Anna Esman
@crie.ru
Central Research Institute of Epidemiology
EDUCATION
I.M. Sechenov First Moscow State Medical University
RESEARCH, TEACHING, or OTHER INTERESTS
Virology, Infectious Diseases, Epidemiology
Scopus Publications
Scopus Publications
Anna Esman, Dmitry Dubodelov, Kamil Khafizov, Ivan Kotov, German Roev, Anna Golubeva, Gasan Gasanov, Marina Korabelnikova, Askar Turashev, Evgeniy Cherkashin,et al.
MDPI AG
The Omicron strain is currently the main dominant variant of SARS-CoV-2, with a large number of sublineages. In this article, we present our experience in tracing it in Russia using molecular diagnostic methods. For this purpose, different approaches were used; for example, we developed multiprimer panels for RT-PCR and Sanger and NGS sequencing methods. For the centralized collection and analysis of samples, the VGARus database was developed, which currently includes more than 300,000 viral sequences.
N. V. Vlasenko, T. A. Loscutova, K. O. Mironov, A. S. Esman, E. A. Dunaeva, T. A. Semenenko, D. B. Dubodelov, M. I. Korabelnikova, Z. B. Ponezheva, V. V. Makashova,et al.
LLC Numicom
Relevance. The identification of determinants of the human genome, such as single nucleotide polymorphisms (SNPs), in association with various disease patterns, including infectious diseases, is one of the most actively developing areas of scientific research in the world.. Hepatitis C (HC), which remains a serious global health problem, belongs to the number of infections that attract the attention of specialists.Aims. Determination of genetic markers of hepatitis C virus (HCV) natural elimination and assessment of their role as a monitoring parameter of the epidemiological surveillance system.Materials and methods. The study included 660 people divided into 2 groups: persons with chronic HC (CHC) and blood donors (indicator group of the healthy population). In the studied groups, the following SNPs were typed: rs1143634, rs1143627 (IL-1B); rs4251961, rs419598 (IL1RN); rs1800795 (IL6); rs1800896 (IL-10); rs4986790 (TLR4); rs4374383 (MERTK). The associative relationship between SNPs and CHC alleles was identified using logistic regression analysis within four models (codominant, dominant, recessive, and overdominant). Additionally, the significance of polymorphisms at the intragenic and intergenic levels was assessed using modern bioinformatic resources in the field of functional genomics.Results. In this study, genotypes associated with the natural elimination of HCV were identified. Paired combinations of IL 1RA/IL-1B genotypes associated with the probability of the formation of CHC have been established. It is shown that synonymous SNPs can be associated with any characteristics of the pathological process, which can be explained by disequilibrium in coupling with functionally significant alleles of other genetic loci.Conclusion. The detection of the association of SNPs with clinical manifestations of the pathological process is not final and requires further study taking into account ONP coupling groups.
T. N. Subbotina, I. E. Maslyukova, K. S. Semashchenko, G. A. Khodos, D. V. Kurochkin, A. A. Shalyova, M. A. Mikhalev, E. V. Vasiliev, M. G. Osadchaya, E. A. Dunaeva,et al.
Publishing House ABV Press
Background. The development of myelofibrosis (MF) is driven by complex molecular genetic events that include driver somatic mutations responsible for the constitutive activation of the JAK/STAT signaling pathway (JAK2, CALR, and MPL), additional mutations affecting epigenetic regulators (TET2, ASXL1, IDH1/2, etc.) and RNA splicing (SRSF2, U2AF1, SF3B1, etc.), as well as genetic aberrations that contribute to genomic instability and disease progression.Aim. To analyze driver (JAK2, CALR, MPL) and prognostic (ASXL1) somatic mutations in patients with MF and evaluate their impact on survival.Materials and methods. The study included 29 patients diagnosed with MF, selected by hematologists from the City Clinical Hospital No. 7 and Regional Clinical Hospital (Krasnoyarsk).Results. 26 (89.6 %) out of 29 examined patients had some driver mutations in JAK2, CALR, MPL genes. The p.V617F mutation in the JAK2 gene was found in 20 (68.9 %) patients. Mutations in the CALR gene were detected in 4 (13.8 %) patients, mutations in the MPL gene were found in 3 patients (10.3 %). In 1 of 26 patients, 2 driver mutations were present simultaneously. 3 (10.3 %) patients were triple negative. Mutations in the ASXL1 gene were detected in 12 (41.4 %) out of 29 examined patients. Conducted targeted NGS (next generation sequencing) for 13 out of 29 patients revealed additional genetic variants that contribute to the understanding of the development mechanism and disease course. When evaluating the overall survival in the groups of patients diagnosed with MF examined by us, depending on the combination of driver (JAK2, CALR, MPL) and prognostic (ASXL1) mutations, no statistically significant differences were found (p = 0.12). This appears to be due to the small sample size. At the same time, assessment of patient survival depending on ASXL1 status showed that in the presence of mutations in the ASXL1 gene, the median survival was 45 months (range 7–120 months), while in the absence of mutations it was 48 months (range 21–359 months) (p = 0.03).Conclusion. The results obtained allow us to assume that the presence of mutations in the ASXL1 gene is an unfavorable factor in the course of the disease.
Anna Esman, Anna Cherkashina, Konstantin Mironov, Dmitry Dubodelov, Svetlana Salamaikina, Anna Golubeva, Gasan Gasanov, Kamil Khafizov, Natalya Petrova, Evgeniy Cherkashin,et al.
MDPI AG
According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory technique to differentiate the main circulating SARS-CoV-2 variants in 2021–2022, when a sharp increase in morbidity was observed with the appearance of the Omicron variant. Real-time PCR methodology is available for use in the majority of scientific and diagnostic institutions in Russia, which makes it possible to increase the coverage of monitoring of variants in the territories of all 85 regions in order to accumulate information for the Central Services and make epidemiological decisions. With the methodology developed by the Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (FSSCRP Human Wellbeing) (CRIE), more than 6000 biological samples have been typed, and 7% of samples with the Delta variant and 92% of samples with the Omicron variant have been identified as of 25 August 2022. Reagents for 140,000 definitions have been supplied to regional organizations.
V. G. Akimkin, A. Yu. Popova, K. F. Khafizov, D. V. Dubodelov, S. V. Ugleva, T. A. Semenenko, A. A. Ploskireva, A. V. Gorelov, N. Yu. Pshenichnaya, E.B. Yezhlova,et al.
Central Research Institute for Epidemiology
Background. The ongoing pandemic of the novel coronavirus infection (COVID-19) draws attention to the significance of molecular and genetic monitoring of the SARS-CoV-2 spread among the population of the Russian Federation. The aim of the study was to analyze the dynamics of circulation of SARS-CoV-2 genetic variants in Russia.Materials and methods. The analysis of the circulation dynamics for SARS-CoV-2 genetic variants in Russia was carried out, covering the period from 28/12/2020 to 26/6/2022. The analysis included the data from Rospotrebnadzor Report No. 970 "Information about Infectious Diseases in Individuals with Suspected Novel Coronavirus Infection" and the Virus Genome Aggregator of Russia (VGARus). The presence of SARS-CoV-2 RNA was confirmed by the real-time reverse transcription polymerase chain reaction. The primer panels developed at the Central Research Institute of Epidemiology were used for amplification of genomic fragments and the subsequent sequencing.Results and discussion. Using the Russian VGARus platform developed by the Central Research Institute of Epidemiology, we received the data on mutational variability of SARS-CoV-2. By monitoring the circulation of SARS-CoV-2 genetic variants in Russia from 28/12/2020 to 26/6/2022, we found that Delta and Omicron genetic variants prevailed at different stages of the epidemic.Conclusion. The data of molecular and genetic studies are an essential component of epidemiological surveillance, being critically important for making executive decisions aimed at prevention of further spread of SARS-CoV-2 and laying the groundwork for creating new vaccines.
V. G. Akimkin, A. Yu. Popova, A. A. Ploskireva, S. V. Ugleva, T. A. Semenenko, N. Yu. Pshenichnaya, E. B. Ezhlova, A. N. Letyushev, Yu. V. Demina, S. N. Kuzin,et al.
Central Research Institute for Epidemiology
Background. The ongoing pandemic of a new coronavirus infection (COVID-19) determines the relevance of the analysis of epidemiological patterns of SARS-CoV-2 spread among the population of the Russian Federation.Aim — study of the manifestations of the epidemic process of COVID-19 in the Russian Federation in 2020–2022.Materials and methods. A retrospective epidemiological analysis of the incidence of COVID-19 in the Russian Federation was carried out from 03/30/2020 to 04/24/2022. The data from the Rospotrebnadzor report No. 970 “Information on cases of infectious diseases in persons with suspected new coronavirus infection”, information portal Stopcoronavirus.rf, etc. were used. The presence of SARS-CoV-2 RNA was confirmed by real-time RT-PCR.Results and discussion. The analysis of the manifestations of the epidemic process of COVID-19 in the Russian Federation in 2020–2022 showed the presence of two stages which differed depending on the influence of the biological factor and the ongoing anti-epidemic measures. There was a pronounced trend in the development of the epidemic process, starting from megacities (Moscow, Moscow region and St. Petersburg), which are major transport hubs and centers of migration activity of the population, to the regions of the Russian Federation. The SARS-CoV-2 pathogenicity has been shown to decrease with each subsequent cycle of the rise in the incidence of COVID-19 against the background of the increased contagiousness of the virus.Conclusion. As a result of the study, risk areas (megacities) and risk groups were identified.
O.P. Dribnokhodova, A.S. Esman, V.I. Korchagin, A.Yu. Bukharina, E.A. Dunaeva, G.V. Leshkina, E.V. Borisova, Ya.A. Voiciehovskaya, A.I. Daoud, V.N. Khlyavich,et al.
Journal Sovremennye Tehnologii v Medicine
The aim of the study is to develop methods for the differentiation of mutations in the BRAF codon 600 and to increase the sensitivity of the K601E mutation detection. Materials and Methods The nucleotide sequence of the BRAF codons 592–602 was identified using the PyroMark Q24 genetic analysis system. The mutations search in codon 600 was conducted using the 600-S primer in line with the following order of adding nucleotides: GCTGTCАTCTGCTAGCTAGAC (corresponding to nucleotides 1799–1786). The K601E mutation was detected using the 601-S primer in line with the following order of nucleotide addition: GCTACTCACTGTAG (corresponding to nucleotides 1801–1793). The analytical characteristics of the proposed methods for somatic mutations’ detection were determined using dilutions of plasmid DNA samples containing the BRAF gene region without mutations or with one of the following mutations: V600E, V600R, V600K, V600M, and K601E. Validation was performed on 132 samples of biological material obtained from the thyroid nodules. Results The developed methods allow to determine 2% of the V600E or V600M mutations, 1% of the V600K and V600R mutations, and 3% of the K601E mutations in samples with high DNA concentration; it is also possible to confidently detect at least 5% of the mutant allele for all mutations in low concentration samples (less than 500 copies/PCR). During biological material testing, 53 samples with the V600E mutation were detected; the proportion of the mutant allele was 4.9–50.0%. Conclusion A complex of methods for determination of the nucleotide sequence of the BRAF codons 592–601 and the algorithm for testing samples and analyzing mutations in the BRAF codons 600–601 was developed. The method provides sufficient sensitivity to detect frequent mutations in codons 600 and 601 and allows them to be precisely differentiated.
N. V. Vlasenko, N. S. Churilova, T. A. Loskutova, K. O. Mironov, A. S. Esman, E. A. Dunaeva, T. A. Semenenko, Z. S. Rodionova, I. G. Nikitin, A. V. Tutelian,et al.
Central Research Institute for Epidemiology
Introduction. Hepatitis B retains the status of socially significant infection and remains a major health problem worldwide, including the Russian Federation. The improvement of the effectiveness of the current complex of preventive measures, especially vaccination, is an important task for public health. Although vaccination against hepatitis B is highly successful, 5% to 10% of individuals do not experience a response to vaccine with an adequate level of antibodies to hepatitis B surface antigen (anti-HBs). One of the key factors determining the absence or insufficiency of post-vaccination immunity against hepatitis B may be the single-nucleotide polymorphisms (SNPs) that change gene sequences, including those that determine the mechanism of immunogenesis. Such genetic changes may affect the signaling pathways and result in significant decrease in antibody response to hepatitis B vaccine. Assessment of epidemiological significance of such SNPs is an important task, considering its possible associations with failure to respond adequately to vaccination.The aim of the study was to determine the effect of SNPs of IL1B (rs1143634, rs1143627), IL1RN (rs4251961, rs419598), IL6 (rs1800795), IL10 (rs1800896), TULP1 (rs9380516), TLR4 (rs4986790), MERTK (rs4374383) genes on the formation of post-vaccination immunity against hepatitis B.Materials and methods. Healthcare workers (n = 271) of the Treatment and Rehabilitation Center of the Ministry of Health of the Russian Federation with known vaccination history, data on age, work experience and department of the medical institution were included in this research. The presence and levels of anti-HBs and anti-HBcore IgG antibodies were determined by the ELISA method using the DS-ELISA-ANTI-HBs and DS-ELISA-ANTI-HBc kits, according to the manufacturer’s instructions. Genotyping was performed by real time polymerase chain reaction. Statistical analysis of data was carried out using the "Statistica 6.0" software.Results. Statistically significant differences in the frequencies of CC (rs9380516) genotypes (p = 0.034; OR 0.497; 95% CI 0.261–0.949) and CT (p = 0.044; OR 1.967; 95% CI 1.015–3.812) of the TULP1 gene in the group of individuals with anti-HBs concentrations of 10–100 IU/l were found in association with the intensity of the post-vaccination response against hepatitis B. Also, for this group, differences were found in the structure of the TT/CT genotype pair of IL-10/TULP1 genes (rs1800896/rs9380516) (p = 0.003; OR = 5.39; 95% CI 1.7–17.4) and for the combination of AA/TT SNP MERTK/IL1RN genotypes (rs4374383/rs4251961) (p = 0.003; OR = 7.96; 95% CI 1.7–37.6).Conclusion. Our study revealed that above variants of genotypes could play a role in predicting an increased risk of low (or absence) post-vaccination immune response against hepatitis B. It seems appropriate to use the relationship between the gene polymorphisms and a low concentration of post-vaccination anti-HBs antibodies in assessing scenarios for the development of the epidemic process of hepatitis B, since the identified associations allow to quantify the risks of poor herd immunity against this infection.
M. A. Koroleva, M. I. Gritsay, K. O. Mironov, N. N. Fomkina, I. S. Koroleva, I. I. Gaponova, A. S. Esman, V. P. Bulanenko, Yu. G. Yanushevich, A. A. Shelenkov,et al.
LLC Numicom
Relevance. Population migration can play a crucial role in the spread of invasive strains of meningococcus, initiating outbreaks of meningococcal infection, and changing the incidence at the local level.Aim. To assess the prevalence of meningococcal carriage among migrants arriving in Moscow and to characterize the antigenic and genetic properties of carrier strains of meningococcus.Materials and methods. The study was conducted in March 2020 at the bases of the Multifunctional Migration Center of Moscow and the Federal Budget Institution of Science «Central Research Institute of Epidemiology». Samples of nasopharyngeal mucus were collected from 352 people. Nasopharyngeal strains of meningococcus were identified and identified using microbiological, serological, and molecular biological methods.Results. The overall level of the carriage was 5.7%. Of the twenty selected strains, 10 have a serogroup defined: Y – 5 strains, W - 3, A, and B – 1 each. The obtained genetic and antigenic characteristics do not allow talking about the import into the RF of representatives of known hypervirulent clonal complexes. In this study, strains were identified that are part of the clonal complex ST-175 complex, which has not been previously described in the Russian Federation.Conclusion. It seems promising to continue the dynamic monitoring of carriage of meningococcus in various groups, including among people entering the country to obtain a migration patent, as well as identifying risk factors for acquiring carriage. The data obtained will supplement current information on the incidence of the generalized form of meningococcal infection and will be crucial for determining the epidemiology at the country level, the population groups responsible for the transmission of the disease, and the need for targeted vaccination.