recent HIV-1 cases in routine clinical practice. This algorithm will enable the detection of new HIV cases, thereby improving the disease control. Key words: HIV-1, HIV infection, genetic variability, time since infection, duration of infection, recent infection, early infection, seroconversion

The activity of genes and noncoding RNAs was studied in 183 hybrid mice (CBA × C57Bl) F1 after a prolonged low-power irradiation (within 21 h at a dose 12.6 Gy with a dose rate 10 mGy/min). The analysis of the studied parameters was carried out in the bone marrow of mice in the eighth and tenth months after irradiation. After ten month, radiation-induced malignant lymphomas in the liver, abdominal cavity, and subcutaneously were found in 14 out of 94 animals. The studied molecular genetic parameters were divided into two groups: oncogenes and tumor suppressors, the activation of which was compared at eighth and tenth months after irradiation. It was detected that the activity of tumor suppressors (PTEN gene and lncp21 long noncoding RNA) in the groups of mice with tumors was lower in comparison with the group of mice without cancer, while the activity of oncogenes (NFkB(p65), IkBα, iNOS, TAL1, CTCF, NEAT1 lncRNAs, and miR-125b) increased. The studied parameters can be considered as potential biomarkers of radiation-induced cancer.

The processes of detection and quantification by real-time PCR in blood of mature microRNAs, including miR-21, should be standardized and validated. Our studies show that the specificity of PCR method for miR-21 in the blood of healthy donors can be demonstrated by the formation of a 67 bp amplicon product, precision under conditions of convergence and reproducibility, expressed using the coefficient of variation, is less than 2% and 3%, respectively, and the linearity of PCR method for miR-21 is confirmed by the correlation coefficient r≥0.99.

Процессы обнаружения и количественного определения методом ПЦР в реальном времени в крови пациентов зрелых микроРНК, в том числе и miR-21, должны быть стандартизированы и валидированы. Проведенные нами исследования, показывают, что специфичность метода ПЦР для miR-21 в крови здоровых доноров может быть демонстрирована образованием продукта-ампликона размером 67 нуклеотидов, прецизионность в условиях сходимости и воспроизводимости, выраженная в виде коэффициента вариации, составляет менее 2% и 3 % соответственно, а линейность метода подтверждается коэффицентом корреляции r≥0,99. The processes of detection and quantification by real-time PCR in blood of mature microRNAs, including miR-21, should be standardized and validated. Our studies show that the specificity of PCR method for miR-21 in the blood of healthy donors can be demonstrated by the formation of a 67 bp amplicon product, precision under conditions of convergence and reproducibility, expressed using the coefficient of variation, is less than 2% and 3%, respectively, and the linearity of PCR method for miR-21 is confirmed by the correlation coefficient r≥0.99.

Objective. To develop and validate the method of dual HIV infection detection based on the results of Sanger sequencing and to evaluate of dual HIV infection frequency in Russia. Materials and methods. We carried out the sequencing of HIV-1 pol gene fragment in model samples of dual HIV infection, the calculation of degeneracy bases index (DB-index), and the index of synonymity (SM-index) and determination of their threshold values for dual HIV infection detection. We analyzed nucleotide sequences of the pol gene fragment in HIV-1 samples (n = 1561) taken from Russian patients. Results. The threshold values of 34 for the DB-index and 0.05 for the SM-index allow detecting effectively the dual HIV infection using reverse transcriptase (RT) and protease-reverse transcriptase (PR-RT) fragments of the pol gene correspondingly. At total 21 (1.35%) dual HIV-infected samples (18 of which were collected in 2014 and later) were revealed in the collection studied; 12 of them were obtained from patients residing in the Central Federal District. An inverse correlation between the likelihood of dual HIV infection detecting and the duration of the patient's infection was found. In total, 11 out of 21 samples with dual HIV infection had mutations associated with drug resistance; 7 of them (33.3%) had substitutions that were not associated with natural polymorphism of HIV-1. Conclusion. The problem of dual HIV infection in Russia is actual and requires further study. Key words: HIV, dual HIV infection, drug resistance, nucleotide sequence, DB-index, SM-index, PR-RT region

We used 183 F1 CBA×C57Bl hybrid mice to study the delayed effects of low-power long-term γ-irradiation at a dose of 12.6 Gy (10 mGy/min) 8 and 10 months after the treatment. Eight months after the treatment we found the increased expression of the transcription factor NFκB and its target genes iNOS and G-SCF in the bone marrow (BM). Ten months after the treatment malignant lymphomas were revealed in 14 of 94 mice in the liver, abdominal cavity, and subcutaneously. In the BM of these mice, the transcription of the PTEN, NFκB, and iNOS genes was inhibited and the contents of long non-coding RNAs (lncRNAs) lnc p21, NEAT1, and microRNA miR-125b were decreased. The expression of the NFκB(p65) gene and miR-125b was inhibited in the BM of irradiated mice without tumors ten months after the treatment. These data show the deregulation of the P53 system supporting the genome stability in the BM of irradiated mice. These indices will be studied as potential markers of risk of development of irradiation-induced tumors.

The effect of X-ray radiation (0.1 Gy) on the expression of a number of genes and regulatory RNA (miRNA and long noncoding RNA) in human lymphocytes and T-lymphoblastic cells (Jurkat cells) was studied. One hour after cell irradiation with a low dose of radiation, lymphocytes displayed p53 expression and a decreased level of mature miR-27a and miR-181a having mRNA of gene p53 as target. These cells also had inhibited NFkB activity, which was found from reduced mRNA content of RhoAcdc42 and IL6 genes. By 4 h, their expression was normalized. Unlike in the case of normal cells, increased content of mRNA of NFkB gene (p65) and mRNA of its target IL6 gene was observed in Jurkat cells during this period. Repeated irradiation of cells with 5 Gy carried out after 4 h showed the radiation adaptive response (AO) according to the criterion of lymphocyte survival and its absence in Jurkat cells. The difference between groups of 5 Gy and 0.1 + 5 Gy in lymphocytes that survived after 20 h revealed common AO features (mRNA of p53 gene, NEAT1, miR-181a, miR-107). The results indicate the activation of various intracellular systems after the stress with low doses of radiation on lymphocytes and Jurkat cells. This approach can be used to optimize the efficacy of radiation therapy when preirradiation with a small dose of radiation increases the radioresistance of normal tissues surrounding a tumor.

Abstract—Various authors have shown that the numerous instances of spontaneous DNA damage (DNA breaks, change in bases) that occur daily in a cell as a result of the metabolism of the human body are the basis of mutational selection. Mutant cells have certain advantages in the microenvironment, which changes due to age characteristics. This contributes to the formation of cancer clones and their dissemination. A significant role in this process belongs to hereditary factors; at the same time, there are a number of hereditary diseases (Xeroderma pigmentosum, etc.) that in most cases lead to the occurrence of cancer. Herein, we describe a number of associated genes that control cellular homeostasis and, at the same time, are suppressor genes; changes in their activity or mutations in their structure contribute to carcinogenesis. The role of epigenetic factors, including noncoding regulatory RNAs, the organization of the chromatin structure, and methylation in the carcinogenesis processes is considered. Modulation of the functional activity of genes is carried out by noncoding RNAs; each RNA can have several target genes and can, in turn, be affected by different genes. Regulatory RNAs include microRNAs and long noncoding RNA proteins, changes in the activity of which can serve as biomarkers of disease onset, have a predictive value, and can be used as a target for therapy. New data on the role of noncoding RNAs, methylation, and chromatin organization in carcinogenesis are presented. Our data on the use of the expression level of some genes and noncoding RNAs as prognostic indicators suitable for the evaluation of treatment efficacy for a number of tumors are presented. Special attention is paid to the structural organization of chromatin and methylation in carcinogenesis, as well as to the interaction of cellular structures that affect the activity of genes and their regulation in carcinogenesis. A brief assessment of the carcinogenic effect of exogenous factors such as natural (cosmic factors and some natural compounds) and anthropogenic ones (radiation, chemicals, and cancer viruses) is given.