1
|
Bogoslovskaya EV, Tsyganova GM, Nosova AO, Shipulin GA. Analysis of the Frequency of Mutations at Diagnostic Oligonucleotide Sites and Their Impact on the Efficiency of PCR for HIV-1. Microorganisms 2023; 11:2838. [PMID: 38137981 PMCID: PMC10746099 DOI: 10.3390/microorganisms11122838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
The development of effective diagnostic kits for HIV-1 remains a pressing concern. We designed diagnostic oligonucleotides for HIV-1 real-time PCR to target the most conserved region of the HIV-1 genome and assessed the mutation frequency at annealing sites. Two databases of nucleotide sequences, Los Alamos and NCBI, were analyzed, revealing that more than 99% of the sequences either lack mutations or contain 1-2 mutations at the binding site of the forward and reverse primers. Additionally, 98.5% of the sequences either lack mutations or contain 1-2 mutations at the binding site of the TaqMan probe. To evaluate the efficiency of primers and the probe in real-time PCR in the case of mutations at their binding sites, we constructed several plasmids containing the most common mutations and, in a model experiment, showed how different mutations affect the efficiency of PCR. Our analysis demonstrated that about 98.5% of HIV-1 strains can be efficiently detected using a single pair of selected primers. For the remaining 1.5% of strains, a more careful selection of the second target is needed.
Collapse
Affiliation(s)
- Elena V. Bogoslovskaya
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (G.M.T.); (A.O.N.); (G.A.S.)
| | | | | | | |
Collapse
|
2
|
Korobeinikova AV, Zlobovskaya OA, Sheptulina AF, Ashniev GA, Bobrova MM, Yafarova AA, Akasheva DU, Kabieva SS, Bakoev SY, Zagaynova AV, Lukashina MV, Abramov IA, Pokrovskaya MS, Doludin YV, Tolkacheva LR, Kurnosov AS, Zyatenkova EV, Lavrenova EA, Efimova IA, Glazunova EV, Kiselev AR, Shipulin GA, Kontsevaya AV, Keskinov AA, Yudin VS, Makarov VV, Drapkina OM, Yudin SM. Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods. Int J Mol Sci 2023; 24:15272. [PMID: 37894951 PMCID: PMC10607775 DOI: 10.3390/ijms242015272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 10/29/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.
Collapse
Affiliation(s)
- Anna V. Korobeinikova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Olga A. Zlobovskaya
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anna F. Sheptulina
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - German A. Ashniev
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Maria M. Bobrova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Adel A. Yafarova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Dariga U. Akasheva
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Shuanat Sh. Kabieva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Siroj Yu. Bakoev
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anjelica V. Zagaynova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Maria V. Lukashina
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Ivan A. Abramov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Mariya S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Yurii V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Larisa R. Tolkacheva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Alexander S. Kurnosov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Elena V. Zyatenkova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Evgeniya A. Lavrenova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Irina A. Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Evgeniya V. Glazunova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anton R. Kiselev
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Anna V. Kontsevaya
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Anton A. Keskinov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Vladimir S. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Valentin V. Makarov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| | - Oxana M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigskyj Lane 10, bld.3, 101990 Moscow, Russia; (A.F.S.); (A.A.Y.); (D.U.A.)
| | - Sergey M. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (A.V.K.); (S.S.K.); (S.Y.B.); (M.V.L.); (A.S.K.)
| |
Collapse
|
3
|
Chernyaeva EN, Ayginin AA, Kosenkov AV, Romanova SV, Tsypkina AV, Luparev AR, Stetsenko IF, Gnusareva NI, Matsvay AD, Savochkina YA, Shipulin GA. SARS-CoV-2 Recombination and Coinfection Events Identified in Clinical Samples in Russia. Viruses 2023; 15:1660. [PMID: 37632003 PMCID: PMC10458065 DOI: 10.3390/v15081660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Recombination is one of the mechanisms of SARS-CoV-2 evolution along with the occurrence of point mutations, insertions, and deletions. Recently, recombinant variants of SARS-CoV-2 have been registered in different countries, and some of them have become circulating forms. In this work, we performed screening of SARS-CoV-2 genomic sequences to identify recombination events and co-infections with various strains of the SARS-CoV-2 virus detected in Russia from February 2020 to March 2022. The study included 9336 genomes of the COVID-19 pathogen obtained as a result of high-throughput sequencing on the Illumina platform. For data analysis, we used an algorithm developed by our group that can identify viral recombination variants and cases of co-infections by estimating the frequencies of characteristic substitutions in raw read alignment files and VCF files. The detected cases of recombination were confirmed by alternative sequencing methods, principal component analysis, and phylogenetic analysis. The suggested approach allowed for the identification of recombinant variants of strains BA.1 and BA.2, among which a new recombinant variant was identified, as well as a previously discovered one. The results obtained are the first evidence of the spread of recombinant variants of SARS-CoV-2 in Russia. In addition to cases of recombination we identified cases of coinfection: eight of them contained the genome of the Omicron line as one of the variants, six of them the genome of the Delta line, and two with the genome of the Alpha line.
Collapse
|
4
|
Devyatov AA, Davydova EE, Luparev AR, Karseka SA, Shuryaeva AK, Zagainova AV, Shipulin GA. Design of a Protocol for Soil-Transmitted Helminths (in Light of the Nematode Toxocara canis) DNA Extraction from Feces by Combining Commercially Available Solutions. Diagnostics (Basel) 2023; 13:2156. [PMID: 37443549 DOI: 10.3390/diagnostics13132156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
One of the main challenges for the mass introduction of the molecular diagnostics of soil-transmitted helminths (STHs) into clinical practice is the lack of a generally recognized effective method for isolating parasitic DNA from fecal samples. In the present study, we assessed the effects of various pretreatment procedures on the efficiency of removing PCR inhibitors and extracting Toxocara canis DNA from feces. We evaluated the effectiveness of four destructive methods (bead beating, the action of temperature-dependent enzymes, freeze-heat cycles, and incubation in a lysis buffer) on the integrity of T. canis eggs and the efficiency of DNA extraction. Also, we evaluated the effects of prewashes and the use of commercial concentrators on DNA extraction from fecal samples contaminated with T. canis eggs. A bead beating procedure was sufficient to destroy the T. canis eggs, while the effects of enzymes and freeze-heat cycles did not lead to a significant destruction of the eggs or the release of Toxocara DNA. Helminth DNA isolation protocols that do not include a bead beating step are not preferred. The preconcentration of STH eggs from feces using a commercial concentrator and subsequent washing can significantly increase the yield of DNA from STHs and reduce PCR inhibition.
Collapse
Affiliation(s)
- Alexander A Devyatov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Ekaterina E Davydova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Andrey R Luparev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Sofia A Karseka
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Anna K Shuryaeva
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Angelica V Zagainova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - German A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| |
Collapse
|
5
|
Leontyev DS, Glazkova DV, Bezborodova OA, Tsyganova GM, Urusov FA, Pankratov AA, Shipulin GA, Bogoslovskaya EV. Humanized Mouse Model of HIV Infection. Bull Exp Biol Med 2023:10.1007/s10517-023-05812-3. [PMID: 37338766 DOI: 10.1007/s10517-023-05812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 06/21/2023]
Abstract
The development of new drugs for the treatment of HIV infection requires testing of their efficacy in a relevant animal model, such as humanized mice, which, unfortunately, are not yet available in Russia. In the present study, we have developed conditions for the humanization of immunodeficient NSG mice with human hematopoietic stem cells. Humanized animals generated during the study showed a high degree of chimerism and harbored repopulation of the entire range of human lymphocytes required for HIV replication in the blood and organs. Inoculation of these mice with HIV-1 virus led to stable viremia, which was confirmed by the presence of viral RNA in blood plasma throughout the entire period of observation and proviral DNA in the organs of animals 4 weeks after HIV infection.
Collapse
Affiliation(s)
- D S Leontyev
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia.
| | - D V Glazkova
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - O A Bezborodova
- P. A. Hertsen Moscow Oncology Research Institute - Affiliated Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - G M Tsyganova
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - F A Urusov
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia
- N. F. Izmerov Research Institute of Occupational Health, Moscow, Russia
| | - A A Pankratov
- P. A. Hertsen Moscow Oncology Research Institute - Affiliated Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - G A Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - E V Bogoslovskaya
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical-Biological Agency of Russia, Moscow, Russia
| |
Collapse
|
6
|
Shipulin GA, Savochkina Y, Shuryaeva AK, Glushchenko EE, Luparev AR, Polyakova VA, Danilov DI, Davydova EE, Vinogradov KS, Stetsenko IF, Aiginin AA, Matsvay AD, Kolbutova KB, Bogdan SA, Vashukova MA, Yudin SM. Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2. Heliyon 2023; 9:e16917. [PMID: 37287602 PMCID: PMC10234363 DOI: 10.1016/j.heliyon.2023.e16917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/04/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses. In 2020, a new variant of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world. To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions. It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х103 copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1-100% for Omicron and 91.3-100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2-100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022.
Collapse
Affiliation(s)
- G A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - YuA Savochkina
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A K Shuryaeva
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - E E Glushchenko
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A R Luparev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - V A Polyakova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - D I Danilov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - E E Davydova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - K S Vinogradov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - I F Stetsenko
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A A Aiginin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - A D Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - K B Kolbutova
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - S A Bogdan
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - M A Vashukova
- Clinical Infectious Diseases Hospital Named After S.P. Botkin, St. Petersburg, Russia
| | - S M Yudin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| |
Collapse
|
7
|
Nasyrova RF, Shnayder NA, Osipova SM, Khasanova AK, Efremov IS, Al-Zamil M, Petrova MM, Narodova EA, Garganeeva NP, Shipulin GA. Genetic Predictors of Antipsychotic Efflux Impairment via Blood-Brain Barrier: Role of Transport Proteins. Genes (Basel) 2023; 14:genes14051085. [PMID: 37239445 DOI: 10.3390/genes14051085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Antipsychotic (AP)-induced adverse drug reactions (ADRs) are a current problem of biological and clinical psychiatry. Despite the development of new generations of APs, the problem of AP-induced ADRs has not been solved and continues to be actively studied. One of the important mechanisms for the development of AP-induced ADRs is a genetically-determined impairment of AP efflux across the blood-brain barrier (BBB). We present a narrative review of publications in databases (PubMed, Springer, Scopus, Web of Science E-Library) and online resources: The Human Protein Atlas; GeneCards: The Human Gene Database; US National Library of Medicine; SNPedia; OMIM Online Mendelian Inheritance in Man; The PharmGKB. The role of 15 transport proteins involved in the efflux of drugs and other xenobiotics across cell membranes (P-gp, TAP1, TAP2, MDR3, BSEP, MRP1, MRP2, MRP3, MRP4, MRP5, MRP6, MRP7, MRP8, MRP9, BCRP) was analyzed. The important role of three transporter proteins (P-gp, BCRP, MRP1) in the efflux of APs through the BBB was shown, as well as the association of the functional activity and expression of these transport proteins with low-functional and non-functional single nucleotide variants (SNVs)/polymorphisms of the ABCB1, ABCG2, ABCC1 genes, encoding these transport proteins, respectively, in patients with schizophrenia spectrum disorders (SSDs). The authors propose a new pharmacogenetic panel "Transporter protein (PT)-Antipsychotic (AP) Pharmacogenetic test (PGx)" (PTAP-PGx), which allows the evaluation of the cumulative contribution of the studied genetic biomarkers of the impairment of AP efflux through the BBB. The authors also propose a riskometer for PTAP-PGx and a decision-making algorithm for psychiatrists. Conclusions: Understanding the role of the transportation of impaired APs across the BBB and the use of genetic biomarkers for its disruption may make it possible to reduce the frequency and severity of AP-induced ADRs, since this risk can be partially modified by the personalized selection of APs and their dosing rates, taking into account the genetic predisposition of the patient with SSD.
Collapse
Affiliation(s)
- Regina F Nasyrova
- Institute of Personalized Psychiatry and Neurology, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, Saint-Petersburg 192019, Russia
- International Centre for Education and Research in Neuropsychiatry, Samara State Medical University, Samara 443016, Russia
| | - Natalia A Shnayder
- Institute of Personalized Psychiatry and Neurology, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, Saint-Petersburg 192019, Russia
- Shared Core Facilities "Molecular and Cell Technologies", V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Sofia M Osipova
- Institute of Personalized Psychiatry and Neurology, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, Saint-Petersburg 192019, Russia
| | - Aiperi K Khasanova
- Department of Psychiatry, Russian Medical Academy for Continual Professional Education, Moscow 125993, Russia
| | - Ilya S Efremov
- Department of Psychiatry and Addiction, Bashkir State Medical University, Ufa 450008, Russia
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples' Friendship University of Russia, Moscow 117198, Russia
| | - Marina M Petrova
- Shared Core Facilities "Molecular and Cell Technologies", V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Ekaterina A Narodova
- Shared Core Facilities "Molecular and Cell Technologies", V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Natalia P Garganeeva
- Department of General Medical Practice and Outpatient Therapy, Siberian State Medical University, Tomsk 634050, Russia
| | - German A Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks Management, Moscow 119121, Russia
| |
Collapse
|
8
|
Mintaev RR, Glazkova DV, Orlova OV, Ignatyev GM, Oksanich AS, Shipulin GA, Bogoslovskaya EV. Development of MVA-d34 Tetravalent Dengue Vaccine: Design and Immunogenicity. Vaccines (Basel) 2023; 11:vaccines11040831. [PMID: 37112743 PMCID: PMC10142911 DOI: 10.3390/vaccines11040831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Dengue fever, an infectious disease that affects more than 100 million people every year, is a global health problem. Vaccination may be the most effective prevention strategy for the disease. However, the development of vaccines against dengue fever is complicated by the high risk of developing an antibody-dependent increase in infection. This article describes the development of an MVA-d34 vaccine against the dengue virus based on a safe and effective MVA viral vector. The DIII domains of the envelope protein (E) of the dengue virus are used as vaccine antigens, as antibodies against these domains do not cause an enhancement of infection. The use of the DIII domains of each of the four dengue virus serotypes made it possible to generate a humoral response against all four dengue virus serotypes in immunized mice. We also showed that the sera of vaccinated mice present virus-neutralizing activity against dengue serotype 2. Thus, the developed MVA-d34 vaccine is a promising candidate vaccine against dengue fever.
Collapse
Affiliation(s)
- Ramil R Mintaev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| | - Dina V Glazkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| | - Olga V Orlova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| | - Georgiy M Ignatyev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| | - Alexey S Oksanich
- I. Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - German A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| | - Elena V Bogoslovskaya
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119833 Moscow, Russia
| |
Collapse
|
9
|
Shaidullina ER, Schwabe M, Rohde T, Shapovalova VV, Dyachkova MS, Matsvay AD, Savochkina YA, Shelenkov AA, Mikhaylova YV, Sydow K, Lebreton F, Idelevich EA, Heiden SE, Becker K, Kozlov RS, Shipulin GA, Akimkin VG, Lalk M, Guenther S, Zautner AE, Bohnert JA, Mardanova AM, Bouganim R, Marchaim D, Hoff KJ, Schaufler K, Edelstein MV. Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395. Genome Med 2023; 15:9. [PMID: 36782220 PMCID: PMC9926764 DOI: 10.1186/s13073-023-01159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. METHODS We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. RESULTS Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. CONCLUSIONS To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
Collapse
Affiliation(s)
- Elvira R. Shaidullina
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - Michael Schwabe
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Rohde
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Valeria V. Shapovalova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Marina S. Dyachkova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Alina D. Matsvay
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Yuliya A. Savochkina
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Katharina Sydow
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - François Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA
| | - Evgeny A. Idelevich
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany ,grid.16149.3b0000 0004 0551 4246Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan E. Heiden
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Roman S. Kozlov
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - German A. Shipulin
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | - Michael Lalk
- grid.5603.0Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastian Guenther
- grid.5603.0Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas E. Zautner
- grid.5807.a0000 0001 1018 4307Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jürgen A. Bohnert
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ayslu M. Mardanova
- grid.77268.3c0000 0004 0543 9688Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ruth Bouganim
- grid.413990.60000 0004 1772 817XDepartment of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Dror Marchaim
- grid.12136.370000 0004 1937 0546Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katharina J. Hoff
- grid.5603.0Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany. .,Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Mikhail V. Edelstein
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| |
Collapse
|
10
|
Shnayder NA, Grechkina VV, Khasanova AK, Bochanova EN, Dontceva EA, Petrova MM, Asadullin AR, Shipulin GA, Altynbekov KS, Al-Zamil M, Nasyrova RF. Therapeutic and Toxic Effects of Valproic Acid Metabolites. Metabolites 2023; 13:metabo13010134. [PMID: 36677060 PMCID: PMC9862929 DOI: 10.3390/metabo13010134] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Valproic acid (VPA) and its salts are psychotropic drugs that are widely used in neurological diseases (epilepsy, neuropathic pain, migraine, etc.) and psychiatric disorders (schizophrenia, bipolar affective disorder, addiction diseases, etc.). In addition, the indications for the appointment of valproate have been expanding in recent years in connection with the study of new mechanisms of action of therapeutic and toxic metabolites of VPA in the human body. Thus, VPA is considered a component of disease-modifying therapy for multiple tumors, neurodegenerative diseases (Huntington's disease, Parkinson's disease, Duchenne progressive dystrophy, etc.), and human immunodeficiency syndrome. The metabolism of VPA is complex and continues to be studied. Known pathways of VPA metabolism include: β-oxidation in the tricarboxylic acid cycle (acetylation); oxidation with the participation of cytochrome P-450 isoenzymes (P-oxidation); and glucuronidation. The complex metabolism of VPA explains the diversity of its active and inactive metabolites, which have therapeutic, neutral, or toxic effects. It is known that some active metabolites of VPA may have a stronger clinical effect than VPA itself. These reasons explain the relevance of this narrative review, which summarizes the results of studies of blood (serum, plasma) and urinary metabolites of VPA from the standpoint of the pharmacogenomics and pharmacometabolomics. In addition, a new personalized approach to assessing the cumulative risk of developing VPA-induced adverse reactions is presented and ways for their correction are proposed depending on the patient's pharmacogenetic profile and the level of therapeutic and toxic VPA metabolites in the human body fluids (blood, urine).
Collapse
Affiliation(s)
- Natalia A. Shnayder
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-620-0222 (N.A.S. & R.F.N.)
| | - Violetta V. Grechkina
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
| | - Aiperi K. Khasanova
- Department of Psychiatry, Russian Medical Academy for Continual Professional Education, 125993 Moscow, Russia
| | - Elena N. Bochanova
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Evgenia A. Dontceva
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Marina M. Petrova
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Azat R. Asadullin
- Department of Psychiatry and Addiction, Bashkir State Medical University, 45000 Ufa, Russia
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks, 119121 Moscow, Russia
| | - Kuanysh S. Altynbekov
- Republican Scientific and Practical Center of Mental Health, Almaty 050022, Kazakhstan
- Department of Psychiatry and Narcology, S.D. Asfendiarov Kazakh National Medical University, Almaty 050022, Kazakhstan
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples’ Friendship University of Russia, 11798 Moscow, Russia
| | - Regina F. Nasyrova
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-620-0222 (N.A.S. & R.F.N.)
| |
Collapse
|
11
|
Matsvay A, Klink GV, Safina KR, Nabieva E, Garushyants SK, Biba D, Bazykin GA, Mikhaylov IM, Say AV, Zakamornaya AI, Khakhina AO, Lisitsa TS, Ayginin AA, Abramov IS, Bogdan SA, Kolbutova KB, Oleynikova DU, Avdeenko TF, Shipulin GA, Yudin SM, Skvortsova VI. Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020. PLoS One 2023; 18:e0285664. [PMID: 37192187 DOI: 10.1371/journal.pone.0285664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/22/2023] [Indexed: 05/18/2023] Open
Abstract
In 2020, SARS-CoV-2 has spread rapidly across the globe, with most nations failing to prevent or substantially delay its introduction. While many countries have imposed some limitations on trans-border passenger traffic, the effect of these measures on the global spread of COVID-19 strains remains unclear. Here, we report an analysis of 3206 whole-genome sequences of SARS-CoV-2 samples from 78 regions of Russia covering the period before the spread of variants of concern (between March and November 2020). We describe recurring imports of multiple COVID-19 strains into Russia throughout this period, giving rise to 457 uniquely Russian transmission lineages, as well as repeated cross-border transmissions of local circulating variants out of Russia. While the phylogenetically inferred rate of cross-border transmissions was somewhat reduced during the period of the most stringent border closure, it still remained high, with multiple inferred imports that each led to detectable spread within the country. These results indicate that partial border closure has had little effect on trans-border transmission of variants, which helps explain the rapid global spread of newly arising SARS-CoV-2 variants throughout the pandemic.
Collapse
Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Galya V Klink
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Elena Nabieva
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Biba
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Georgii A Bazykin
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Ivan M Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Anna V Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Anastasiya I Zakamornaya
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Anastasiya O Khakhina
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana S Lisitsa
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Andrey A Ayginin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Ivan S Abramov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Sergey A Bogdan
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - Kseniya B Kolbutova
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - Daria U Oleynikova
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana F Avdeenko
- Chief Federal State Budgetary Healthcare Institution "Centre of Hygiene and Epidemiology" of the Federal Medical Biological Agency, Moscow, Russia
| | - German A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Sergey M Yudin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | | |
Collapse
|
12
|
Vaiman EE, Shnayder NA, Zhuravlev NM, Petrova MM, Asadullin AR, Al-Zamil M, Garganeeva NP, Shipulin GA, Cumming P, Nasyrova RF. Genetic Biomarkers of Antipsychotic-Induced Prolongation of the QT Interval in Patients with Schizophrenia. Int J Mol Sci 2022; 23:ijms232415786. [PMID: 36555428 PMCID: PMC9785058 DOI: 10.3390/ijms232415786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Antipsychotics (AP) induced prolongation of the QT interval in patients with schizophrenia (Sch) is an actual interdisciplinary problem as it increases the risk of sudden death syndrome. Long QT syndrome (LQTS) as a cardiac adverse drug reaction is a multifactorial symptomatic disorder, the development of which is influenced by modifying factors (APs' dose, duration of APs therapy, APs polytherapy, and monotherapy, etc.) and non-modifying factors (genetic predisposition, gender, age, etc.). The genetic predisposition to AP-induced LQTS may be due to several causes, including causal mutations in the genes responsible for monoheme forms of LQTS, single nucleotide variants (SNVs) of the candidate genes encoding voltage-dependent ion channels expressed both in the brain and in the heart, and SNVs of candidate genes encoding key enzymes of APs metabolism. This narrative review summarizes the results of genetic studies on AP-induced LQTS and proposes a new personalized approach to assessing the risk of its development (low, moderate, high). We recommend implementation in protocols of primary diagnosis of AP-induced LQTS and medication dispensary additional observations of the risk category of patients receiving APs, deoxyribonucleic acid profiling, regular electrocardiogram monitoring, and regular therapeutic drug monitoring of the blood APs levels.
Collapse
Affiliation(s)
- Elena E. Vaiman
- Institute of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
| | - Natalia A. Shnayder
- Institute of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Shared Core Facilities “Molecular and Cell Technologies”, V. F. Voyno-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-670-02-20 (N.A.S. & R.F.N.)
| | - Nikita M. Zhuravlev
- Institute of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
| | - Marina M. Petrova
- Shared Core Facilities “Molecular and Cell Technologies”, V. F. Voyno-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Azat R. Asadullin
- Department of Psychiatry and Addiction, Bashkir State Medical University, 450008 Ufa, Russia
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Natalia P. Garganeeva
- Department of General Medical Practice and Outpatient Therapy, Siberian State Medical University, 634050 Tomsk, Russia
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks Management, 119121 Moscow, Russia
| | - Paul Cumming
- Department of Nuclear Medicine, Bern University Hospital, 3010 Bern, Switzerland
- School of Psychology and Counselling, Queensland University of Technology, Brisbane 4000, Australia
| | - Regina F. Nasyrova
- Institute of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- International Centre for Education and Research in Neuropsychiatry, Samara State Medical University, 443016 Samara, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-670-02-20 (N.A.S. & R.F.N.)
| |
Collapse
|
13
|
Chernyaeva EN, Ayginin AA, Bulusheva IA, Vinogradov KS, Stetsenko IF, Romanova SV, Tsypkina AV, Matsvay AD, Savochkina YA, Shipulin GA. Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022. Pathogens 2022; 11:pathogens11121461. [PMID: 36558796 PMCID: PMC9786029 DOI: 10.3390/pathogens11121461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (n = 589) and downloaded from GISAID (n = 397), and identified that the BA.1 lineage was predominant in Russia during this period. The BA.2 lineage was also identified early in December 2021. We identified three cases of BA.1/BA.2 coinfections and one case of Delta/Omicron coinfection. A comparative genomic analysis of SARS-CoV-2 viral variants that spread in other countries allowed us to identify possible cases of transmission. We also found that some mutations that are quite rare in the Global Omicron dataset have a higher incidence rate, and identified genetic markers that could be associated with ways of Omicron transmission in Russia. We give the genomic variability of single nucleotide variations across the genome and give a characteristic of haplotype variability of Omicron strains in both Russia and around the world, and we also identify them.
Collapse
|
14
|
Drapkina OM, Ashniev GA, Zlobovskaya OA, Yafarova AA, Dementeva EV, Kaburova AN, Meshkov IO, Sheptulina AF, Kiselev AR, Kontsevaya AV, Zhamalov LM, Koretskiy SN, Pokrovskaya MS, Akinshina AI, Zagaynova AV, Lukashina MV, Kirillov AV, Abramov IA, Tolkacheva LR, Bikaeva IO, Glazunova EV, Shipulin GA, Bobrova MM, Makarov VV, Keskinov AA, Yudin VS, Yudin SM. Diversities in the Gut Microbial Patterns in Patients with Atherosclerotic Cardiovascular Diseases and Certain Heart Failure Phenotypes. Biomedicines 2022; 10:2762. [PMID: 36359282 PMCID: PMC9687836 DOI: 10.3390/biomedicines10112762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 03/02/2024] Open
Abstract
To continue progress in the treatment of cardiovascular disease, there is a need to improve the overall understanding of the processes that contribute to the pathogenesis of cardiovascular disease (CVD). Exploring the role of gut microbiota in various heart diseases is a topic of great interest since it is not so easy to find such reliable connections despite the fact that microbiota undoubtedly affect all body systems. The present study was conducted to investigate the composition of gut microbiota in patients with atherosclerotic cardiovascular disease (ASCVD) and heart failure syndromes with reduced ejection fraction (HFrEF) and HF with preserved EF (HFpEF), and to compare these results with the microbiota of individuals without those diseases (control group). Fecal microbiota were evaluated by three methods: living organisms were determined using bacterial cultures, total DNA taxonomic composition was estimated by next generation sequencing (NGS) of 16S rRNA gene (V3-V4) and quantitative assessment of several taxa was performed using qPCR (quantitative polymerase chain reaction). Regarding the bacterial culture method, all disease groups demonstrated a decrease in abundance of Enterococcus faecium and Enterococcus faecalis in comparison to the control group. The HFrEF group was characterized by an increased abundance of Streptococcus sanguinus and Streptococcus parasanguinis. NGS analysis was conducted at the family level. No significant differences between patient's groups were observed in alpha-diversity indices (Shannon, Faith, Pielou, Chao1, Simpson, and Strong) with the exception of the Faith index for the HFrEF and control groups. Erysipelotrichaceae were significantly increased in all three groups; Streptococcaceae and Lactobacillaceae were significantly increased in ASCVD and HFrEF groups. These observations were indirectly confirmed with the culture method: two species of Streptococcus were significantly increased in the HFrEF group and Lactobacillus plantarum was significantly increased in the ASCVD group. The latter observation was also confirmed with qPCR of Lactobacillus sp. Acidaminococcaceae and Odoribacteraceae were significantly decreased in the ASCVD and HFrEF groups. Participants from the HFpEF group showed the least difference compared to the control group in all three study methods. The patterns found expand the knowledge base on possible correlations of gut microbiota with cardiovascular diseases. The similarities and differences in conclusions obtained by the three methods of this study demonstrate the need for a comprehensive approach to the analysis of microbiota.
Collapse
Affiliation(s)
- Oxana M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - German A. Ashniev
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Olga A. Zlobovskaya
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Adel A. Yafarova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Elena V. Dementeva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Anastasia N. Kaburova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Ivan O. Meshkov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Anna F. Sheptulina
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Anton R. Kiselev
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Anna V. Kontsevaya
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Linar M. Zhamalov
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Sergey N. Koretskiy
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Mariya S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia
| | - Alexandra I. Akinshina
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Anjelica V. Zagaynova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Mariia V. Lukashina
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Andrey V. Kirillov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan A. Abramov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Larisa R. Tolkacheva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Irina O. Bikaeva
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Evgeniya V. Glazunova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Maria M. Bobrova
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Valentin V. Makarov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Anton A. Keskinov
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Vladimir S. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Sergey M. Yudin
- Centre for Strategic Planning and Management of Biomedical Health Risks of Federal Medical Biological Agency, 119121 Moscow, Russia
| |
Collapse
|
15
|
Shnayder NA, Khasanova AK, Strelnik AI, Al-Zamil M, Otmakhov AP, Neznanov NG, Shipulin GA, Petrova MM, Garganeeva NP, Nasyrova RF. Cytokine Imbalance as a Biomarker of Treatment-Resistant Schizophrenia. Int J Mol Sci 2022; 23:ijms231911324. [PMID: 36232626 PMCID: PMC9570417 DOI: 10.3390/ijms231911324] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
Abstract
Treatment-resistant schizophrenia (TRS) is an important and unresolved problem in biological and clinical psychiatry. Approximately 30% of cases of schizophrenia (Sch) are TRS, which may be due to the fact that some patients with TRS may suffer from pathogenetically “non-dopamine” Sch, in the development of which neuroinflammation is supposed to play an important role. The purpose of this narrative review is an attempt to summarize the data characterizing the patterns of production of pro-inflammatory and anti-inflammatory cytokines during the development of therapeutic resistance to APs and their pathogenetic and prognostic significance of cytokine imbalance as TRS biomarkers. This narrative review demonstrates that the problem of evaluating the contribution of pro-inflammatory and anti-inflammatory cytokines to maintaining or changing the cytokine balance can become a new key in unlocking the mystery of “non-dopamine” Sch and developing new therapeutic strategies for the treatment of TRS and psychosis in the setting of acute and chronic neuroinflammation. In addition, the inconsistency of the results of previous studies on the role of pro-inflammatory and anti-inflammatory cytokines indicates that the TRS biomarker, most likely, is not the serum level of one or more cytokines, but the cytokine balance. We have confirmed the hypothesis that cytokine imbalance is one of the most important TRS biomarkers. This hypothesis is partially supported by the variable response to immunomodulators in patients with TRS, which were prescribed without taking into account the cytokine balance of the relation between serum levels of the most important pro-inflammatory and anti-inflammatory cytokines for TRS.
Collapse
Affiliation(s)
- Natalia A. Shnayder
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-620-02-20-78-13 (N.A.S. & R.F.N.)
| | - Aiperi K. Khasanova
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
| | - Anna I. Strelnik
- International Centre for Education and Research in Neuropsychiatry, Samara State Medical University, 443016 Samara, Russia
- Department of Psychiatry, Narcology and Psychotherapy, Samara State Medical University, 443016 Samara, Russia
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Andrey P. Otmakhov
- Basic Department of Psychological and Social Support, St. Petersburg State Institute of Psychology and Social Work, 199178 Saint Petersburg, Russia
- St. Nikolay Psychiatric Hospital, 190121 Saint Petersburg, Russia
| | - Nikolay G. Neznanov
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
| | - German A. Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks Management, 119121 Moscow, Russia
| | - Marina M. Petrova
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Natalia P. Garganeeva
- Department of General Medical Practice and Outpatient Therapy, Siberian State Medical University, 634050 Tomsk, Russia
| | - Regina F. Nasyrova
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia
- International Centre for Education and Research in Neuropsychiatry, Samara State Medical University, 443016 Samara, Russia
- Correspondence: (N.A.S.); (R.F.N.); Tel.: +7-(812)-620-02-20-78-13 (N.A.S. & R.F.N.)
| |
Collapse
|
16
|
Glazkova DV, Bogoslovskaya EV, Urusov FA, Kartashova NP, Glubokova EA, Gracheva AV, Faizuloev EB, Trunova GV, Khokhlova VA, Bezborodova OA, Pankratov AA, Leneva IA, Shipulin GA. [Generation of SARS-CoV-2 Mouse Model by Transient Expression of the Human ACE2 Gene Mediated by Intranasal Administration of AAV-hACE2]. Mol Biol (Mosk) 2022; 56:774-782. [PMID: 36165016 DOI: 10.31857/s0026898422050068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/12/2022] [Indexed: 06/16/2023]
Abstract
One of the most important steps in the development of drugs and vaccines against a new coronavirus infection is their testing on a relevant animal model. The laboratory mouse, with well-studied immunology, is the preferred mammalian model in experimental medicine. However, mice are not susceptible to infection with SARS-CoV-2 due to the lack of human angiotensin-converting enzyme (hACE2), which is the cell receptor of SARS-CoV-2 and necessary for the entry of the virus into the cell. In present work, it was shown that intranasal administration of the adeno-associated vectors AAV9 and AAV-DJ encoding the hACE2 provided a high level of expression of ACE2 gene in the lungs of mice. In contrast, the introduction of the AAV6 vector led to a low level ACE2 expression. Infection with SARS-CoV-2 of mice expressing hACE2 in the lungs led to virus replication and development of bronchopneumonia on the 7th day after infection. Thus, a simple method for delivering the human ACE2 gene to mouse lungs by intranasal administration of the AAV vector has been proposed. This approach enabled rapid generation of mouse model for studying coronavirus infection.
Collapse
Affiliation(s)
- D V Glazkova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - E V Bogoslovskaya
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - F A Urusov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
- Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia
| | - N P Kartashova
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - E A Glubokova
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - A V Gracheva
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - E B Faizuloev
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - G V Trunova
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - V A Khokhlova
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - O A Bezborodova
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - A A Pankratov
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - I A Leneva
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - G A Shipulin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| |
Collapse
|
17
|
Tikhonov AS, Mintaev RR, Glazkova DV, Bogoslovskaya EV, Shipulin GA. [HIV Restriction Factor APOBEC3G and Prospects for Its Use in Gene Therapy for HIV]. Mol Biol (Mosk) 2022; 56:546-556. [PMID: 35964311 DOI: 10.31857/s0026898422040115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/17/2022] [Indexed: 06/15/2023]
Abstract
The mechanisms for the protection of the human body from viral or bacterial agents are extremely diverse. In one such mechanism, an important role belongs to the cytidine deaminase APOBEC3 family, which is the factor of congenital immunity and protects the organism from numerous viral agents. One of the proteins of this family, APOBEC3G, is able to protect against Human Immunodeficiency Virus type 1 in the absence of viral protein Vif. In turn, Vif opposes APOBEC3G action, causing polyubiquity of the protein and degradation in the proteasome. The review describes possible ways to increase the anti-HIV activity of APOBEC3G, giving it resistance to viral protein Vif, as well as potential approaches to the use of modified APOBEC3G in gene therapy for HIV.
Collapse
Affiliation(s)
- A S Tikhonov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119833 Russia
| | - R R Mintaev
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119833 Russia
- Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - D V Glazkova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119833 Russia
| | - E V Bogoslovskaya
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119833 Russia
| | - G A Shipulin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119833 Russia
| |
Collapse
|
18
|
Urusov FA, Glazkova DV, Tsyganova GM, Pozdyshev DV, Bogoslovskaya EV, Shipulin GA. [The Titer of the Lentiviral Vector Encoding Chimeric TRIM5α-HRH Gene is Reduced Due to Expression of TRIM5α-HRH in Producer Cells and the Negative Effect of Efla Promoter]. Mol Biol (Mosk) 2022; 56:147-156. [PMID: 35082263 DOI: 10.31857/s0026898422010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/11/2021] [Indexed: 06/14/2023]
Abstract
The chimeric protein TRIM5α-HRH is a promising antiviral factor for HIV-1 gene therapy. This protein is able to protect cells from HIV-1 by blocking the virus in the cytoplasm. We are developing protocol of HIV-1 gene therapy, which involves the delivery of the TRIM5α-HRH gene into CD4^(+) T-lymphocytes by lentiviral vectors (LVs). However, LVs containing TRIM5α-HRH have a low infectious titer, which prevents effective T cell modification. Here, we found that the expression of TRIM5α-HRH during pseudoviral particle production in HEK293 T cells, as well as the presence of the Eflα promoter in our construction are responsible for titer reduction. These results allow us to determine the directions for further optimization of LV with the TRIM5α-HRH gene to improve its infectious titer.
Collapse
Affiliation(s)
- F A Urusov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
- Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia
| | - D V Glazkova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - G M Tsyganova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - D V Pozdyshev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
| | - E V Bogoslovskaya
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - G A Shipulin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| |
Collapse
|
19
|
Kireev DE, Chulanov VP, Shipulin GA, Semenov AV, Tivanova EV, Kolyasnikova NM, Zueva EB, Pokrovskiy VV, Galli C. Serological diagnosis and prevalence of HIV-1 infection in Russian metropolitan areas. BMC Infect Dis 2021; 21:24. [PMID: 33413197 PMCID: PMC7791727 DOI: 10.1186/s12879-020-05695-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND HIV infection is a major health problem in Russia. We aimed to assess HIV prevalence in different population groups and to compare the characteristics of 4th generation immunoassays from Abbott, Bio-Rad, Vector-Best, Diagnostic Systems, and Medical Biological Unit. METHODS The study included 4452 individuals from the general population (GP), 391 subjects at high risk of HIV infection (HR) and 699 with potentially interfering conditions. HIV positivity was confirmed by immunoblot and by HIV RNA, seroconversion and virus diversity panels were also used. HIV avidity was employed to assess recent infections. RESULTS The prevalence in GP was 0.40%, higher in males (0.62%) and in people aged < 40 years (0.58%). Patients attending dermo-venereal centers and drug users had a high prevalence (34.1 and 58.8%). Recent infections were diagnosed in 20% of GP and in 4.2% of HR. Assay sensitivity was 100% except for one false negative (99,54%, MBU). Specificity was 99.58-99.89% overall, but as low as 93.26% on HR (Vector-Best). Small differences on early seroconversion were recorded. Only the Abbott assay detected all samples on the viral diversity panel. CONCLUSION HIV infection rate in the high-risk groups suggests that awareness and screening campaigns should be enhanced. Fourth generation assays are adequate but performance differences must be considered.
Collapse
Affiliation(s)
- D E Kireev
- Federal Budget Institute of Science Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Novogireyevskaya St., 3A, 111123, Moscow, Russia.
| | - V P Chulanov
- Federal Budget Institute of Science Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Novogireyevskaya St., 3A, 111123, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - G A Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, Moscow, Russia
| | - A V Semenov
- St. Petersburg Pasteur Research Institute of Epidemiology and Microbiology, St. Petersburg, Russia
- North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Russia
| | - E V Tivanova
- Federal Budget Institute of Science Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Novogireyevskaya St., 3A, 111123, Moscow, Russia
| | - N M Kolyasnikova
- Federal Budget Institute of Science Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Novogireyevskaya St., 3A, 111123, Moscow, Russia
| | - E B Zueva
- St. Petersburg Pasteur Research Institute of Epidemiology and Microbiology, St. Petersburg, Russia
| | - V V Pokrovskiy
- Federal Budget Institute of Science Central Research Institute of Epidemiology Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor), Novogireyevskaya St., 3A, 111123, Moscow, Russia
| | - C Galli
- Abbott Diagnostics, Rome, Italy
| |
Collapse
|
20
|
Glazkova DV, Urusov FA, Bogoslovskaya EV, Shipulin GA. [Retrovirus Restriction Factor TRIM5α: The Mechanism of Action and Prospects for Use in Gene Therapy of HIV Infection]. Mol Biol (Mosk) 2020; 54:707-717. [PMID: 33009785 DOI: 10.31857/s0026898420050031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/16/2020] [Indexed: 11/24/2022]
Abstract
It is commonly known that the antiviral activity of the TRIM5α protein, the intracellular retrovirus restriction factor, underlies the resistance of the Old World monkeys to HIV-1. This fact suggests that TRIM5α can potentially be used to cure HIV-1 infection in humans. The present review considers the mechanisms of HIV-1 replication inhibition by the TRIM5a protein and the prospects for using it in gene therapy of HIV infection.
Collapse
Affiliation(s)
- D V Glazkova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia.,Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia
| | - F A Urusov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia.,Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia.,
| | - E V Bogoslovskaya
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| | - G A Shipulin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of the Russian Federation, Moscow, 119992 Russia
| |
Collapse
|
21
|
Orlova OV, Glazkova DV, Tsyganova GM, Antoshkina IV, Mintaev RR, Tikhonov AS, Bogoslovskaya EV, Shipulin GA. Application of real-time PCR to significantly reduce the time to obtain recombinant MVA virus. J Virol Methods 2020; 289:114056. [PMID: 33359615 DOI: 10.1016/j.jviromet.2020.114056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
Obtaining a pure recombinant Modified Vaccinia Ankara (MVA) virus is a multistage, time-consuming procedure. We describe a novel single-tube real-time PCR which enables determination of the amount of wild type and recombinant viruses and their ratio in plaques. Use of the real-time PCR significantly reduce the time and efforts needed to obtain purified recombinant MVA. The new approach has been applied to generate recombinant MVAs encoding different SARS-COV-2 antigens.
Collapse
Affiliation(s)
- O V Orlova
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia.
| | - D V Glazkova
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| | - G M Tsyganova
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| | - I V Antoshkina
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| | - R R Mintaev
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia; I. Mechnikov Research Institute of Vaccines and Sera, 105064, Moscow, Russia
| | - A S Tikhonov
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| | - E V Bogoslovskaya
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| | - G A Shipulin
- Federal State Budgetary Institution «Centre for Strategic Planning and Management of Biomedical Health Risks» of the Federal Medical Biological Agency", 119121, Moscow, Russia
| |
Collapse
|
22
|
Kireev DE, Farzan VM, Shipulin GA, Korshun VA, Zatsepin TS. RT-qPCR Detection of Low-Copy HIV RNA with Yin-Yang Probes. Methods Mol Biol 2020; 2063:27-35. [PMID: 31667760 DOI: 10.1007/978-1-0716-0138-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Accurate monitoring of low levels of viral load (the number of viral particles per milliliter of plasma) in HIV-infected patients is important in terms of evaluation of the progress of antiretroviral therapy. The general approach for detection of low copy HIV RNA is reverse transcription combined with quantitative real-time PCR based on fluorescence detection. The selection of primers and the structure of fluorogenic oligonucleotide probes are crucial for sensitivity and accuracy of the assay. In this chapter, we report the RT-qPCR protocol for detection of low copy HIV RNA using double stranded Yin-Yang DNA probes containing identical fluorescent dyes on each strand of the probe. Dye residues attached to the 3'-end of an oligonucleotide and 5'-end of the complementary oligonucleotide form a self-quenched aggregate in a Yin-Yang duplex probe, and display fluorescence light up upon probe strand displacement with the target sequence amplified in the course of PCR. Among several fluorescent dyes tested (R6G, ROX, Cy5) the ROX labeled Yin-Yang probes showed better fluorescence increase and lower Ct values. All the homo Yin-Yang probes were superior to corresponding dye-quencher probes and allowed reliable detection of 10-10,000 copies of HIV RNA per mL.
Collapse
Affiliation(s)
| | | | - German A Shipulin
- Federal State Budgetary Institution "Center for Strategic Planning and Management of Biomedical Health Risks" of the Ministry of Health, Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Gause Institute of New Antibiotics, Moscow, Russia.,Department of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Moscow, Russia. .,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
| |
Collapse
|
23
|
Kuleshov KV, Margos G, Fingerle V, Koetsveld J, Goptar IA, Markelov ML, Kolyasnikova NM, Sarksyan DS, Kirdyashkina NP, Shipulin GA, Hovius JW, Platonov AE. Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome. BMC Genomics 2020; 21:16. [PMID: 31906865 PMCID: PMC6945570 DOI: 10.1186/s12864-019-6388-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the causative agents of Lyme borreliosis and relapsing fever group Borrelia. Borrelia miyamotoi belongs to the relapsing fever group of spirochetes and forms distinct populations in North America, Asia, and Europe. As all Borrelia species B. miyamotoi possess an unusual and complex genome consisting of a linear chromosome and a number of linear and circular plasmids. The species is considered an emerging human pathogen and an increasing number of human cases are being described in the Northern hemisphere. The aim of this study was to produce a high quality reference genome that will facilitate future studies into genetic differences between different populations and the genome plasticity of B. miyamotoi. RESULTS We used multiple available sequencing methods, including Pacific Bioscience single-molecule real-time technology (SMRT) and Oxford Nanopore technology (ONT) supplemented with highly accurate Illumina sequences, to explore the suitability for whole genome assembly of the Russian B. miyamotoi isolate, Izh-4. Plasmids were typed according to their potential plasmid partitioning genes (PF32, 49, 50, 57/62). Comparing and combining results of both long-read (SMRT and ONT) and short-read methods (Illumina), we determined that the genome of the isolate Izh-4 consisted of one linear chromosome, 12 linear and two circular plasmids. Whilst the majority of plasmids had corresponding contigs in the Asian B. miyamotoi isolate FR64b, there were only four that matched plasmids of the North American isolate CT13-2396, indicating differences between B. miyamotoi populations. Several plasmids, e.g. lp41, lp29, lp23, and lp24, were found to carry variable major proteins. Amongst those were variable large proteins (Vlp) subtype Vlp-α, Vlp-γ, Vlp-δ and also Vlp-β. Phylogenetic analysis of common plasmids types showed the uniqueness in Russian/Asian isolates of B. miyamotoi compared to other isolates. CONCLUSIONS We here describe the genome of a Russian B. miyamotoi clinical isolate, providing a solid basis for future comparative genomics of B. miyamotoi isolates. This will be a great impetus for further basic, molecular and epidemiological research on this emerging tick-borne pathogen.
Collapse
Affiliation(s)
- Konstantin V Kuleshov
- Central Research Institute of Epidemiology, Moscow, 111123, Russia. .,Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia.
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764, Oberschleissheim, Germany.
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764, Oberschleissheim, Germany
| | - Joris Koetsveld
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Irina A Goptar
- Izmerov Research Institute of Occupational Health, Moscow, Russia
| | | | - Nadezhda M Kolyasnikova
- Central Research Institute of Epidemiology, Moscow, 111123, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and- Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Denis S Sarksyan
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Izhevsk State Medical Academy, Izhevsk, Russia
| | | | - German A Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, Moscow, Russia
| | - Joppe W Hovius
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | |
Collapse
|
24
|
Karan LS, Makenov MT, Korneev MG, Sacko N, Boumbaly S, Yakovlev SA, Kourouma K, Bayandin RB, Gladysheva AV, Shipovalov AV, Yurganova IA, Grigorieva YE, Fedorova MV, Scherbakova SA, Kutyrev VV, Agafonov AP, Maksyutov RA, Shipulin GA, Maleev VV, Boiro M, Akimkin VG, Popova AY. Bombali Virus in Mops condylurus Bats, Guinea. Emerg Infect Dis 2019; 25. [PMID: 31310231 PMCID: PMC6711222 DOI: 10.3201/eid2509.190581] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In 2018, a previously unknown Ebola virus, Bombali virus, was discovered in Sierra Leone. We describe detection of Bombali virus in Guinea. We found viral RNA in internal organs of 3 Angolan free-tailed bats (Mops condylurus) trapped in the city of N’Zerekore and in a nearby village.
Collapse
|
25
|
Zatsepin TS, Varizhuk AM, Dedkov VG, Shipulin GA, Aralov AV. Oligonucleotide Primers with G 8AE-Clamp Modifications for RT-qPCR Detection of the Low-Copy dsRNA. Methods Mol Biol 2019; 1973:281-297. [PMID: 31016709 DOI: 10.1007/978-1-4939-9216-4_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a new technique suitable for improved detection of low-copy dsRNA using modified oligonucleotides as primers in RT-qPCR. Insertion of G8AE-clamp residues into primers significantly improves thermal stability of duplexes with RNA without decrease of hybridization selectivity. The applicability of modified primers is demonstrated for detection of low-copy Kemerovo virus dsRNA.
Collapse
Affiliation(s)
- Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - German A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia.,Federal State Budgetary Institution "Center for Strategic Planning and Management of Biomedical Health Risks" of the Ministry of Health, Moscow, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
26
|
Dribnokhodova OP, Korchagin VI, Mironov KO, Dunaeva EA, Titkov AV, Akselrod EV, Raskurazhev AA, Tanashyan MM, Illarioshkin SN, Platonov AE, Shipulin GA. [A comparative analysis of allele frequencies of rs1801133 and rs1801131 of MTHFR in patients with stroke and healthy people from the Moscow region]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:18-23. [PMID: 31184621 DOI: 10.17116/jnevro201911903218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM To study genetic characteristics of the population of the Moscow region and analyze the association of rs1801133 and rs1801131 of MTHFR with the risk of ischemic stroke (IS). MATERIAL AND METHODS A sample of 170 and 115 patients with atherothrombotic and cardioembolic subtypes of IS and 360 residents of the Moscow region without IS were examined. MTHFR alleles were determined by a multiplex real-time polymerase chain reaction. RESULTS AND CONCLUSION No association between the frequencies of MTHFR alleles and the risk of ischemic stroke was found. The comparison of allele frequencies with those in Caucasian populations published in the dbSNP (NCBI) and 1000 Genomes Project databases revealed significant differences for rs1801133 from the EUR 1000 Genomes Project. The allele frequency data for MTHFR could increase the accuracy and reliability of the individual risk calculation for multifactorial diseases in the Russian population.
Collapse
Affiliation(s)
| | - V I Korchagin
- Central Research Institute of Epidemiology, Moscow, Russia
| | - K O Mironov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - E A Dunaeva
- Central Research Institute of Epidemiology, Moscow, Russia
| | - A V Titkov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - E V Akselrod
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | | | | | - A E Platonov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia
| |
Collapse
|
27
|
Litov AG, Deviatkin AA, Goptar IA, Dedkov VG, Gmyl AP, Markelov ML, Shipulin GA, Karganova GG. Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing. J Gen Virol 2019; 99:240-245. [PMID: 29393021 DOI: 10.1099/jgv.0.001003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.
Collapse
Affiliation(s)
- Alexander G Litov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Lomonosov MSU, Faculty of Biology, Lenin Hills, 1/12, Moscow 119234, Russia
| | - Andrey A Deviatkin
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Research Institute of Occupational Health, Moscow, Russia
| | - Irina A Goptar
- Research Institute of Occupational Health, Moscow, Russia
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Vladimir G Dedkov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - German A Shipulin
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Galina G Karganova
- Lomonosov MSU, Faculty of Biology, Lenin Hills, 1/12, Moscow 119234, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
| |
Collapse
|
28
|
Farzan VM, Kvach MV, Aparin IO, Kireev DE, Prikazchikova TA, Ustinov AV, Shmanai VV, Shipulin GA, Korshun VA, Zatsepin TS. Novel homo Yin-Yang probes improve sensitivity in RT-qPCR detection of low copy HIV RNA. Talanta 2019; 194:226-232. [DOI: 10.1016/j.talanta.2018.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/31/2022]
|
29
|
Gorbenko AS, Stolyar MA, Olkhovskiy IA, Abdullaev AO, Sudarikov AB, Dunaeva EA, Mironov KO, Shipulin GA. [Allele-specific polymerase chain reaction and electrophoretic detection in the detection algorithm clinically significant somatic mutations in the gene of calreticulin (calr).]. Klin Lab Diagn 2019; 63:588-592. [PMID: 30735328 DOI: 10.18821/0869-2084-2018-63-8-588-592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/11/2018] [Indexed: 11/17/2022]
Abstract
The detection of somatic mutations in the 9 exon of the calreticulin gene (CALR) is regulated by the clinical recommendations as a diagnostic criterion for chronic Ph-negative myeloproliferative neoplasms (MPN). Some methods of nucleic acids testing are used to identify CALR gene mutations with different requirements for special skills of personnel and expensive equipment. The purpose of this work is to compare the results of the detection of CALR gene mutations in venous blood samples by allele-specific RT-PCR with subsequent electrophoresis, fragment analysis and Sanger- or pyro- sequencing. We used 1284 blood samples of patients with suspected MPN and 20 blood donor samples. Mutations in the CALR gene of the I and II type were identified using PCR-RT with the original primers and TaqMan probes. Also, all samples were tested for mutations in the CALR gene by electrophoretic detection of PCR results in an agarose gel. The use of allele-specific RT-PCR followed by electrophoretic detection made it possible to determine clinically significant mutations in the CALR gene in 81 venous blood samples of JAK2- and MPL-negative patients, including 42 cases of type I mutation, 33 cases of type II mutation and 8 rare CALR mutations. Mutations in the 9 exon of the CALR gene were not detected in any of the 20 blood donor samples or in 121 blood samples of patients with polycythemia vera. In randomly selected 20 negative samples, CALR gene mutations were also not detected using Sanger sequencing. All positive samples were confirmed by fragment analysis, as well as with Sanger- sequencing and pyro- sequencing. The described combined approach to detect mutations of the CALR gene in peripheral blood samples can be used in clinical diagnostic laboratories that have a standard set of equipment for electrophoresis of nucleic acids and a PCR-RT. We also propose a confirmatory test based on the pyrosequencing of DNA using the system of genetic analysis "PyroMark Q24".
Collapse
Affiliation(s)
- A S Gorbenko
- Krasnoyarsk branch of the "National Research Center for Hematology", 660036, Krasnoyarsk, Russia
| | - M A Stolyar
- Krasnoyarsk branch of the "National Research Center for Hematology", 660036, Krasnoyarsk, Russia.,Federal Research Center "Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences", 660036, Krasnoyarsk, Russia
| | - I A Olkhovskiy
- Krasnoyarsk branch of the "National Research Center for Hematology", 660036, Krasnoyarsk, Russia.,Federal Research Center "Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences", 660036, Krasnoyarsk, Russia
| | - A O Abdullaev
- National Research Center for Hematology, 125167, Moscow, Russian Federation
| | - A B Sudarikov
- National Research Center for Hematology, 125167, Moscow, Russian Federation
| | - E A Dunaeva
- Central Research Institute of Epidemiology, 111123, Moscow, Russia
| | - K O Mironov
- Central Research Institute of Epidemiology, 111123, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, 111123, Moscow, Russia
| |
Collapse
|
30
|
Omelchenko DO, Speranskaya AS, Ayginin AA, Khafizov K, Krinitsina AA, Fedotova AV, Pozdyshev DV, Shtratnikova VY, Kupriyanova EV, Shipulin GA, Logacheva MD. Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products. Genes (Basel) 2019; 10:genes10020122. [PMID: 30736447 PMCID: PMC6409534 DOI: 10.3390/genes10020122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity. However, this method’s application in food analysis requires several methodology optimizations in DNA extraction, amplification and library preparation. In this study, we present such optimizations. The most important methodological outcomes are the following: (1) the DNA extraction method greatly influences amplification success; (2) the main problem for the application of metabarcoding is DNA purity, not integrity or quantity; and (3) the “non-amplifiable” samples can be amplified with polymerases resistant to inhibitors. Using this optimized workflow, we analysed a broad set of plant products (teas, spices and herbal remedies) using two NGS platforms. The analysis revealed the problem of both the presence of extraneous components and the absence of labelled ones. Notably, for teas, no correlation was found between the price and either the absence of labelled components or presence of unlabelled ones; for spices, a negative correlation was found between the price and presence of unlabelled components.
Collapse
Affiliation(s)
- Denis O Omelchenko
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
| | - Anna S Speranskaya
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Central Research Institute of Epidemiology, Novogireevskaya St. 3а, Moscow 111123, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Andrey A Ayginin
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Moscow Institute of Physics and Technology, Institutskiy Ln. 9, Dolgoprudny 141701, Moscow Region, Russia.
| | - Kamil Khafizov
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Central Research Institute of Epidemiology, Novogireevskaya St. 3а, Moscow 111123, Russia.
- Moscow Institute of Physics and Technology, Institutskiy Ln. 9, Dolgoprudny 141701, Moscow Region, Russia.
- Center for Strategic Planning, Ministry of Health of the Russian Federation, Pogodinskaya St. 10, build.1, Moscow 119121, Russia.
| | - Anastasia A Krinitsina
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Anna V Fedotova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Denis V Pozdyshev
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Viktoria Y Shtratnikova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - Evgenia V Kupriyanova
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| | - German A Shipulin
- Center for Strategic Planning, Ministry of Health of the Russian Federation, Pogodinskaya St. 10, build.1, Moscow 119121, Russia.
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.
- Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia.
| |
Collapse
|
31
|
Akselrod EV, Mironov KO, Mikhailenko DS, Efremov GD, Perepechin DV, Alekseiev BY, Potekhina ES, Shipulin GA. [The development and approbation of methodology on the basis of multiplex polymerase chain reaction in real-time to determine clinically significant micro-deletion in Y-chromosome.]. Klin Lab Diagn 2019; 63:124-128. [PMID: 30672679 DOI: 10.18821/0869-2084-2018-63-2-124-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/17/2017] [Indexed: 11/17/2022]
Abstract
One of the prevalent genetic causes of idiopathic male sterility is related to micro-deletions in AZF locus located in Y-chromosome. In total population, rate of such micro-deletions makes up to 1:4000. however, in infertile males their rate varies from 2% to 10%. In AZF locus three subregions are distinguished: AZFa, AZFb and AZFc. The loss of one or several subregions can result in disorder of spermatogenesis of various degree - from decreasing of its activity to Sertoli-cell syndrome manifested by azoospermia or oligospermia of severe degree. Therefore, implementation of genetic testing for presence of micro-deletions in AZF locus is a necessary test in case of prognosis of male sterility and its treatment. The purpose of study is to develop and test a diagnostic system of detection of micro-deletions in subregions of AZF locus using multiplex polymerase chain reaction in real-time. As a reference method a technique was implemented described in guidelines of the European Academy of Andrology conjointly with European Molecular Genetics Quality Network. The technique testing specified analysis of 33 samples of DNA separated from blood of males with azoospermia and oligospermia of severe degree. No discordant results were received as compared with reference method. In 27 DNA samples the deletions were detected in AZF locus: 4 AZFa deletions (15%), 2 AZFb deletions (7%), 17 AZFc deletions (63%) and 6 combined deletions of AZFb+candи AZFa+b+с (22%). The proposed technique permits detect micro-deletions of subregions of AZF locus.
Collapse
Affiliation(s)
- E V Akselrod
- The Federal Budget Institution of Science "The Central Research Institute of Epidemiology" of Rospotrebnadzor, 111123, Moscow, Russia
| | - K O Mironov
- The Federal Budget Institution of Science "The Central Research Institute of Epidemiology" of Rospotrebnadzor, 111123, Moscow, Russia
| | - D S Mikhailenko
- The Federal State Autonomous Educational Institution of Higher Education "The I.M. Sechenov First Moscow State Medical University" of Minzdrav of Russia, 119991, Moscow, Russia.,The N.A. Lopatkin research institute of urology and intervention radiology - the Branch of The Federal State Budget Scientific Institution "The National Medical Research Center" of Minzdrav of Russia, 105425, Moscow, Russia
| | - G D Efremov
- The N.A. Lopatkin research institute of urology and intervention radiology - the Branch of The Federal State Budget Scientific Institution "The National Medical Research Center" of Minzdrav of Russia, 105425, Moscow, Russia
| | - D V Perepechin
- The N.A. Lopatkin research institute of urology and intervention radiology - the Branch of The Federal State Budget Scientific Institution "The National Medical Research Center" of Minzdrav of Russia, 105425, Moscow, Russia
| | - B Ya Alekseiev
- The N.A. Lopatkin research institute of urology and intervention radiology - the Branch of The Federal State Budget Scientific Institution "The National Medical Research Center" of Minzdrav of Russia, 105425, Moscow, Russia
| | - E S Potekhina
- The Federal Budget Institution of Science "The Central Research Institute of Epidemiology" of Rospotrebnadzor, 111123, Moscow, Russia
| | - G A Shipulin
- The Federal Budget Institution of Science "The Central Research Institute of Epidemiology" of Rospotrebnadzor, 111123, Moscow, Russia
| |
Collapse
|
32
|
Abstract
Characterization of the within-host genetic diversity of viral pathogens is required for selection of effective treatment of some important viral infections, e.g. HIV, HBV and HCV. Despite the technical ability of detection, there are conflicting data regarding the clinical significance of low-frequency variants, partially because of the difficulty of their distinguishing from experimental artifacts. The issue of cross-contamination is relevant for all highly sensitive techniques, including deep sequencing: even trace contamination leads to a significant increase of false positives in identified SNVs. Determination of infections by multiple genotypes of some viruses, the incidence of which can be considerable, especially in risk groups, is also clinically significant in some cases. We developed a new viral reference-guided assembler, VirGenA, that can separate mixtures of strains of different intraspecies genetic groups (genotypes, subtypes, clades, etc.) and assemble a separate consensus sequence for each group in a mixture. It produced long assemblies for mixture components of extremely low frequencies (<1%) allowing detection of cross-contamination of samples by divergent genotypes. We tested VirGenA on both clinical and simulated data. On both types of data, VirGenA shows better or similar results than the existing de novo assemblers. Cross-platform implementation (including source code) is freely available at https://github.com/gFedonin/VirGenA/releases.
Collapse
Affiliation(s)
- Gennady G Fedonin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Yury S Fantin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexnader V Favorov
- Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University
| | - German A Shipulin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexey D Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| |
Collapse
|
33
|
Omelchenko DO, Glazkova DV, Bogoslovskaya EV, Urusov FA, Zhogina YA, Tsyganova GM, Shipulin GA. [Protection of Lymphocytes Against HIV using Lentivirus Vector Carrying a Combination of TRIM5α-HRH Genes and microRNA Against CCR5]. Mol Biol (Mosk) 2018; 52:294-305. [PMID: 29695698 DOI: 10.7868/s0026898418020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/24/2017] [Indexed: 11/23/2022]
Abstract
Gene therapy is considered a promising approach to treating infections caused by human immunodeficiency virus (HIV). One strategy is to introduce antiviral genes into cells in order to impart resistance to HIV. In this work, the antiviral activity of new anti-HIV lentiviral vector pT has been studied. The vector carries a combination that consists of two identical artificial miRNA mic13lg and the TRIM5α-HRH gene. Two mic13lg microRNAs suppress the expression of the CCR5 gene, which encodes the HIV coreceptor and, thus, prevents the penetration of R5-tropic HIV strains into the cell. It has been shown that pT effectively inhibits the expression of CCR5 in both the HT1080 CCR5-EGFP model cell line and in human primary lymphocytes. The second line of protection against R5- and X4-tropic HIV is provided by the TRIM5α-HRH protein, which binds virus capsids after the virus enters the cell. Indeed, when infecting cells of the SupT1 line, which contains four copies of the vector per cell, with the X-4 tropic HIV, more than 1000-fold suppression of viral replication has been observed. The process of generation of the pT vector and conditions of transduction of CD4^(+) lymphocytes were optimized for testing the antiviral activity of the vector on primary human lymphocytes. As a result, the transduction efficiency for the pT vector was 28%. After infection with the R5-tropic strain of the virus, the survival of cells in the culture of lymphocytes with the vector was significantly higher than in the control. However, the complete suppression of HIV replication was not achieved, presumably due to the inadequate fraction of cells that carry the vector in culture. In the future, it is planned to find the best way to enrich the lymphocyte culture with modified cells to increase resistance to HIV.
Collapse
Affiliation(s)
- D O Omelchenko
- Central Research Institute of Epidemiology, Moscow, 111123 Russia.,
| | - D V Glazkova
- Central Research Institute of Epidemiology, Moscow, 111123 Russia
| | | | - F A Urusov
- Central Research Institute of Epidemiology, Moscow, 111123 Russia
| | - Y A Zhogina
- Central Research Institute of Epidemiology, Moscow, 111123 Russia
| | - G M Tsyganova
- Central Research Institute of Epidemiology, Moscow, 111123 Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, 111123 Russia
| |
Collapse
|
34
|
Speranskaya AS, Khafizov K, Ayginin AA, Krinitsina AA, Omelchenko DO, Nilova MV, Severova EE, Samokhina EN, Shipulin GA, Logacheva MD. Comparative analysis of Illumina and Ion Torrent high-throughput sequencing platforms for identification of plant components in herbal teas. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.04.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
35
|
Shelenkov AA, Karan LS, Mihaylova YV, Yanushevich YG, Shipulin GA, Shagin DA. First whole genome sequencing of Russian isolate of Capnocytophaga canimorsus, opportunistic pathogen causing lethal sepsis. Microb Pathog 2018; 125:493-496. [PMID: 30342910 DOI: 10.1016/j.micpath.2018.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
Abstract
Capnocytophaga canimorsus is a part of healthy oral flora of dogs and cats. However, when it is transmitted to human subjects via animal bites or scratches, it can cause severe complications like endocarditis or even lethal septic shock, especially in immunocompromised persons. In this study, we performed the first whole-genome sequencing on Illumina HiSeq platform of Russian isolate of C. canimorsus that have caused lethal sepsis in 51-old male from Moscow. We believe that the availability of genomic sequence and annotation for the given strain could be useful for future epidemiological surveillance studies in Russia and other countries.
Collapse
Affiliation(s)
- Andrey A Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia
| | - Lyudmila S Karan
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia
| | - Yulia V Mihaylova
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia
| | - Yuri G Yanushevich
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia
| | - Dmitriy A Shagin
- Central Research Institute of Epidemiology, Novogireevskaya str. 3a, Moscow, 111123, Russia.
| |
Collapse
|
36
|
Bagautdinova LI, Platonov AE, Sarksyan DS, Stukolova OV, Shipulin GA, Maleev VV, Dudarev MV. [Follow-up of patients with Ixodes tick-borne borrelioses caused by Borrelia miyamotoi or Borrelia burgdorferi sensu lato]. TERAPEVT ARKH 2018; 88:43-54. [PMID: 28005031 DOI: 10.17116/terarkh2016881143-54] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Ixodes tick-borne borrelioses (ITBB) are caused by two different spirochetes: Borrelia from the group of Borrelia burgdorferi sensu lato, the agents of the classic Lyme borreliosis (LB), and Borrelia miyamotoi that belongs to the group of Borrelia causing tick-borne relapsing fevers. ITBB caused by B. miyamotoi (BM-ITBB) is a previously unknown infectious disease discovered in Russia. It is known that the LB sequelae may reduce the long-term life guality of convalescents. AIM To study the follow-up of those who have recovered from new BM-ITBB infection in comparison with persons who have had LB. SUBJECTS AND METHODS The investigation enrolled 41 patients with BM-ITBB and 41 patients with LB who were treated at the Republican Infectious Diseases Hospital of Udmurtia. Within a year after the disease, they were followed up through clinical and instrumental examination of cardiac performance, expanded biochemical analysis of blood and urine, which could; estimate kidney and liver functions, and psychological questioning. RESULTS Asthenic syndrome and complaints about and objective signs of cardiac dysfunctions persisted supraventricular extrasystoles, left ventricular diastolic dysfunction, and elevated and/or unstable systolic blood pressure were detected in 20-30% of the convalescents for a long time. Kidney dysfunctions were manifested in albuminuria and the decrease of glomerular filtration rate. A year following the disease, 10-20% patients had persistently elevated concentrations of alanine aminotransferase, aspartate aminotransferase, and C-reactive protein and had higher levels of total cholesterol and low-density lipoproteins. The pathological consequences of ITBB were polymorphic and varied in different patients; in general, only 68% of them showed health improvement. CONCLUSION We assume that a significant role in the pathogenesis of BM-ITBB and LB is played by vascular endothelial damage possibly associated with the inflammatory and autoimmune aspects of an immune response in Borrelia infection. The consequences of this damage may persist and even intensify during a year, which provokes chronic dysfunction of the heart, kidney, or liver in a number of convalescents.
Collapse
Affiliation(s)
- L I Bagautdinova
- Izhevsk State Medical Academy, Ministry of Health of Russia, Izhevsk, Republic of Udmurtia, Russia
| | - A E Platonov
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - D S Sarksyan
- Izhevsk State Medical Academy, Ministry of Health of Russia, Izhevsk, Republic of Udmurtia, Russia
| | - O V Stukolova
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V V Maleev
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - M V Dudarev
- Izhevsk State Medical Academy, Ministry of Health of Russia, Izhevsk, Republic of Udmurtia, Russia
| |
Collapse
|
37
|
Lapovok IA, Lopatukhin AE, Kireev DE, Kazennova EV, Lebedev AV, Bobkova MR, Kolomeets AN, Turbina GI, Shipulin GA, Ladnaya NN, Pokrovsky VV. [Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015]. TERAPEVT ARKH 2018; 89:44-49. [PMID: 29260745 DOI: 10.17116/terarkh2017891144-49] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. SUBJECTS AND METHODS The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. RESULTS The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. CONCLUSION The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.
Collapse
Affiliation(s)
- I A Lapovok
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - A E Lopatukhin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - D E Kireev
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - E V Kazennova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A V Lebedev
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
| | - A N Kolomeets
- Omsk Research Institute of Natural Focal Infections, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G I Turbina
- Lipetsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Lipetsk, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - N N Ladnaya
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V V Pokrovsky
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| |
Collapse
|
38
|
Kostyushev DS, Zueva AP, Brezgin SA, Lipatnikov AD, Simirskii VN, Glebe D, Volchkova EV, Shipulin GA, Chulanov VP. [Overexpression of DNA-methyltransferases in persistency of cccDNA pool in chronic hepatitis B]. TERAPEVT ARKH 2018; 89:21-26. [PMID: 29260742 DOI: 10.17116/terarkh2017891121-26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AIM To define the role of DNA-methyltransferases of type 1 and type 3A in hepatitis B viral cycle. MATERIAL AND METHODS Human hepatoma cells HepG2 with stable expression of 1.1-mer HBV genome were transfected with vectors encoding DNA-methyltransferase 1 (DNMT1), DNA-methyltransferase 3A (DNMT3A) or were co-transfected with these vectors. Total HBV DNA copy number, relative expression of pregenomic RNA (pgRNA), S-protein-encoding RNA (S-RNA) and cccDNA were analyzed by quantitative and semi-quantitative real-time PCR-analysis with TaqMan probes for assessment of DNMTs-mediated effects on HBV. RESULTS DNMT1 and DNMT3A suppress HBV transcription and replication, though to different magnitude. cccDNA pool is enlarged statistically significantly ≈2-fold (P<0.005) after transfection of DNMT3A, but is unaltered under DNMT1 treatment. CONCLUSION DNMT3A regulates the size of cccDNA pool and is important for persistency of HBV infection.
Collapse
Affiliation(s)
- D S Kostyushev
- Central Research Institute of Epidemiology, Moscow, Russia
| | - A P Zueva
- Central Research Institute of Epidemiology, Moscow, Russia; M.V. Lomonosov Moscow State University, Moscow, Russia
| | - S A Brezgin
- Central Research Institute of Epidemiology, Moscow, Russia; I.M. Sechenov First State Medical University, Moscow, Russia
| | - A D Lipatnikov
- Central Research Institute of Epidemiology, Moscow, Russia; D.I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - V N Simirskii
- N.K. Koltzov Institute of Developmental Biology, Moscow, Russia
| | - D Glebe
- Justus-Liebig University of Giessen, Institute of Medical Virology, Giessen, Germany
| | - E V Volchkova
- I.M. Sechenov First State Medical University, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia
| | - V P Chulanov
- Central Research Institute of Epidemiology, Moscow, Russia; I.M. Sechenov First State Medical University, Moscow, Russia
| |
Collapse
|
39
|
Korchagin VI, Mironov KO, Platonov AE, Dribnokhodova OP, Akselrod EV, Dunaeva EA, Raskurazhev AA, Tanashyan MM, Maksimova MY, Illarioshkin SN, Shipulin GA. [Complex assessment of the contribution of genetic factors to the risk of ischemic stroke]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 117:11-18. [PMID: 29411740 DOI: 10.17116/jnevro201711712211-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AIM To develop a method of the complex assessment of genetic risk for ischemic stroke (IS) and evaluate its effectiveness. MATERIAL AND METHODS Genotyping of 182 patients with atherothrombotic and cardioembolic subtypes of IS and 360 healthy individuals of 48 single nucleotide polymorphic loci (SNP) associated with the risk of II and its subtypes was performed. RESULTS AND CONCLUSION In each group of SNPs, composite indicators of genetic risk of IS in groups of patients and healthy controls were identified. Differences between the calculated values of the genetic risk in these groups were significant (p <0,05). The quality of the binary classification validated by ROC-analysis confirmed the predictive potential of the proposed method of risk calculation for determining the genetic predisposition to the development of IS.
Collapse
Affiliation(s)
- V I Korchagin
- Central Research Institute of Epidemiology, Moscow, Russia
| | - K O Mironov
- Central Research Institute of Epidemiology, Moscow, Russia
| | - A E Platonov
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | - E V Akselrod
- Central Research Institute of Epidemiology, Moscow, Russia
| | - E A Dunaeva
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | | | | | | | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia
| |
Collapse
|
40
|
Dedkov VG, Magassouba N, Safonova MV, Bodnev SA, Pyankov OV, Camara J, Sylla B, Agafonov AP, Maleev VV, Shipulin GA. Sensitive Multiplex Real-time RT-qPCR Assay for the Detection of Filoviruses. Health Secur 2018; 16:14-21. [DOI: 10.1089/hs.2017.0027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
41
|
Kuleshov KV, Vodop'ianov SO, Dedkov VG, Markelov ML, Deviatkin AA, Kruglikov VD, Vodop'ianov AS, Pisanov RV, Mazrukho AB, Titova SV, Maleev VV, Shipulin GA. Travel-Associated Vibrio cholerae O1 El Tor, Russia. Emerg Infect Dis 2018; 22:2006-2008. [PMID: 27767910 PMCID: PMC5088018 DOI: 10.3201/eid2211.151727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
42
|
Platonov AE, Toporkova MG, Kolyasnikova NM, Stukolova OA, Dolgova AS, Brodovikova AV, Makhneva NA, Karan LS, Koetsveld J, Shipulin GA, Maleev VV. Clinical presentation of Ixodes tick-borne borreliosis caused by Borrelia miyamotoi in the context of an immune response to the pathogen. TERAPEVT ARKH 2017; 89:35-43. [DOI: 10.17116/terarkh2017891135-43] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ixodes tick-borne borreliosis caused by Borrelia miyamotoi (ITBB-BM) is a previously unknown infectious disease discovered in Russia. Aim. The present study continues the investigation of the clinical features of ITBB-BM in the context of an immune system-pathogen interaction. Subjects and methods. The study enrolled 117 patients with ITBB-BM and a comparison group of 71 patients with Lyme disease (LD) that is ITBB with erythema migrans. All the patients were treated at the New Hospital, Yekateringburg. More than 100 clinical, epidemiological and laboratory parameters were obtained from each patient’s medical history and included in the general database. A subset of patients hospitalized in 2015 and 2016 underwent additional laboratory examinations. Namely, the levels of B. miyamotoi-specific IgM and IgG antibodies were measured by the protein microarray containing GlpQ protein and four variable major proteins (VMPs): Vlp15/16, Vlp18, Vsp1, and Vlp5. The blood concentration of Borrelia was estimated by quantitative real-time PCR. Results. In contrast to LD, first of all (p
Collapse
|
43
|
Farzan VM, Ulashchik EA, Martynenko-Makaev YV, Kvach MV, Aparin IO, Brylev VA, Prikazchikova TA, Maklakova SY, Majouga AG, Ustinov AV, Shipulin GA, Shmanai VV, Korshun VA, Zatsepin TS. Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Bioconjug Chem 2017; 28:2599-2607. [PMID: 28921968 DOI: 10.1021/acs.bioconjchem.7b00462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a novel technique for the efficient conjugation of oligonucleotides with various alkyl azides such as fluorescent dyes, biotin, cholesterol, N-acetylgalactosamine (GalNAc), etc. using copper-catalysed alkyne-azide cycloaddition on the solid phase and CuI·P(OEt)3 as a catalyst. Conjugation is carried out in an oligonucleotide synthesizer in fully automated mode and is coupled to oligonucleotide synthesis and on-column deprotection. We also suggest a set of reagents for the construction of diverse conjugates. The sequential double-click procedure using a pentaerythritol-derived tetraazide followed by the addition of a GalNAc or Tris-GalNAc alkyne gives oligonucleotide-GalNAc dendrimer conjugates in good yields with minimal excess of sophisticated alkyne reagents. The approach is suitable for high-throughput synthesis of oligonucleotide conjugates ranging from fluorescent DNA probes to various multi-GalNAc derivatives of 2'-modified siRNA.
Collapse
Affiliation(s)
- Valentina M Farzan
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Yury V Martynenko-Makaev
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Maksim V Kvach
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Tatiana A Prikazchikova
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Svetlana Yu Maklakova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia
| | - Alexander G Majouga
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,National University of Science and Technology "MISiS" , Leninskiy Prospect 4, Moscow 119991, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Gause Institute of New Antibiotics , Bolshaya Pirogovskaya 11, Moscow 119021, Russia
| | - Timofei S Zatsepin
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia.,Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
| |
Collapse
|
44
|
Dedkov VG, Shchelkanov MY, Bushkieva BT, Rudenko TA, Kurdyukova OV, Galkina IV, Sapotsky MV, Blinova EA, Dzhambinov SD, Shipulin GA. A neonatal death associated with Crimean-Congo hemorrhagic fever (Republic of Kalmykia, Russia, June 2016). Antiviral Res 2017; 146:146-148. [PMID: 28870741 DOI: 10.1016/j.antiviral.2017.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Vladimir G Dedkov
- Central Research Institute for Epidemiology, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia; Research Institute of Occupational Health, Moscow, Russia.
| | - Mikhail Yu Shchelkanov
- Far Eastern Federal University, Vladivostok, Russia; Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, Russia; National Scientific Center of Marine Biology, Vladivostok, Russia
| | - Bella Tc Bushkieva
- Center for Hygiene and Epidemiology in the Republic of Kalmykia, Elista, Russia
| | - Tatyana A Rudenko
- Center of Specialized Types of Medical Care in the Republic of Kalmykia, Elista, Russia
| | | | | | - Mikhail V Sapotsky
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, Russia
| | - Ekaterina A Blinova
- Central Research Institute for Epidemiology, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | | | - German A Shipulin
- Central Research Institute for Epidemiology, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| |
Collapse
|
45
|
Deviatkin AA, Lukashev AN, Markelov MM, Gmyl LV, Shipulin GA. Enrichment of Viral Nucleic Acids by Solution Hybrid Selection with Genus Specific Oligonucleotides. Sci Rep 2017; 7:9752. [PMID: 28852181 PMCID: PMC5575070 DOI: 10.1038/s41598-017-10342-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Despite recent advances, our knowledge of potential and rare human pathogens is far from exhaustive. Current molecular diagnostic tools mainly rely on the specific amplification of marker sequences and may overlook infections caused by unknown and rare pathogens. Using high-throughput sequencing (HTS) can solve this problem; but, due to the extremely low fraction of pathogen genetic material in clinical samples, its application is only cost-effective in special, rather than routine, cases. In this study, we present a method for the semi-specific enrichment of viral conservative sequences in a HTS library by hybridization in solution with genus-specific degenerate biotinylated oligonucleotides. Nucleic acids of the test viruses (yellow fever virus and Japanese encephalitis virus) were enriched by solution hybrid selection using pan-flavivirus oligonucleotides. Moreover, enterovirus (family: Picornaviridae, genus: Enterovirus) sequences were successfully enriched using foot-and-mouth disease virus (family: Picornaviridae, genus: Aphthovirus) oligonucleotide. The enrichment factor relative to the background nucleic acid was about 1,000-fold. As hybridization has less stringent oligonucleotide match requirements than PCR, few oligonucleotides are sufficient to cover the potential sequence variation in the whole genus and may even enrich nucleic acids of viruses of other related genera. Efficient enrichment of viral sequences makes its use in diagnostics cost-efficient.
Collapse
Affiliation(s)
- Andrei A Deviatkin
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, Moscow, Russian Federation. .,Research Institute of Occupational Health, Moscow, Russian Federation.
| | - Alexander N Lukashev
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Larisa V Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, Moscow, Russian Federation
| | - German A Shipulin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
| |
Collapse
|
46
|
Dedkov VG, Simonova EG, Beshlebova OV, Safonova MV, Stukolova OA, Verigina EV, Savinov GV, Karaseva IP, Blinova EA, Granitov VM, Arsenjeva IV, Shipulin GA. The burden of tick-borne diseases in the Altai region of Russia. Ticks Tick Borne Dis 2017. [PMID: 28648773 DOI: 10.1016/j.ttbdis.2017.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This article presents the results of a comprehensive survey of the burden of tick-borne infectious diseases (TBIDs) in the Altai region of Russia. Official data for TBID incidence were analyzed and 201 samples from patients with suspected TBID were studied. Furthermore, questing ticks and ticks recovered from humans were examined to estimate prevalence of TBID-causative agents. The Altai region was determined to have a heightened risk for TBIDs in Russia. The most epidemiologically significant tick-borne illness in this area is spotted fever group rickettsiosis, while nationally in Russia, the leading TBID is Lyme borreliosis. The prevalence of mixed infection was 12.4% among the studied cases. Additionally, the prevalence of poorly studied pathogens - Kemerovo virus (KEMV) and Rickettsia tarasevichiae - in ticks from the Altai region was determined.
Collapse
Affiliation(s)
- V G Dedkov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia; Research Institute of Occupational Health, Moscow, Russia.
| | - E G Simonova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia; I.M. Sechenov First Moscow Medical University, Moscow, Russia
| | | | - M V Safonova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - O A Stukolova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - E V Verigina
- I.M. Sechenov First Moscow Medical University, Moscow, Russia
| | - G V Savinov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - I P Karaseva
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - E A Blinova
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | | | | | - G A Shipulin
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| |
Collapse
|
47
|
Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
Collapse
Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
| |
Collapse
|
48
|
Deviatkin AA, Lukashev AN, Poleshchuk EM, Dedkov VG, Tkachev SE, Sidorov GN, Karganova GG, Galkina IV, Shchelkanov MY, Shipulin GA. The phylodynamics of the rabies virus in the Russian Federation. PLoS One 2017; 12:e0171855. [PMID: 28225771 PMCID: PMC5321407 DOI: 10.1371/journal.pone.0171855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/26/2017] [Indexed: 12/25/2022] Open
Abstract
Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split into three groups (C0-C2) with discrete geographic prevalence. A single strain of the steppe rabies virus lineage was isolated in the far eastern part of Russia (Primorsky Krai), likely as a result of a recent anthropogenic introduction. For the first time the polar rabies virus group A2, previously reported in Alaska, was described in the northern part of European Russia and at the Franz Josef Land. Phylogenetic analysis suggested that all currently circulating rabies virus groups in the Russian Federation were introduced within the few last centuries, with most of the groups spreading in the 20th century. The dating of evolutionary events was highly concordant with the historical epidemiological data.
Collapse
Affiliation(s)
- Andrei A. Deviatkin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Alexander N. Lukashev
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- RUDN University, Moscow, Russia
| | | | - Vladimir G. Dedkov
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Sergey E. Tkachev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk, Russian Federation
| | - Gennadiy N. Sidorov
- Institute for Natural Foci Infections, Omsk, Russian Federation
- Omsk State Pedagogical University, Omsk, Russian Federation
| | - Galina G. Karganova
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
| | | | - Mikhail Yu. Shchelkanov
- Far Eastern Federal University, Vladivostok, Russian Federation
- Institute of Biology and Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russian Federation
| | - German A. Shipulin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
| |
Collapse
|
49
|
Dunaeva EA, Mironov KO, Subbotina TN, Olkhovsky IA, Shipulin GA. [The development and comparative approbation of methods of increasing sensitivity of detection of mutation V617F in gene JAK2 by pyro-sequencing]. Klin Lab Diagn 2017; 62:125-128. [PMID: 30615403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The possibilities of early detection of chronic myelo-proliferative tumors (MPT) are determined by sensitivity of techniques implemented for finding somatic mutation V617F in gene JAK2. The mutation V617F can also be found in individuals without unfolded picture of hematological diseases. The detection of mutation even in low concentrations is associated with increasing of risk of cerebral stroke and thrombosis of arterial and venous vessels. The study was carried out to develop techniques based on COLD polymerase chain reaction and allele-specific polymerase chain reaction targeted to increasing of sensitivity of finding mutation V617F detected using pyro-sequencing. The analytical sensitivity of techniques was evaluated by control samples with different ratio of alleles. For allele-specific polymerase chain reaction analytical sensitivity amounted to 0.25% of mutant allele at concentration of analyzed control sample 10 copies of DNA per mkl. For COLD polymerase chain reaction sensitivity amounted to 0.5% at concentration 10 copies of DNA per mkl. The comparative approbation of techniques was implemented using clinical material obtained from 106 patients with suspicion on MPT. The analysis of clinical samples using COLD polymerase chain reaction revealed 13 (14%) and using technique of allele-specific polymerase chain reaction - 15 (16%) positive samples. In all 15 cases of detection of mutation clinical confirmations of diagnosis of MPT was received. The proposed techniques permit increasing efficiency of amplification of mutant DNA in analyzed samples and hence to increase sensitivity of subsequent analysis of products of amplification using technique of pyro-sequencing. Therefore, the mentioned techniques can be recommended to be applied for confirmation of diagnosis of MPT and early identification of individuals with increased risk of development of venous and arterial thromboses.
Collapse
|
50
|
Farzan VM, Markelov ML, Skoblov AY, Shipulin GA, Zatsepin TS. Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers. Analyst 2017; 142:945-950. [DOI: 10.1039/c6an02441f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dissection of stem and loop regions in molecular beacons by nucleotide or non-nucleotide linkers minimizes nonspecific recognition in SNP discrimination.
Collapse
Affiliation(s)
- Valentina M. Farzan
- Skolkovo Institute of Science and Technology
- 3 Nobel Street
- Innovation Center “Skolkovo”
- 143026 Skolkovo
- Russia
| | | | | | | | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology
- 3 Nobel Street
- Innovation Center “Skolkovo”
- 143026 Skolkovo
- Russia
| |
Collapse
|