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Ivanova OE, Eremeeva TP, Morozova NS, Mikhailova YM, Kozlovskaya LI, Baikova OY, Shakaryan AK, Krasota AY, Korotkova EA, Yakovchuk EV, Shustova EY, Lukashev AN. Non-Polio Enteroviruses Isolated by Acute Flaccid Paralysis Surveillance Laboratories in the Russian Federation in 1998-2021: Distinct Epidemiological Features of Types. Viruses 2024; 16:135. [PMID: 38257835 PMCID: PMC10819661 DOI: 10.3390/v16010135] [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: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
More than 100 types of non-polio enteroviruses (NPEVs) are ubiquitous in the human population and cause a variety of symptoms ranging from very mild to meningitis and acute flaccid paralysis (AFP). Much of the information regarding diverse pathogenic properties of NPEVs comes from the surveillance of poliovirus, which also yields NPEV. The analysis of 265 NPEV isolations from 10,433 AFP cases over 24 years of surveillance and more than 2500 NPEV findings in patients without severe neurological lesions suggests that types EV-A71, E13, and E25 were significantly associated with AFP. EV-A71 was also significantly more common among AFP patients who had fever at the onset and residual paralysis compared to all AFP cases. In addition, a significant disparity was noticed between types that were common in humans (CV-A2, CVA9, EV-A71, E9, and E30) or in sewage (CVA7, E3, E7, E11, E12, and E19). Therefore, there is significant evidence of non-polio viruses being implicated in severe neurological lesions, but further multicenter studies using uniform methodology are needed for a definitive conclusion.
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Affiliation(s)
- Olga E. Ivanova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia
| | - Tatiana P. Eremeeva
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
| | - Nadezhda S. Morozova
- The Federal Budgetary Health Institution “Federal Center of Hygiene and Epidemiology” of the Federal Office for Inspectorate in the Field of Customers and Human Well-Being Protection”(FBHI FCH&E), 117105 Moscow, Russia
| | - Yulia M. Mikhailova
- The Federal Budgetary Health Institution “Federal Center of Hygiene and Epidemiology” of the Federal Office for Inspectorate in the Field of Customers and Human Well-Being Protection”(FBHI FCH&E), 117105 Moscow, Russia
| | - Liubov I. Kozlovskaya
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia
| | - Olga Y. Baikova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
| | - Armen K. Shakaryan
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
- Department of Childrenʹs Infectious Diseases, Pediatric Faculty, Pirogov Russian National Research Medical University, 119121 Moscow, Russia
| | - Alexandr Y. Krasota
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Ekaterina A. Korotkova
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Elizaveta V. Yakovchuk
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
| | - Elena Y. Shustova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia (E.V.Y.); (E.Y.S.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia
- Research Institute for Systems Biology and Medicine, 117246 Moscow, Russia
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Novozhilova TS, Chistyakov DS, Akhmadishina LV, Lukashev AN, Gerasimov ES, Yurchenko V. Genomic analysis of Leishmania turanica strains from different regions of Central Asia. PLoS Negl Trop Dis 2023; 17:e0011145. [PMID: 36877735 PMCID: PMC10019736 DOI: 10.1371/journal.pntd.0011145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/16/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023] Open
Abstract
The evolution in Leishmania is governed by the opposite forces of clonality and sexual reproduction, with vicariance being an important factor. As such, Leishmania spp. populations may be monospecific or mixed. Leishmania turanica in Central Asia is a good model to compare these two types. In most areas, populations of L. turanica are mixed with L. gerbilli and L. major. Notably, co-infection with L. turanica in great gerbils helps L. major to withstand a break in the transmission cycle. Conversely, the populations of L. turanica in Mongolia are monospecific and geographically isolated. In this work, we compare genomes of several well-characterized strains of L. turanica originated from monospecific and mixed populations in Central Asia in order to shed light on genetic factors, which may drive evolution of these parasites in different settings. Our results illustrate that evolutionary differences between mixed and monospecific populations of L. turanica are not dramatic. On the level of large-scale genomic rearrangements, we confirmed that different genomic loci and different types of rearrangements may differentiate strains originated from mixed and monospecific populations, with genome translocations being the most prominent example. Our data suggests that L. turanica has a significantly higher level of chromosomal copy number variation between the strains compared to its sister species L. major with only one supernumerary chromosome. This suggests that L. turanica (in contrast to L. major) is in the active phase of evolutionary adaptation.
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Affiliation(s)
| | - Daniil S. Chistyakov
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (ESG); (VY)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- * E-mail: (ESG); (VY)
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Ivanova OE, Shakaryan AK, Morozova NS, Vakulenko YA, Eremeeva TP, Kozlovskaya LI, Baykova OY, Shustova EY, Mikhailova YM, Romanenkova NI, Rozaeva NR, Dzhaparidze NI, Novikova NA, Zverev VV, Golitsyna LN, Lukashev AN. Cases of Acute Flaccid Paralysis Associated with Coxsackievirus A2: Findings of a 20-Year Surveillance in the Russian Federation. Microorganisms 2022; 10:microorganisms10010112. [PMID: 35056561 PMCID: PMC8780984 DOI: 10.3390/microorganisms10010112] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Surveillance for acute flaccid paralysis syndrome (AFP) in children under 15 is the backbone of the Global Polio Eradication Initiative. Laboratory examination of stool samples from AFP cases allows the detection of, along with polioviruses, a variety of non-polio enteroviruses (NPEV). The etiological significance of these viruses in the occurrence of AFP cases has been definitively established only for enteroviruses A71 and D68. Enterovirus Coxsackie A2 (CVA2) is most often associated with vesicular pharyngitis and hand, foot and mouth disease. Among 7280 AFP cases registered in Russia over 20 years (2001–2020), CVA2 was isolated only from five cases. However, these included three children aged 3 to 4 years, without overt immune deficiency, immunized with 4–5 doses of poliovirus vaccine in accordance with the National Vaccination Schedule. The disease resulted in persistent residual paralysis. Clinical and laboratory data corresponded to poliomyelitis developing during poliovirus infection. These findings are compatible with CVA2 being the cause of AFP. Molecular analysis of CVA2 from these patients and a number of AFP cases in other countries did not reveal association with a specific phylogenetic group, suggesting that virus genetics is unlikely to explain the pathogenic profile. The overall results highlight the value of AFP surveillance not just for polio control but for studies of uncommon AFP agents.
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Affiliation(s)
- Olga E. Ivanova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
| | - Armen K. Shakaryan
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Pirogov Russian National Research Medical University, 119121 Moscow, Russia
| | - Nadezhda S. Morozova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Tatyana P. Eremeeva
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Liubov I. Kozlovskaya
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Olga Y. Baykova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Elena Y. Shustova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Yulia M. Mikhailova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | | | - Nadezhda R. Rozaeva
- Saint-Petersburg Pasteur Institute, 197101 Saint-Petersburg, Russia; (N.I.R.); (N.R.R.)
| | - Natela I. Dzhaparidze
- Federal Budgetary Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in the Vladimir Region”, 600005 Vladimir, Russia;
| | - Nadezhda A. Novikova
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Vladimir V. Zverev
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Lyudmila N. Golitsyna
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
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Deviatkin AA, Vakulenko YA, Dashian MA, Lukashev AN. Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses. Viruses 2021; 14:66. [PMID: 35062270 PMCID: PMC8777955 DOI: 10.3390/v14010066] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hundred years ago and is responsible for several current outbreaks. A systematic analysis of aberrant long-distance events in the steppe and Arctic-like groups of rabies virus was performed using statistical (Bayesian) phylogeography and plots of genetic vs. geographic distances. The two approaches produced similar results but had some significant differences and complemented each other. No phylogeographic analysis could be performed for the Arctic group because polar foxes transfer the virus across the whole circumpolar region at high velocity, and there was no correlation between genetic and geographic distances in this virus group. In the Arctic-like group and the steppe subgroup of the cosmopolitan group, a significant number of known sequences (15-20%) was associated with rapid long-distance transfers, which mainly occurred within Eurasia. Some of these events have been described previously, while others have not been documented. Most of the recent long-distance transfers apparently did not result in establishing the introduced virus, but a few had important implications for the phylogeographic history of rabies. Thus, human-mediated long-distance transmission of the rabies virus remains a significant threat that needs to be addressed.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mariia A. Dashian
- Faculty of Biomedicine, Pirogov Medical University, 117997 Moscow, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
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de la Fuente J, Armas O, Sánchez-Rodríguez L, Gortázar C, Lukashev AN. Citizen science initiative points at childhood BCG vaccination as a risk factor for COVID-19. Transbound Emerg Dis 2021; 68:3114-3119. [PMID: 33825348 PMCID: PMC8251061 DOI: 10.1111/tbed.14097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/30/2020] [Revised: 03/01/2021] [Accepted: 04/01/2021] [Indexed: 12/14/2022]
Abstract
Current results do not provide conclusive evidence on the effect of BCG vaccination on COVID-19 alone or in combination with other factors. To address this limitation, in this study we used a citizen science initiative on the COVID-19 pandemic to collect data worldwide during 2 October 2020-30 October 2020 (1,233 individuals) in a structured way for analysing factors and characteristics of affected individuals in relation to BCG vaccination. For the first time, the results of our study suggested that vaccination with BCG may increase the risk for COVID-19 at certain age, particularly in individuals vaccinated at childhood. Childhood BCG vaccination increased the likelihood of being diagnosed with COVID-19 fivefold in COVID-19 low-incidence countries and threefold in high-incidence countries. A reasonable explanation for this effect is the activation of certain innate immunity mechanisms associated with inflammatory reactions. These factors should be considered when analysing the risks associated with this global pandemic.
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Affiliation(s)
- José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Octavio Armas
- Escuela de Ingeniería Industrial y Aeroespacial, University of Castilla La Mancha, Toledo, Spain
| | - Luis Sánchez-Rodríguez
- Escuela de Ingeniería Industrial y Aeroespacial, University of Castilla La Mancha, Toledo, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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Pokrovsky VS, Lukashev AN, Babayeva G, Karshieva SS, Arinbasarova AY, Medentzev AG, Komarova MV, Lukasheva EV. Plasma pharmacokinetics and tissue distribution of L-lysine α-oxidase from Trichoderma cf. aureoviride RIFAI VKM F- 4268D in mice. Amino Acids 2021; 53:111-118. [PMID: 33398529 DOI: 10.1007/s00726-020-02930-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
L-lysine α-oxidase (LO) is an L-amino acid oxidase with antitumor, antimicrobial and antiviral properties. Pharmacokinetic (PK) studies were carried out by measuring LO concentration in plasma and tissue samples by enzyme immunoassay. L-lysine concentration in samples was measured spectrophotometrically using LO. After single i.v. injection of 1.0, 1.5, 3.0 mg/kg the circulating T1/2 of enzyme in mice varied from 51 to 74 min and the AUC0-inf values were 6.54 ± 0.46, 8.66 ± 0.59, 9.47 ± 1.45 μg/ml × h, respectively. LO was distributed in tissues and determined within 48 h after administration with maximal accumulation in liver and heart tissues. Mean time to reach the maximum concentration was highest for the liver-9 h, kidney-1 h and 15 min for the tissues of heart, spleen and brain. T1/2 of LO in tissues ranged from 7.75 ± 0.73 to 26.10 ± 2.60 h. In mice, plasma L-lysine decreased by 79% 15 min after LO administration in dose 1.6 mg/kg. The serum L-lysine levels remained very low from 1 to 9 h (< 25 μM, 17%), indicating an acute lack of L-lysine in animals for at least 9 h. Concentration of L-lysine in serum restored only 24 h after LO administration. The results of LO PK study show that it might be considered as a promising enzyme for further investigation as a potential anticancer agent.
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Affiliation(s)
- V S Pokrovsky
- Department of Biochemistry, Peoples' Friendship University, Moscow, Russia. .,Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Moscow, Russia.
| | - A N Lukashev
- Tropical and Vector Borne Diseases, Martsinovsky Institute of Medical Parasitology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - G Babayeva
- Department of Biochemistry, Peoples' Friendship University, Moscow, Russia.,Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - S Sh Karshieva
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - A Yu Arinbasarova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow Region, Russia
| | - A G Medentzev
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow Region, Russia
| | - M V Komarova
- Department of Laser and Biotechnical Systems, Samara University, Samara, Russia
| | - E V Lukasheva
- Department of Biochemistry, Peoples' Friendship University, Moscow, Russia
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Lukasheva EV, Makletsova MG, Lukashev AN, Babayeva G, Arinbasarova AY, Medentsev AG. Fungal Enzyme l-Lysine α-Oxidase Affects the Amino Acid Metabolism in the Brain and Decreases the Polyamine Level. Pharmaceuticals (Basel) 2020; 13:E398. [PMID: 33212812 PMCID: PMC7698073 DOI: 10.3390/ph13110398] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/08/2020] [Accepted: 11/14/2020] [Indexed: 11/16/2022] Open
Abstract
The fungal glycoprotein l-lysine α-oxidase (LO) catalyzes the oxidative deamination of l-lysine (l-lys). LO may be internalized in the intestine and shows antitumor, antibacterial, and antiviral effects in vivo. The main mechanisms of its effects have been shown to be depletion of the essential amino acid l-lys and action of reactive oxidative species produced by the reaction. Here, we report that LO penetrates into the brain and is retained there for up to 48 h after intravenous injection, which might be explained by specific pharmacokinetics. LO actively intervenes in amino acid metabolism in the brain. The most significant impact of LO was towards amino acids, which are directly exposed to its action (l-lys, l-orn, l-arg). In addition, the enzyme significantly affected the redistribution of amino acids directly associated with the tricarboxylic acid (TCA) cycle (l-asp and l-glu). We discovered that the depletion of l-orn, the precursor of polyamines (PA), led to a significant and long-term decrease in the concentration of polyamines, which are responsible for regulation of many processes including cell proliferation. Thus, LO may be used to reduce levels of l-lys and PA in the brain.
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Affiliation(s)
- Elena V. Lukasheva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia;
| | - Marina G. Makletsova
- Department of Biology and General Pathology, Don State Technical University, Gagarin Square 1, Rostov-on-Don 344011, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), 20 M. Pirogovskaya str., Moscow 119435, Russia;
| | - Gulalek Babayeva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia;
| | - Anna Yu. Arinbasarova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Pr. Nauki, Pushchino, Moscow Region 142290, Russia; (A.Y.A.); (A.G.M.)
| | - Alexander G. Medentsev
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Pr. Nauki, Pushchino, Moscow Region 142290, Russia; (A.Y.A.); (A.G.M.)
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Deviatkin AA, Karganova GG, Vakulenko YA, Lukashev AN. TBEV Subtyping in Terms of Genetic Distance. Viruses 2020; 12:E1240. [PMID: 33142676 PMCID: PMC7692686 DOI: 10.3390/v12111240] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/10/2020] [Revised: 10/24/2020] [Accepted: 10/29/2020] [Indexed: 01/07/2023] Open
Abstract
Currently, the lowest formal taxon in virus classification is species; however, unofficial lower-level units are commonly used in everyday work. Tick-borne encephalitis virus (TBEV) is a species of mammalian tick-borne flaviviruses that may cause encephalitis. Many known representatives of TBEV are grouped into subtypes, mostly according to their phylogenetic relationship. However, the emergence of novel sequences could dissolve this phylogenetic grouping; in the absence of strict quantitative criterion, it may be hard to define the borders of the first TBEV taxonomic unit below the species level. In this study, the nucleotide/amino-acid space of all known TBEV sequences was analyzed. Amino-acid sequence p-distances could not reliably distinguish TBEV subtypes. Viruses that differed by less than 10% of nucleotides in the polyprotein-coding gene belonged to the same subtype. At the same time, more divergent viruses were representatives of different subtypes. According to this distance criterion, TBEV species may be divided into seven subtypes: TBEV-Eur, TBEV-Sib, TBEV-FE, TBEV-2871 (TBEV-Ob), TBEV-Him, TBEV-178-79 (TBEV-Bkl-1), and TBEV-886-84 (TBEV-Bkl-2).
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
| | - Galina G. Karganova
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
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Bure IV, Mikhaylenko DS, Kuznetsova EB, Alekseeva EA, Bondareva KI, Kalinkin AI, Lukashev AN, Tarasov VV, Zamyatnin AA, Nemtsova MV. Analysis of miRNA Expression in Patients with Rheumatoid Arthritis during Olokizumab Treatment. J Pers Med 2020; 10:jpm10040205. [PMID: 33142700 PMCID: PMC7712090 DOI: 10.3390/jpm10040205] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/11/2023] Open
Abstract
Rheumatoid arthritis (RA) is the most common autoimmune disease worldwide. Epigenetic alternations of microRNAs (miRNAs) can contribute to its pathogenesis and progression. As the first line therapy with DMARDs is not always successful, other drugs and therapeutic targets should be applied. This study aims to measure the expression level of plasma miRNAs in RA patients treated with olokizumab and to evaluate their potential as prognostic biomarkers. The expression of 9 miRNAs was quantified in 103 RA patients before treatment and at weeks 12 and 24 of olokizumab therapy by reverse transcription-polymerase chain reaction (RT-PCR) assay and analyzed in groups of responders and non-responders. Almost all miRNAs changed their expression during therapy. The ROC curve analysis of the most prominent of them together with consequent univariate and multivariate regression analysis revealed statistically significant associations with the olokizumab therapy efficiency scores for miR-26b, miR-29, miR-451, and miR-522. Therefore, these miRNAs might be a potential therapeutic response biomarker.
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Affiliation(s)
- Irina V. Bure
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
| | - Dmitry S. Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia;
| | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia;
| | - Ekaterina A. Alekseeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia;
| | - Kristina I. Bondareva
- Biostatistics Department, OCT Rus, Bolshaya Moskovskaya str., 8/2, 191002 Saint-Petersburg, Russia;
| | - Alexey I. Kalinkin
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia;
| | - Alexander N. Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Vadim V. Tarasov
- Department of Pharmacology and Pharmacy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: (A.A.Z.J.); (M.V.N.)
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya str., 8-2, 119992 Moscow, Russia; (I.V.B.); (D.S.M.); (E.B.K.); (E.A.A.); (A.N.L.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechye str. 1, 115478 Moscow, Russia;
- Correspondence: (A.A.Z.J.); (M.V.N.)
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Deviatkin AA, Kholodilov IS, Belova OA, Bugmyrin SV, Bespyatova LA, Ivannikova AY, Vakulenko YA, Lukashev AN, Karganova GG. Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances. Microorganisms 2020; 8:microorganisms8101589. [PMID: 33076346 PMCID: PMC7602664 DOI: 10.3390/microorganisms8101589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/07/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 10/26/2022] Open
Abstract
Tick-Borne Encephalitis Virus (TBEV) is a dangerous arbovirus widely distributed in Northern Eurasia. The area of this pathogen changes over time. At the beginning of the 2000s, the Ixodes tick populations in Karelia increased. At the same time, the area of I. persulcatus, the main vector of the Siberian TBEV subtype, also expanded. Herein, we sequenced 10 viruses isolated from ticks collected in three locations from the Karelia region in 2008-2018. PCR positive samples were passaged in suckling mice or pig embryo kidney cells (PEK). After the second passage in suckling, mice viral RNA was isolated and E-gene fragment was sequenced. Viral sequences were expected to be similar or nearly identical. Instead, there was up to a 4.8% difference in nucleotide sequence, comparable with the most diverse viruses belonging to the Baltic subgroup in Siberian TBEV subtype (Baltic TBEV-Sib). To reveal whether this was systemic or incidental, a comprehensive phylogeographical analysis was conducted. Interestingly, viruses within each geographic region demonstrated comparable diversity to the whole Baltic TBEV-Sib. Moreover, Baltic TBEV-Sib has a distribution area limited by three ecological regions. This means that active virus mixing occurs in the vast geographic area forming one common virus pool. The most plausible explanation is the involvement of flying animals in the TBEV spread.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Correspondence: (A.A.D.); (G.G.K.)
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Sergey V. Bugmyrin
- Laboratory for Animal and Plant Parasitology, Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (S.V.B.); (L.A.B.)
| | - Lubov A. Bespyatova
- Laboratory for Animal and Plant Parasitology, Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (S.V.B.); (L.A.B.)
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
| | - Yulia A. Vakulenko
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.Y.I.)
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (A.A.D.); (G.G.K.)
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11
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Klimentov AS, Belova OA, Kholodilov IS, Butenko AM, Bespyatova LA, Bugmyrin SV, Chernetsov N, Ivannikova AY, Kovalchuk IV, Nafeev AA, Oorzhak ND, Pilikova OM, Polienko AE, Purmak KA, Romanenko EN, Romanova LI, Saryglar AA, Solomashchenko NI, Shamsutdinov AF, Vakalova EV, Lukashev AN, Karganova GG, Gmyl AP. Phlebovirus sequences detected in ticks collected in Russia: Novel phleboviruses, distinguishing criteria and high tick specificity. Infect Genet Evol 2020; 85:104524. [PMID: 32891876 DOI: 10.1016/j.meegid.2020.104524] [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] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Phlebovirus is an abundant and rather heterogeneous genus within the Phenuiviridae family (order Bunyavirales). The genus Phlebovirus is divided into two antigenic complexes, which also correspond to the main vector: sandflies/mosquitoes and ticks. Previously, only sandfly/mosquito-borne phleboviruses were associated with human disease, such as Rift Valley fever virus, Toscana virus, Sicilian and Naples Sandfly fever viruses and others. Until recently, tick-borne phleboviruses were not considered as human pathogens. After the discovery of severe fever with thrombocytopenia syndrome, interest to tick-borne phleboviruses has increased dramatically. In the last decade, many novel phleboviruses have been reported in different regions. Despite this, the diversity, ecology and pathogenicity of these viruses still remain obscure. The aim of this work was to study the diversity of phleboviruses in ticks collected in several regions of Russia. We used pan-phlebovirus RT-PCR assays based on multiple degenerate primers targeting the polymerase gene fragment. Arthropod specimens were collected from 2005 to 2018. A total of 5901 Ixodidae ticks combined into 1116 pools were screened. A total of 160 specific amplicons were produced. In three cases RT-PCR assays amplified two distinct viruses from same tick pools. Direct sequencing of amplicons and subsequent phylogenetic analysis revealed twelve representatives of divergent phlebovirus groups. Based on the distribution of pairwise nucleotide sequence identity values, a cut-off (88%) was suggested to distinguish tick-borne phleboviruses. According to this provisional criterion, two viruses found here could be termed novel, while ten viruses have been described in previous studies. Detected phleboviruses demonstrated almost perfect specificity to a tick species or, at least, a genus. The same pattern was observed for tick-borne phleboviruses found in different studies around the world. Viruses that grouped together on a phylogenetic tree and differed less than this sequence identity threshold suggested above were hosted by ticks from the same genus.
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Affiliation(s)
- Alexander S Klimentov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia.
| | - Oxana A Belova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Ivan S Kholodilov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Alexander M Butenko
- Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia
| | - Liubov A Bespyatova
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Sergey V Bugmyrin
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Nikita Chernetsov
- Zoological Institute of RAS, St. Petersburg 199034, Russia; Dept. Vertebrate Zoology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Anna Y Ivannikova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Irina V Kovalchuk
- Office of Rospotrebnadzor in the Stavropol Territory, Stavropol 355008, Russia; Stavropol State Medical University, Stavropol 355017, Russia
| | - Alexander A Nafeev
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, Ulyanovsk 432005, Russia
| | | | - Olga M Pilikova
- Black Sea Anti-Plague Station of Rospotrebnadzor, Novorossiysk 353919, Russia
| | - Alexandra E Polienko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Kristina A Purmak
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Evgeniya N Romanenko
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Lidiya Iu Romanova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | | | - Nataliya I Solomashchenko
- Stavropol State Medical University, Stavropol 355017, Russia; Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Anton F Shamsutdinov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, Kazan 420015, Russia
| | - Elena V Vakalova
- Astrakhan Anti-Plague Station of Rospotrebnadzor, Astrakhan 414000, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow 119435, Russia
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | - Anatoly P Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
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Mikhaylenko DS, Nemtsova MV, Bure IV, Kuznetsova EB, Alekseeva EA, Tarasov VV, Lukashev AN, Beloukhova MI, Deviatkin AA, Zamyatnin AA. Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response. Int J Mol Sci 2020; 21:E4911. [PMID: 32664585 PMCID: PMC7402327 DOI: 10.3390/ijms21144911] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthropathy worldwide. Possible manifestations of RA can be represented by a wide variability of symptoms, clinical forms, and course options. This multifactorial disease is triggered by a genetic predisposition and environmental factors. Both clinical and genealogical studies have demonstrated disease case accumulation in families. Revealing the impact of candidate gene missense variants on the disease course elucidates understanding of RA molecular pathogenesis. A multivariate genomewide association study (GWAS) based analysis identified the genes and signalling pathways involved in the pathogenesis of the disease. However, these identified RA candidate gene variants only explain 30% of familial disease cases. The genetic causes for a significant proportion of familial RA have not been determined until now. Therefore, it is important to identify RA risk groups in different populations, as well as the possible prognostic value of some genetic variants for disease development, progression, and treatment. Our review has two purposes. First, to summarise the data on RA candidate genes and the increased disease risk associated with these alleles in various populations. Second, to describe how the genetic variants can be used in the selection of drugs for the treatment of RA.
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Affiliation(s)
- Dmitry S. Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Irina V. Bure
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Ekaterina A. Alekseeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Vadim V. Tarasov
- Department of Pharmacology and Pharmacy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alexander N. Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Marina I. Beloukhova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrei A. Deviatkin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Dezhurko-Korol VA, Novozhilova NE, Makeeva IM, Arkhipova AY, Moisenovich MM, Akhmadishina LV, Lukashev AN, Semenov AM, Leontieva MR, Byakova SF. The influence of centrifugation and inoculation time on the number, distribution, and viability of intratubular bacteria and surface biofilm in deciduous and permanent bovine dentin. Arch Oral Biol 2020; 114:104716. [PMID: 32325265 DOI: 10.1016/j.archoralbio.2020.104716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/10/2020] [Revised: 03/11/2020] [Accepted: 03/27/2020] [Indexed: 11/27/2022]
Abstract
The present study aimed to assess the influence of centrifugation and inoculation time on the number, distribution, and viability of intratubular bacteria and surface monospecies E. faecalis biofilm. MATERIALS AND METHODS Forty-four semicylindrical specimens cut from primary (n = 22) and permanent (n = 22) bovine teeth were randomly assigned to the experimental groups. Teeth of each type were inoculated with E. faecalis with and without centrifugation for 1 and 14 days. The number, localization, viability of bacteria and depth of their penetration were assessed with bacterial culturing of dentin shavings, scanning electron microscopy (SEM) and confocal laser electron microscopy (CLSM). Three-way ANOVA with post-hoc Tukey test were used to assess the influence of different experimental setups on dentin infection. RESULTS Severe dentin infection was observed in permanent and deciduous teeth after centrifugation and 1-day incubation: bacteria reached the full length of dentinal tubules and colony-forming units were too numerous to count. The volume of green fluorescence didn't differ significantly in permanent teeth compared with deciduous (p = 1.0). After 1-day stationary inoculation, small number of cultivable bacteria and few viable bacteria in dentinal tubules were found in both groups. After 14-day stationary inoculation, the dentin infection according to CLSM was deeper in deciduous teeth compared with permanent (p = 0.006 and p = 0.019 for centrifugation and stationary inoculation, respectively). CONCLUSION The most even and dense dentin infection was observed in primary and permanent bovine teeth after centrifugation and 1-day inoculation, and in deciduous teeth after 14-day stationary inoculation.
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Affiliation(s)
- Viktoria A Dezhurko-Korol
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
| | - Nina E Novozhilova
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia.
| | - Irina M Makeeva
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
| | - Anastasia Yu Arkhipova
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Mihail M Moisenovich
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Ludmila V Akhmadishina
- E.I. Martsinovsky Institute of Medical Parasitology and Tropical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), M. Pirogovskaya str., 20-1, 119435, Moscow, Russia
| | - Alexander N Lukashev
- E.I. Martsinovsky Institute of Medical Parasitology and Tropical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), M. Pirogovskaya str., 20-1, 119435, Moscow, Russia
| | - Alexander M Semenov
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Maria R Leontieva
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Svetlana F Byakova
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
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14
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Abstract
The toxocariasis incidence in Russia is relatively low (1.8 cases per 100,000 individuals) and the parasite is not a major healthcare concern. However, the proportion of primary hosts testing positive for the parasite is high and varies between 3% and 100% in dogs (on average 33%), and between 6% and 52% in cats. Higher prevalence was observed in Volga, Urals and Siberia regions. Levels of contamination of soil, children's playgrounds and sandboxes is also high, with up to 100% contamination rates determined in some studies, but more commonly prevalence of contamination around 40% was reported. There is a pronounced seasonality in the prevalence of Toxocara in primary hosts and the soil, with peaks in the summer and autumn. Most likely, a lack of permissive conditions for the development of eggs in the winter determines observed seasonal patterns, which are different than those observed in most other countries. Toxocara eggs were found in 4-10% of vegetables and greenery samples tested, suggesting that they can contribute to the transmission of Toxocara.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia.
| | - Maria N Ruzina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Lyudmila V Akhmadishina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
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15
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Akhmadishina LV, Ruzina MN, Lukasheva MA, Kyuregyan KK, Mikhailov MI, Lukashev AN. Seroprevalence and incidence of human toxocarosis in Russia. Adv Parasitol 2020; 109:419-432. [PMID: 32381210 DOI: 10.1016/bs.apar.2020.01.015] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Overall incidence of toxocariasis in Russia is low and varies between 1.6 and 2.7 per 100,000, while in several hyper-endemic regions, such as Altay, Kurgan, Perm and Udmurtia, it reaches 43 per 100,000. The seroprevalence of toxocariasis in published references was on average 16% and varied across the regions of Russia from negligible in North Siberia to 40% in southern regions of West Siberia. Seroprevalence in adults in five regions of Russia identified in this study was on average 20%, and varied from 3% in Yakutia (north of East Siberia) to 36% in Rostov-on-Don, South Russia. There was no correlation between seroprevalence and reported incidence of toxocariasis; however, the pattern of seroprevalence variation could be linked to Toxocara prevalence in dogs. Toxocariasis seroprevalence has more than doubled over the last 20 years. Diagnostic antibody titres (1:800 or more) were found in 3.6% of sera, suggesting about five million of acute Toxocara invasions per year.
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Affiliation(s)
- Lyudmila V Akhmadishina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Maria N Ruzina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Maria A Lukasheva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| | - Karen K Kyuregyan
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia; Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - Mikhail I Mikhailov
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia; Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia.
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16
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Bronstein AM, Fedyanina LV, Maximova MS, Lukashev AN, Sergeev AR. Nine cases of human dipylidiasis in Moscow region during 1987 to 2017. Trop Biomed 2020; 37:194-200. [PMID: 33612730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dipylidium caninum is a parasite that commonly infects dogs and cats worldwide. The large population of wild and stray dogs and cats may potentially transmit D. caninum to humans via their flea and lice. Humans are an accidental host, and dipylidiasis is more commonly seen in infants and children. There is scant information about human dipylidiasis in Russia. We report nine cases of dipylidiasis - eight in children and one in an adult. The patients were asymptomatic, except for excreting active proglottids in their faeces, which was the most common complaint. The clinical significance of asymptomatic dipylidiasis is not understood, except mothers were anxious because of the continuous appearance of active worms in the faeces of their children. The patients were successfully treated with praziquantel (15 mg/kg). Preventing dipylidiasis in pets and humans requires the control of fleas and lice, avoiding the outdoor defecation of definitive hosts, deworming pets, preventing children from playing with stray animals and spread of information about dipylidiasis among pet owners. Dogs and cats in many places in Russia breed freely, defecate outdoors in any area, and are not subjected to deworming and insect control. These circumstances favour the fact that, although this zoonosis is rare, it is a re-emerging disease and might reach important levels in Russia.
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Affiliation(s)
- A M Bronstein
- I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Trubetskaya St., 8/2, Russian Federation
- Pigorov Russian National Research Medical University (Department of Infectious Diseases and Epidemiology), 119121 Moscow, Ostrovityaninova St., 1, Russian Federation
| | - L V Fedyanina
- I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Trubetskaya St., 8/2, Russian Federation
| | - M S Maximova
- I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Trubetskaya St., 8/2, Russian Federation
| | - A N Lukashev
- I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Trubetskaya St., 8/2, Russian Federation
| | - A R Sergeev
- I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Trubetskaya St., 8/2, Russian Federation
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17
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Deviatkin AA, Kholodilov IS, Vakulenko YA, Karganova GG, Lukashev AN. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses 2020; 12:v12020247. [PMID: 32102228 PMCID: PMC7077300 DOI: 10.3390/v12020247] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 12/31/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Tick-borne encephalitis (TBE) is one of the most important viral zoonosis transmitted by the bite of infected ticks. In this study, all tick-borne encephalitis virus (TBEV) E gene sequences available in GenBank as of June 2019 with known date of isolation (n = 551) were analyzed. Simulation studies showed that a sample bias could significantly affect earlier studies, because small TBEV datasets (n = 50) produced non-overlapping intervals for evolutionary rate estimates. An apparent lack of a temporal signal in TBEV, in general, was found, precluding molecular clock analysis of all TBEV subtypes in one dataset. Within all subtypes and most of the smaller groups in these subtypes, there was evidence of many medium- and long-distance virus transfers. These multiple random events may play a key role in the virus spreading. For some groups, virus diversity within one territory was similar to diversity over the whole geographic range. This is best exemplified by the virus diversity observed in Switzerland or Czech Republic. These two countries yielded most of the known European subtype Eu3 subgroup sequences, and the diversity of viruses found within each of these small countries is comparable to that of the whole Eu3 subgroup, which is prevalent all over Central and Eastern Europe. Most of the deep tree nodes within all three established TBEV subtypes dated less than 300 years back. This could be explained by the recent emergence of most of the known TBEV diversity. Results of bioinformatics analysis presented here, together with multiple field findings, suggest that TBEV may be regarded as an emerging disease.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Laboratory of Postgenomic Technologies, Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia
- Correspondence: ; Tel.: +7-906-739-0860
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (G.G.K.)
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (G.G.K.)
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
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18
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Grybchuk D, Macedo DH, Kleschenko Y, Kraeva N, Lukashev AN, Bates PA, Kulich P, Leštinová T, Volf P, Kostygov AY, Yurchenko V. The First Non-LRV RNA Virus in Leishmania. Viruses 2020; 12:v12020168. [PMID: 32024293 PMCID: PMC7077295 DOI: 10.3390/v12020168] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/06/2020] [Revised: 01/21/2020] [Accepted: 01/29/2020] [Indexed: 12/25/2022] Open
Abstract
In this work, we describe the first Leishmania-infecting leishbunyavirus-the first virus other than Leishmania RNA virus (LRV) found in trypanosomatid parasites. Its host is Leishmania martiniquensis, a human pathogen causing infections with a wide range of manifestations from asymptomatic to severe visceral disease. This virus (LmarLBV1) possesses many characteristic features of leishbunyaviruses, such as tripartite organization of its RNA genome, with ORFs encoding RNA-dependent RNA polymerase, surface glycoprotein, and nucleoprotein on L, M, and S segments, respectively. Our phylogenetic analyses suggest that LmarLBV1 originated from leishbunyaviruses of monoxenous trypanosomatids and, probably, is a result of genomic re-assortment. The LmarLBV1 facilitates parasites' infectivity in vitro in primary murine macrophages model. The discovery of a virus in L. martiniquensis poses the question of whether it influences pathogenicity of this parasite in vivo, similarly to the LRV in other Leishmania species.
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Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Central European Institute of Technology, Masaryk University, 60177 Brno, Czech Republic
| | - Diego H. Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
| | - Yulia Kleschenko
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
| | - Paul A. Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YE, UK;
| | - Pavel Kulich
- Laboratory of Electron Microscopy, Veterinary Research Institute, 62100 Brno, Czech Republic;
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (T.L.); (P.V.)
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (T.L.); (P.V.)
| | - Alexei Y. Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg 199034, Russia
- Correspondence: (A.Y.K.); (V.Y.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic; (D.G.); (D.H.M.); (N.K.)
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow 119435, Russia, (A.N.L.)
- Correspondence: (A.Y.K.); (V.Y.)
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19
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Deviatkin AA, Vakulenko YA, Akhmadishina LV, Tarasov VV, Beloukhova MI, Zamyatnin Jr. AA, Lukashev AN. Emerging Concepts and Challenges in Rheumatoid Arthritis Gene Therapy. Biomedicines 2020; 8:biomedicines8010009. [PMID: 31936504 PMCID: PMC7168286 DOI: 10.3390/biomedicines8010009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 12/03/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic inflammatory joint disease affecting about 1% of the population worldwide. Current treatment approaches do not ensure a cure for every patient. Moreover, classical regimens are based on nontargeted systemic immune suppression and have significant side effects. Biological treatment has advanced considerably but efficacy and specificity issues remain. Gene therapy is one of the potential future directions for RA therapy, which is rapidly developing. Several gene therapy trials done so far have been of moderate success, but experimental and genetics studies have yielded novel targets. As a result, the arsenal of gene therapy tools keeps growing. Currently, both viral and nonviral delivery systems are used for RA therapy. Herein, we review recent approaches for RA gene therapy.
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Affiliation(s)
- Andrei A. Deviatkin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia; (M.I.B.); (A.A.Z.J.); (A.N.L.)
- Correspondence:
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (L.V.A.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ludmila V. Akhmadishina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (L.V.A.)
| | - Vadim V. Tarasov
- Department of Pharmacology and Pharmacy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Marina I. Beloukhova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia; (M.I.B.); (A.A.Z.J.); (A.N.L.)
| | - Andrey A. Zamyatnin Jr.
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia; (M.I.B.); (A.A.Z.J.); (A.N.L.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexander N. Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia; (M.I.B.); (A.A.Z.J.); (A.N.L.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (L.V.A.)
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20
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Safonova MV, Gmyl AP, Lukashev AN, Speranskaya AS, Neverov AD, Fedonin GG, Pimkina EV, Matsvay AD, Khafizov KF, Karganova GG, Kozlovskaya LI, Valdokhina AV, Bulanenko VP, Dedkov VG. Genetic diversity of Kemerovo virus and phylogenetic relationships within the Great Island virus genetic group. Ticks Tick Borne Dis 2019; 11:101333. [PMID: 31787560 DOI: 10.1016/j.ttbdis.2019.101333] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 11/27/2022]
Abstract
Kemerovo virus (KEMV) is a member of the Great Island virus genetic group, belonging to the tick-borne arboviruses of the genus Orbivirus within the family Reoviridae. Nine strains of KEMV, which were isolated from various locations in Russia, were sequenced by high-throughput sequencing to study their intraspecific diversity and the interspecific relationships of viruses within the Great Island genetic group. For the first time, multiple reassortment within KEMV was reliably demonstrated. Different types of independently emerged alternative reading frames in segment 9 and heterogeneity of the viral population in one of the KEMV strains were found. The hypothesis of the role of an alternative open reading frame (ORF) in segment 9 in KEMV cellular tropism was not confirmed in this study.
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Affiliation(s)
- Marina V Safonova
- Plague Control Center, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia.
| | - Anatoly P Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna S Speranskaya
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Alexey D Neverov
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Gennady G Fedonin
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Ekaterina V Pimkina
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Alina D Matsvay
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Kamil F Khafizov
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Lubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna V Valdokhina
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Victoria P Bulanenko
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Vladimir G Dedkov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia; Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia
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21
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Kleschenko Y, Grybchuk D, Matveeva NS, Macedo DH, Ponirovsky EN, Lukashev AN, Yurchenko V. Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan. Genes (Basel) 2019; 10:genes10100830. [PMID: 31640177 PMCID: PMC6826456 DOI: 10.3390/genes10100830] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/19/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.
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Affiliation(s)
- Yuliya Kleschenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Danyil Grybchuk
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
- CEITEC-Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Nadezhda S Matveeva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
- Department of Molecular Biology, Faculty of Biology, Moscow State University, 119991 Moscow, Russia.
| | - Diego H Macedo
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
| | - Evgeny N Ponirovsky
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia.
- Life Sciences Research Centre, Faculty of Science, University of Ostrava, 71000 Ostrava, Czech Republic.
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22
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Nemtsova MV, Zaletaev DV, Bure IV, Mikhaylenko DS, Kuznetsova EB, Alekseeva EA, Beloukhova MI, Deviatkin AA, Lukashev AN, Zamyatnin AA. Epigenetic Changes in the Pathogenesis of Rheumatoid Arthritis. Front Genet 2019; 10:570. [PMID: 31258550 PMCID: PMC6587113 DOI: 10.3389/fgene.2019.00570] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 01/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects about 1% of the world’s population. The etiology of RA remains unknown. It is considered to occur in the presence of genetic and environmental factors. An increasing body of evidence pinpoints that epigenetic modifications play an important role in the regulation of RA pathogenesis. Epigenetics causes heritable phenotype changes that are not determined by changes in the DNA sequence. The major epigenetic mechanisms include DNA methylation, histone proteins modifications and changes in gene expression caused by microRNAs and other non-coding RNAs. These modifications are reversible and could be modulated by diet, drugs, and other environmental factors. Specific changes in DNA methylation, histone modifications and abnormal expression of non-coding RNAs associated with RA have already been identified. This review focuses on the role of these multiple epigenetic factors in the pathogenesis and progression of the disease, not only in synovial fibroblasts, immune cells, but also in the peripheral blood of patients with RA, which clearly shows their high diagnostic potential and promising targets for therapy in the future.
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Affiliation(s)
- Marina V Nemtsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Dmitry V Zaletaev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Irina V Bure
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dmitry S Mikhaylenko
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina A Alekseeva
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Beloukhova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrei A Deviatkin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alexander N Lukashev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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23
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Pokrovsky VS, Chepikova OE, Davydov DZ, Zamyatnin AA, Lukashev AN, Lukasheva EV. Amino Acid Degrading Enzymes and their Application in Cancer Therapy. Curr Med Chem 2019; 26:446-464. [PMID: 28990519 DOI: 10.2174/0929867324666171006132729] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 02/08/2017] [Revised: 09/12/2017] [Accepted: 09/28/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Amino acids are essential components in various biochemical pathways. The deprivation of certain amino acids is an antimetabolite strategy for the treatment of amino acid-dependent cancers which exploits the compromised metabolism of malignant cells. Several studies have focused on the development and preclinical and clinical evaluation of amino acid degrading enzymes, namely L-asparaginase, L-methionine γ-lyase, L-arginine deiminase, L-lysine α-oxidase. Further research into cancer cell metabolism may therefore define possible targets for controlling tumor growth. OBJECTIVE The purpose of this review was to summarize recent progress in the relationship between amino acids metabolism and cancer therapy, with a particular focus on Lasparagine, L-methionine, L-arginine and L-lysine degrading enzymes and their formulations, which have been successfully used in the treatment of several types of cancer. METHODS We carried out a structured search among literature regarding to amino acid degrading enzymes. The main aspects of search were in vitro and in vivo studies, clinical trials concerning application of these enzymes in oncology. RESULTS Most published research are on the subject of L-asparaginase properties and it's use for cancer treatment. L-arginine deiminase has shown promising results in a phase II trial in advanced melanoma and hepatocellular carcinoma. Other enzymes, in particular Lmethionine γ-lyase and L-lysine α-oxidase, were effective in vitro and in vivo. CONCLUSION The findings of this review revealed that therapy based on amino acid depletion may have the potential application for cancer treatment but further clinical investigations are required to provide the efficacy and safety of these agents.
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Affiliation(s)
- Vadim S Pokrovsky
- Blokhin Cancer Research Center, Moscow, Russian Federation.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russian Federation.,People's Friendship University, Russia (RUDN University), Moscow, Russian Federation
| | - Olga E Chepikova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,Belozersky Institute of Physico- Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alexander N Lukashev
- People's Friendship University, Russia (RUDN University), Moscow, Russian Federation.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Elena V Lukasheva
- People's Friendship University, Russia (RUDN University), Moscow, Russian Federation
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24
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Abstract
The enterically transmitted hepatitis A (HAV) and hepatitis E viruses (HEV) are the leading causes of acute viral hepatitis in humans. Despite the discovery of HAV and HEV 40-50 years ago, their evolutionary origins remain unclear. Recent discoveries of numerous nonprimate hepatoviruses and hepeviruses allow revisiting the evolutionary history of these viruses. In this review, we provide detailed phylogenomic analyses of primate and nonprimate hepatoviruses and hepeviruses. We identify conserved and divergent genomic properties and corroborate historical interspecies transmissions by phylogenetic comparisons and recombination analyses. We discuss the likely non-recent origins of human HAV and HEV precursors carried by mammals other than primates, and detail current zoonotic HEV infections. The novel nonprimate hepatoviruses and hepeviruses offer exciting new possibilities for future research focusing on host range and the unique biological properties of HAV and HEV.
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Affiliation(s)
- Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119991 Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, 142782 Moscow, Russia
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
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25
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Goryacheva II, Baranova AM, Lukashev AN, Gordeev MI, Usenbaev NT, Shaikevich EV. Genetic characterization of Plasmodium vivax in the Kyrgyz Republic. Infect Genet Evol 2018; 66:262-268. [PMID: 30339983 DOI: 10.1016/j.meegid.2018.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
At the end of 2016, Kyrgyz Republic was certified by the World Health Organization as a malaria-free country, while only a decade ago this disease posed a serious health threat. The progress achieved by Kyrgyz Republic provides a unique example of tertian (Plasmodium vivax) malaria elimination. This success was based on an integrated approach, including measures for the treatment of infected people and disease prevention, vector control and the development of an effective national epidemiological surveillance system. Lower P. vivax msp-1, msp-3α, csp and dbpII genes polymorphism was revealed in Kyrgyz Republic in compare with that in Tajikistan. Molecular characterization of the causative agent found that P. vivax populations in Kyrgyz Republic was comprised by several lineages, highly divergent in the south-western and genetically homogeneous in the northern regions of Kyrgyz Republic, d. Such profile in the northern regions was compatible with several recent introductions rather than a long-term endemic circulation of the parasite. A low level of genetic variability suggested that the parasitic systems of tertian malaria, were not adapted, which, along with other factors, largely determined the possibility of malaria elimination in northern Kyrgyz Republic. Other determinants included environmental, social, and epidemiological factors that limited the spread of malaria. South-western Kyrgyz Republic, a region with a high level of interstate migration, requires considerable attention to prevent the spread of malaria.
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Affiliation(s)
- I I Goryacheva
- Vavilov Institute of General Genetics, Moscow 119991, Russia
| | | | | | - M I Gordeev
- Moscow Region State University, Moscow 105005, Russia
| | - N T Usenbaev
- Sanitary-Epidemiological Department of Kyrgyz Republic MOH, Bishkek, Kyrgyzstan
| | - E V Shaikevich
- Vavilov Institute of General Genetics, Moscow 119991, Russia.
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26
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Lukashev AN, Vakulenko YA, Turbabina NA, Deviatkin AA, Drexler JF. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Rev Med Virol 2018; 28:e2002. [PMID: 30069956 DOI: 10.1002/rmv.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/05/2022]
Abstract
Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia
| | - Yulia A Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Virology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia A Turbabina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
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27
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Deviatkin AA, Lukashev AN. Recombination in the rabies virus and other lyssaviruses. Infect Genet Evol 2018; 60:97-102. [PMID: 29477551 DOI: 10.1016/j.meegid.2018.02.026] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/06/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022]
Abstract
Recombination is a common event in RNA viruses; however, in the rabies virus there have been only a few reports of isolated recombination events. Comprehensive analysis found traces of recent recombination events within Arctic, Arctic-like and Africa 1b rabies virus groups, as well as recombination between distinct lyssaviruses. Recombination breakpoints were not linked to gene boundaries and could be detected all over the genome. However, there was no evidence that recombination is an important factor in the genetic variability of the rabies virus. It is therefore likely that recombination in the rabies virus is limited by ecological factors (e.g., rare co-circulation of distinguishable lineages and a narrow window for productive coinfection in most carnivore hosts), rather than molecular barriers (e.g., incompatibility of genome fragments).
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Affiliation(s)
- Andrei A Deviatkin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations of Russian Academy of Sciences, Moscow, Russia.
| | - Alexander N Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations of Russian Academy of Sciences, Moscow, Russia
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28
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Lukashev AN, Deviatkin AA. Phylodynamics of Crimean Congo hemorrhagic fever virus in South Russia. Infect Genet Evol 2018; 59:23-27. [PMID: 29413882 DOI: 10.1016/j.meegid.2018.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 11/29/2022]
Abstract
Phylodynamics of Crimean Congo Hemorrhagic fever virus (CCHFV) genotype V in South Russia was analyzed using 244 partial (452-571 nt) sequences in all three genomic segments and 38 complete genomic sequences. Despite increased number of sequences, the Russian lineage of the European genotype V (commonly termed GtVa) was distinct from GtV isolates from Turkey and the Balkan countries. No geographic pattern was observed in phylogenetic subgrouping of CCHFV within South Russia. Identical isolates could be found at distant locations spaced by hundreds of kilometers, while relatively divergent viruses circulated in the same region. Full genome analysis indicated that reassortment events within GtVa occurred every few decades (median half-life of a non-reassortant node 30-40 years) and involved M and S segments. Therefore, in South Russia CCHFV represents a highly dynamic population of frequently reassorting viruses.
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Affiliation(s)
- A N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia.
| | - A A Deviatkin
- Institute of Molecular Medicine, Sechenov University, Moscow, Russia
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29
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Abstract
Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10-2 to 3.07×10-2 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia
| | - Yulia A Vakulenko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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30
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Prostova MA, Deviatkin AA, Tcelykh IO, Lukashev AN, Gmyl AP. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C. PeerJ 2017; 5:e3896. [PMID: 29018627 PMCID: PMC5633025 DOI: 10.7717/peerj.3896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/16/2017] [Indexed: 12/18/2022] Open
Abstract
Background Enteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.
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Affiliation(s)
- Maria A Prostova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Andrei A Deviatkin
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Irina O Tcelykh
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Alexander N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia.,Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Sechenov First Moscow State Medical University, Moscow, Russia
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31
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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.
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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
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32
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Lukashev AN, Corman VM, Schacht D, Gloza-Rausch F, Seebens-Hoyer A, Gmyl AP, Drosten C, Drexler JF. Close genetic relatedness of picornaviruses from European and Asian bats. J Gen Virol 2017; 98:955-961. [PMID: 28555547 DOI: 10.1099/jgv.0.000760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Our investigation of 1004 faecal specimens from European bats for picornaviruses by broadly reactive nested reverse transcription-PCR found picornaviral RNA in 28 samples (2.8 %). Phylogenetic analysis of the partial 3D genomic region suggested that one bat virus belonged to the species Enterovirus G (EV-G, formerly Porcine enterovirus B). Bat infection was supported by relatively high EV-G concentrations of 1.1×106 RNA copies per gram of faeces. All other bat viruses belonged either to the bat-associated genus Mischivirus, or to an unclassified Picornaviridae group distantly related to the genus Sapelovirus. Members of this unclassified sapelovirus-related group had RNA secondary structures in their 3'-nontranslated regions that were typical of enteroviruses and that resembled structures that occur in bat-associated coronaviruses, suggesting ancient recombination events. Based on sequence distances, several picornaviruses from European and Chinese bats were likely conspecific, suggesting connectivity of virus populations. Due to their high mutation rates and their diversity, picornaviruses may be useful tools for studies of bat and virus ecology.
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Affiliation(s)
- Alexander N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Victor Max Corman
- German Centre for Infection Research (DZIF)
- Institute of Virology, Helmut-Ruska-Haus, Charité Medical School, Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Daniel Schacht
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Florian Gloza-Rausch
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany
| | | | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research (DZIF)
- Institute of Virology, Helmut-Ruska-Haus, Charité Medical School, Berlin, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research (DZIF)
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33
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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.
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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
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Abstract
Gene therapy is the straightforward approach for the application of recent advances in molecular biology into clinical practice. One of the major obstacles in the development of gene therapy is the delivery of the effector to and into the target cell. Unfortunately, most methods commonly used in laboratory practice are poorly suited for clinical use. Viral vectors are one of the most promising methods for gene therapy delivery. Millions of years of evolution of viruses have resulted in the development of various molecular mechanisms for entry into cells, long-term survival within cells, and activation, inhibition, or modification of the host defense mechanisms at all levels. The relatively simple organization of viruses, small genome size, and evolutionary plasticity allow modifying them to create effective instruments for gene therapy approaches. This review summarizes the latest trends in the development of gene therapy, in particular, various aspects and prospects of the development of clinical products based on viral delivery systems.
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Affiliation(s)
- A N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, 142782, Russia.
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35
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Lukashev AN, Klimentov AS, Smirnova SE, Dzagurova TK, Drexler JF, Gmyl AP. Phylogeography of Crimean Congo Hemorrhagic Fever Virus. PLoS One 2016; 11:e0166744. [PMID: 27880794 PMCID: PMC5120814 DOI: 10.1371/journal.pone.0166744] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 08/18/2016] [Accepted: 11/02/2016] [Indexed: 11/19/2022] Open
Abstract
Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies. The complete genomic sequence of all three segments of 14 Crimean Congo hemorrhagic fever virus strains isolated from 1958–2000 in Russia, Central Asia and Africa was identified. Each genomic segment was independently subjected to continuous Bayesian phylogeographic analysis. The origin of each genomic segment was traced to Africa about 1,000–5,000 years ago. The virus was first introduced to South and Central Asia in the Middle Ages, and then spread to China, India and Russia. Reverse transfers of genomic segments from Asia to Africa were also observed. The European CCHFV genotype V was introduced to Europe via the Astrakhan region in South Russia 280–400 years ago and subsequently gradually spread westward in Russia, to Turkey and the Balkans less than 150 years ago. Only a few recombination events could be suggested in S and L genomic segments, while segment reassortment was very common. The median height of a non-reassortant phylogenetic tree node was 68–156 years. There were reassortment events within the European CCHFV lineage, but not with viruses from other locations. Therefore, CCHFV in Europe is a recently emerged zoonosis that represents a spillover from the global gene pool.
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Affiliation(s)
- Alexander N. Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- RUDN University, Moscow, Russia
- * E-mail:
| | - Alexander S. Klimentov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya Center of Epidemiology and Microbiology, Moscow, Russia
| | | | - Tamara K. Dzagurova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research (DZIF), Bonn-Cologne, Germany
| | - Anatoly P. Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
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Andreev-Andrievskiy AA, Kolosova NG, Stefanova NA, Lovat MV, Egorov MV, Manskikh VN, Zinovkin RA, Galkin II, Prikhodko AS, Skulachev MV, Lukashev AN. Efficacy of Mitochondrial Antioxidant Plastoquinonyl-decyl-triphenylphosphonium Bromide (SkQ1) in the Rat Model of Autoimmune Arthritis. Oxid Med Cell Longev 2016; 2016:8703645. [PMID: 27293517 PMCID: PMC4887630 DOI: 10.1155/2016/8703645] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/22/2016] [Accepted: 04/18/2016] [Indexed: 12/30/2022]
Abstract
Rheumatoid arthritis is one of the most common autoimmune diseases. Many antioxidants have been tested in arthritis, but their efficacy was, at best, marginal. In this study, a novel mitochondria-targeted antioxidant, plastoquinonyl-decyl-triphenylphosphonium bromide (SkQ1), was tested in vivo to prevent and cure experimental autoimmune arthritis. In conventional Wistar rats, SkQ1 completely prevented the development of clinical signs of arthritis if administered with food before induction. Further, SkQ1 significantly reduced the fraction of animals that developed clinical signs of arthritis and severity of pathological lesions if administration began immediately after induction of arthritis or at the onset of first symptoms (day 14 after induction). In specific pathogen-free Wistar rats, SkQ1 administered via gavage after induction of arthritis did not reduce the fraction of animals with arthritis but decreased the severity of lesions upon pathology examination in a dose-dependent manner. Efficacious doses of SkQ1 were in the range of 0.25-1.25 nmol/kg/day (0.13-0.7 μg/kg/day), which is much lower than doses commonly used for conventional antioxidants. SkQ1 promoted apoptosis of neutrophils in vitro, which may be one of the mechanisms underlying its pharmacological activity. Considering its low toxicity and the wide therapeutic window, SkQ1 may be a valuable additional therapy for rheumatoid arthritis.
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Affiliation(s)
- Alexander A. Andreev-Andrievskiy
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Maxim V. Lovat
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim V. Egorov
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
| | - Vasily N. Manskikh
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
| | - Roman A. Zinovkin
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan I. Galkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Maxim V. Skulachev
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander N. Lukashev
- Institute of Mitoengineering, Lomonosov Moscow State University, Moscow, Russia
- Martsinovsky Institute of Medical Parasitology and Tropical Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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37
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Dedkov VG, Lukashev AN, Deviatkin AA, Kuleshov KV, Safonova MV, Poleshchuk EM, Drexler JF, Shipulin GA. Retrospective diagnosis of two rabies cases in humans by high throughput sequencing. J Clin Virol 2016; 78:74-81. [PMID: 26998568 DOI: 10.1016/j.jcv.2016.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/14/2015] [Revised: 02/27/2016] [Accepted: 03/12/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Rabies is prevalent in 150 countries and is definitely found in Russian Federation. The average registered incidence of rabies infection among animals in Russia is 3000 cases per year. At least 500,000 cases of animal bites and scratches are registered in the Russia every year, but only 2-4 cases of rabies infection in humans are reported per year. This relatively low incidence of rabies infection among humans is the result of a well-organized program of rabies surveillance and control as well as the readily available vaccination and immunoglobulin therapies. However, physician awareness of rabies infection in patients with acute encephalopathy is low, and some cases of rabies remain undiagnosed. OBJECTIVES A retrospective study of autopsy materials from patients who died of encephalitis of unknown etiology in the Astrakhan region of Russia in 2003. STUDY DESIGN A broad-range polymerase chain reaction (PCR) analysis followed by high throughput sequencing were used for the diagnosis. RESULTS Two cases of rabies were detected and subsequently confirmed using a fluorescent antibody test, an enzyme-linked immunosorbent assay (ELISA) and a mouse inoculation test. Two strains of rabies virus were isolated and characterized using virological methods. The entire genome of each strain was sequenced.
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Affiliation(s)
- V G Dedkov
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Right and Human Welfare, Moscow, Russia; RAS Institute of Occupational Health, Moscow, Russia.
| | - A N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia; Martsinovsky Institute of Medical Parasitology and Tropical Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - A A Deviatkin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Right and Human Welfare, Moscow, Russia; RAS Institute of Occupational Health, Moscow, Russia; Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - K V Kuleshov
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Right and Human Welfare, Moscow, Russia
| | - M V Safonova
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Right and Human Welfare, Moscow, Russia; Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - E M Poleshchuk
- Omsk Research Institute of Natural Foci Infections, Omsk, Russia
| | - J F Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany; German Centre for Infection Research, partner site Bonn-Cologne, Germany
| | - G A Shipulin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Russian Inspectorate for Protection of Consumer Right and Human Welfare, Moscow, Russia
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38
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Akhmadishina LV, Govorukhina MV, Kovalev EV, Nenadskaya SA, Ivanova OE, Lukashev AN. Enterovirus A71 Meningoencephalitis Outbreak, Rostov-on-Don, Russia, 2013. Emerg Infect Dis 2016. [PMID: 26196217 PMCID: PMC4517719 DOI: 10.3201/eid2108.141084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Seventy-eight cases of enterovirus infection, including 25 neuroinfections, occurred in Rostov-on-Don, Russia, during May–June 2013. The outbreak was caused by an enterovirus A type 71 (EV-A71) subgenotype C4 lineage that spread to neighboring countries from China ≈3 years earlier. Enterovirus associated neuroinfection may emerge in areas with a preceding background circulation of EV-A71 with apparently asymptomatic infection.
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Klimentov AS, Butenko AM, Khutoretskaya NV, Shustova EY, Larichev VF, Isaeva OV, Karganova GG, Lukashev AN, Gmyl AP. Development of pan-phlebovirus RT-PCR assay. J Virol Methods 2016; 232:29-32. [PMID: 26947398 DOI: 10.1016/j.jviromet.2016.02.009] [Citation(s) in RCA: 6] [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] [Received: 10/16/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 11/17/2022]
Abstract
This study reports the pan-phlebovirus assay capable of detecting both sandfly/mosquito- and tick-borne phleboviruses. Sensitivity and specificity of the assay was verified using a panel of arboviruses. The RT-PCR assay is simple and sensitive, and thus well suited for screening of field samples.
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Affiliation(s)
- Alexander S Klimentov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia; D.I. Ivanovsky Institute of Virology of N.F. Gamaleya Center of Epidemiology and Microbiology, Gamaleya Str. 16, Moscow 123098, Russia
| | - Alexander M Butenko
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya Center of Epidemiology and Microbiology, Gamaleya Str. 16, Moscow 123098, Russia
| | - Natalia V Khutoretskaya
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya Center of Epidemiology and Microbiology, Gamaleya Str. 16, Moscow 123098, Russia
| | - Elena Yu Shustova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia
| | - Victor F Larichev
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya Center of Epidemiology and Microbiology, Gamaleya Str. 16, Moscow 123098, Russia
| | - Olga V Isaeva
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia
| | - Galina G Karganova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia; M.V. Lomonosov Moscow State University, Department of Biology, Leninskiye Gory Str. 1, Moscow 119991, Russia
| | - Alexander N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia
| | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Kievskoe shosse 27km., Moscow 142782, Russia.
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40
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Lukashev AN, Yarmolskaya MS, Shumilina EY, Sychev DA, Kozlovskaya LI. Antibody titers against vaccine and contemporary wild poliovirus type 1 in children immunized with IPV+OPV and young adults immunized with OPV. Virus Res 2016; 213:162-164. [PMID: 26657881 DOI: 10.1016/j.virusres.2015.11.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 09/28/2015] [Revised: 11/30/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
In 2010, a type 1 poliovirus outbreak in Congo with 445 lethal cases was caused by a virus that was neutralized by sera of German adults vaccinated with inactivated polio vaccine with a reduced efficiency. This seroprevalence study was done in two cohorts immunized with other vaccination schedules. Russian children aged 3-6 years immunized with a combination of inactivated and live polio vaccines were reasonably well protected against any wild type poliovirus 1, including the Congolese isolate. Adults aged 20-29 years immunized only with live vaccine were apparently protected against the vaccine strain (92% seropositive), but only 50% had detectable antibodies against the Congo-2010 isolate. Both waning immunity and serological divergence of the Congolese virus could contribute to this result.
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Affiliation(s)
| | - Maria S Yarmolskaya
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Elena Yu Shumilina
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Daniil A Sychev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
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41
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Lomakina NF, Yu Shustova E, Strizhakova OM, Felix Drexler J, Lukashev AN. Epizootic of vesicular disease in pigs caused by coxsackievirus B4 in the Soviet Union in 1975. J Gen Virol 2016; 97:49-52. [DOI: 10.1099/jgv.0.000318] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Natalia F. Lomakina
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Elena Yu Shustova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Olga M. Strizhakova
- National Research Institute for Veterinary Virology and Microbiology of Russia, Pokrov, Vladimir Region, Russia
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- German Centre for Infection Research (DZIF), Bonn-Cologne, Germany
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42
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Yarmolskaya MS, Shumilina EY, Ivanova OE, Drexler JF, Lukashev AN. Molecular epidemiology of echoviruses 11 and 30 in Russia: different properties of genotypes within an enterovirus serotype. Infect Genet Evol 2015; 30:244-248. [PMID: 25562123 DOI: 10.1016/j.meegid.2014.12.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 11/18/2014] [Accepted: 12/26/2014] [Indexed: 11/20/2022]
Abstract
Over 100 known enterovirus serotypes differ in their epidemiological and pathogenic properties. Much less is known about variation of these features on a sub-serotype level, such as genotypes. Echovirus 11 (E11) and E30 are amongst the most frequent causative agents of aseptic meningitis. We studied the molecular epidemiology of these pathogens to evaluate potential epidemiological and pathogenic dissimilarities of their genotypes. The complete VP1 genome region was sequenced for 97 E11 and 62 E30 isolates collected in Russia from 2008 to 2012, and they were studied in comparison with all 140 E11 and 432 E30 sequences available in GenBank. A geographic pattern of genotype prevalence was observed for both types. Russian E11 isolates belonged mainly to A genotype, which is common in Asia, and D5, which is predominant in Europe. For E30, genotype III by classification of Ke et al. (2011), also termed genotype a by Bailly et al. (2009), was endemic in Russia from 2003 to 2012, while it was not detected in Europe and North America during this time. The E30 genotypes VI-B, VI-G, and VI-H (e, f and h) were regularly introduced from different countries, became predominant and vanished after no more than 4years. In addition to geographic patterns, E11 genotypes also differed by isolation source. Genotype A2 viruses were significantly more often found in sewage, compared to genotype D5 that was isolated from both sewage and human samples. In addition, there was evidence of a different capacity for international transfers among E11 GtA subclusters.
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Affiliation(s)
- Maria S Yarmolskaya
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Elena Yu Shumilina
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Olga E Ivanova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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43
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Lukashev AN, Shumilina EY, Belalov IS, Ivanova OE, Eremeeva TP, Reznik VI, Trotsenko OE, Drexler JF, Drosten C. Recombination strategies and evolutionary dynamics of the Human enterovirus A global gene pool. J Gen Virol 2014; 95:868-873. [PMID: 24425417 DOI: 10.1099/vir.0.060004-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We analysed natural recombination in 79 Human enterovirus A strains representing 13 serotypes by sequencing of VP1, 2C and 3D genome regions. The half-life of a non-recombinant tree node in coxsackieviruses 2, 4 and 10 was only 3.5 years, and never more than 9 years. All coxsackieviruses that differed by more than 7 % of the nucleotide sequence in any genome region were recombinants relative to each other. Enterovirus 71 (EV71), on the contrary, displayed remarkable genetic stability. Three major EV71 clades were stable for 19-29 years, with a half-life of non-recombinant viruses between 13 and 18.5 years in different clades. Only five EV71 strains out of over 150 recently acquired non-structural genome regions from coxsackieviruses, while none of 80 contemporary coxsackieviruses had non-structural genes transferred from the three EV71 clades. In contrast to earlier observations, recombination between VP1 and 2C genome regions was not more frequent than between 2C and 3D regions.
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Affiliation(s)
| | - Elena Yu Shumilina
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Ilya S Belalov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Olga E Ivanova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Tatiana P Eremeeva
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Vadim I Reznik
- Center of Hygiene and Epidemiology in Khabarovsk Region, Khabarovsk, Russia
| | - O E Trotsenko
- Khabarovsk Institute of Epidemiology and Microbiology, Khabarovsk, Russia
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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44
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Lukashev AN, Skulachev MV, Ostapenko V, Savchenko AY, Pavshintsev V, Skulachev VP. Advances in Development of Rechargeable Mitochondrial Antioxidants. Progress in Molecular Biology and Translational Science 2014; 127:251-65. [DOI: 10.1016/b978-0-12-394625-6.00010-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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45
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Akhmadishina LV, Koroleva GA, Ivanova OE, Trotsenko OE, Mikhaĭlov MI, Lukashev AN. [Seroepidemiology and molecular epidemiology of enterovirus type 71 in the world and the Russian Federation]. Zh Mikrobiol Epidemiol Immunobiol 2013:112-121. [PMID: 24605685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A review of recent publications on epidemiology and seroepidemiology of enterovirus type 71 in various regions of the world and authors' own results of study of seroepidemiology and molecular epidemiology of EV71 in Russia are presented.
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46
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Abstract
Choice of synonymous codons depends on nucleotide/dinucleotide composition of the genome (termed mutational pressure) and relative abundance of tRNAs in a cell (translational pressure). Mutational pressure is commonly simplified to genomic GC content; however mononucleotide and dinucleotide frequencies in different genomes or mRNAs may vary significantly, especially in RNA viruses. A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. Total GC content was a poor descriptor of viral genome composition and causes of codon usage bias. Genomic nucleotide content was the single most important factor of synonymous codon usage. Moreover, the choice between compatible amino acids (e.g., leucine and isoleucine) was strongly affected by genomic nucleotide composition. Dinucleotide composition at codon positions 2-3 had additional effect on codon usage. Together with mononucleotide composition bias, it could explain almost the entire codon usage bias in RNA viruses. On the other hand, strong dinucleotide content bias at codon position 3-1 found in some viruses had very little effect on codon usage. A hypothetical innate immunity sensor for CpG in RNA could partially explain the codon usage bias, but due to dependence of virus translation upon biased host translation machinery, experimental studies are required to further explore the source of dinucleotide bias in RNA viruses.
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Affiliation(s)
- Ilya S. Belalov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander N. Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow, Russia
- Institute for Virology, University of Bonn Medical Center, Bonn, Germany
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47
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Drexler JF, Corman VM, Müller MA, Lukashev AN, Gmyl A, Coutard B, Adam A, Ritz D, Leijten LM, van Riel D, Kallies R, Klose SM, Gloza-Rausch F, Binger T, Annan A, Adu-Sarkodie Y, Oppong S, Bourgarel M, Rupp D, Hoffmann B, Schlegel M, Kümmerer BM, Krüger DH, Schmidt-Chanasit J, Setién AA, Cottontail VM, Hemachudha T, Wacharapluesadee S, Osterrieder K, Bartenschlager R, Matthee S, Beer M, Kuiken T, Reusken C, Leroy EM, Ulrich RG, Drosten C. Evidence for novel hepaciviruses in rodents. PLoS Pathog 2013; 9:e1003438. [PMID: 23818848 PMCID: PMC3688547 DOI: 10.1371/journal.ppat.1003438] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [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: 02/19/2013] [Accepted: 04/22/2013] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma. Research is complicated by a lack of accessible small animal models. The systematic investigation of viruses of small mammals could guide efforts to establish such models, while providing insight into viral evolutionary biology. We have assembled the so-far largest collection of small-mammal samples from around the world, qualified to be screened for bloodborne viruses, including sera and organs from 4,770 rodents (41 species); and sera from 2,939 bats (51 species). Three highly divergent rodent hepacivirus clades were detected in 27 (1.8%) of 1,465 European bank voles (Myodes glareolus) and 10 (1.9%) of 518 South African four-striped mice (Rhabdomys pumilio). Bats showed anti-HCV immunoblot reactivities but no virus detection, although the genetic relatedness suggested by the serologic results should have enabled RNA detection using the broadly reactive PCR assays developed for this study. 210 horses and 858 cats and dogs were tested, yielding further horse-associated hepaciviruses but none in dogs or cats. The rodent viruses were equidistant to HCV, exceeding by far the diversity of HCV and the canine/equine hepaciviruses taken together. Five full genomes were sequenced, representing all viral lineages. Salient genome features and distance criteria supported classification of all viruses as hepaciviruses. Quantitative RT-PCR, RNA in-situ hybridisation, and histopathology suggested hepatic tropism with liver inflammation resembling hepatitis C. Recombinant serology for two distinct hepacivirus lineages in 97 bank voles identified seroprevalence rates of 8.3 and 12.4%, respectively. Antibodies in bank vole sera neither cross-reacted with HCV, nor the heterologous bank vole hepacivirus. Co-occurrence of RNA and antibodies was found in 3 of 57 PCR-positive bank vole sera (5.3%). Our data enable new hypotheses regarding HCV evolution and encourage efforts to develop rodent surrogate models for HCV.
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Affiliation(s)
- Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Victor Max Corman
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | | | - Anatoly Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Bruno Coutard
- Architectures et Fonctions des Macromolécules Biologiques, UMR 7257 CNRS and Aix-Marseille University, Marseille, France
| | - Alexander Adam
- Institute of Pathology, University of Cologne Medical Centre, Cologne, Germany
| | - Daniel Ritz
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Debby van Riel
- Erasmus MC, Department of Viroscience, Rotterdam, The Netherlands
| | - Rene Kallies
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Stefan M. Klose
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | - Florian Gloza-Rausch
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany
| | - Tabea Binger
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Augustina Annan
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel Oppong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mathieu Bourgarel
- Centre de Cooperation Internationale de Recherche en Agronomie pour le Développement, UPR AGIRs, Montpellier, France
| | - Daniel Rupp
- Department of Infectious Diseases, Molecular Virology, Medical Facility, Heidelberg University, Heidelberg, Germany
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Institute for Virus Diagnostics, Greifswald–Insel Riems, Germany
| | - Mathias Schlegel
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Beate M. Kümmerer
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Detlev H. Krüger
- Institute of Medical Virology (Helmut Ruska Haus), Charité Medical School, Berlin, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, Department of Virology, Hamburg, Germany
| | - Alvaro Aguilar Setién
- Unidad de Investigación Médica en Inmunología, Hospital de Pediatría, México DF, Mexico
| | | | - Thiravat Hemachudha
- Chulalongkorn University, Faculty of Medicine, Neuroscience Center for Research and Development, Bangkok, Thailand
| | - Supaporn Wacharapluesadee
- Chulalongkorn University, Faculty of Medicine, Neuroscience Center for Research and Development, Bangkok, Thailand
| | - Klaus Osterrieder
- Institute of Virology, Free University of Berlin, Department of Veterinary Medicine, Berlin, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Medical Facility, Heidelberg University, Heidelberg, Germany
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute for Virus Diagnostics, Greifswald–Insel Riems, Germany
| | - Thijs Kuiken
- Erasmus MC, Department of Viroscience, Rotterdam, The Netherlands
| | - Chantal Reusken
- Netherlands Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Eric M. Leroy
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier, France
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- * E-mail:
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Trotsenko OE, Lukashev AN, Karavianskaia TN, Reznik VI, Sapega EI, Kotova VO, Amiaga EN, Korita PV. [Molecular-epidemiological monitoring of enterovirus circulation in the Far East and Zabaikalye]. Zh Mikrobiol Epidemiol Immunobiol 2013:70-75. [PMID: 23805656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
6 year molecular-biological monitoring of enteroviruses in the Far East and Zabaikalye was carried out. Nucleotide sequence of 125 strains was determined from 2006 to 2011. Molecular analysis was carried out in VP1 virus genome region. Phylogenetic interactions for ECHO-6, ECHO-30, ECHO-11, Coxsackie B-5 (CB-5), Coxsackie B-1 (CB-1) and Coxsackie A-9 (CA-9) were analyzed. Highly dynamic epidemiology was shown to be inherent for ECHO-6 and ECHO-30 viruses and is characterized by genetic heterogeneity and consequent change of virus variants. On the contrary a relative stability of circulating genotypes is intrinsic for CB-1, CB-5 and ECHO-11 enteroviruses. The results of molecular-biological studies indicate frequent introduction of new enterovirus variants from countries of Europe and Asia.
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Marova AA, Oksanich AS, Kaira AN, Meskina ER, Medvedeva EA, Ivanova OE, Lukashev AN, Kyuregian KK, Kalinkina MA, Egorova OV, Zverev VV, Faĭzuloev EV. [Experience of application of multiplex qPCR for differential diagnostics of intestinal viral infections]. Zh Mikrobiol Epidemiol Immunobiol 2012:39-45. [PMID: 23297630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
AIM Evaluate the effectiveness of multiplex reverse transcription (RT) and polymerase chain reaction with fluorescence detection in real time mode (qPCR) methods for differential detection of 11 groups of intestine viruses (adenoviruses, enteroviruses, polioviruses, hepatitis A and E viruses, group A and C rotaviruses, orthoreoviruses, noroviruses, sapoviruses and astroviruses) in various biological samples. MATERIALS AND METHODS Panels of virus isolates and clinical samples characterized by reference methods were used to evaluate sensitivity of detection of various intestine viruses. Nucleic acids were isolated from study samples and multiplex RT and qPCR were carried out. RESULTS Sensitivity of laboratory reagent kit (LRK) when compared with results obtained from reference methods was 100% for rotavirus A, adenovirus, enterovirus and norovirus, 88.9% for hepatitis E virus and 92.3% for hepatitis A virus, and diagnostic specificity - 99.4%. During analysis of 697 clinical samples from patients with acute intestine infection symptoms nucleic acids of various intestine viruses were isolated in 71.7%. CONCLUSION Multiplex qRT-PCR was shown as an effective method of etiologic diagnostics of an intestine viral infection. Use of LRK was demonstrated to establish etiology of intestine diseases in 63 - 72% and in children with watery diarrhea - in approximately 90% of cases.
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50
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Lukashev AN, Drexler JF, Kotova VO, Amjaga EN, Reznik VI, Gmyl AP, Grard G, Taty Taty R, Trotsenko OE, Leroy EM, Drosten C. Novel serotypes 105 and 116 are members of distinct subgroups of human enterovirus C. J Gen Virol 2012; 93:2357-2362. [PMID: 22894922 DOI: 10.1099/vir.0.043216-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The full coding sequences of two novel human enterovirus (HEV)-C serotypes 105 and 116, sampled in the Republic of the Congo in 2010 and in Russia in 2011, were identified in this study. Enterovirus (EV)-105 was closest to EV-104 in the 5' NTR and to EV-109 in the coding genome region. It had the same unconventional 5' NTR as EV-104 and EV-109. The non-cytopathogenic EV-116 was phylogenetically close to coxsackievirus (CV)-A1, CV-A19 and CV-A22, which also cannot be propagated in routinely used cell cultures. There were signs of recombination within this subgroup of HEV-C; however, recombination with conventional HEV-C was restricted, implying partial reproductive isolation. As there is also evidence of different permissive replication systems and distinct genetic properties of these subgroups, they may represent subspecies of the HEV-C species or different stages of speciation.
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Affiliation(s)
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Valeria O Kotova
- Khabarovsk Institute of Epidemiology and Microbiology, Khabarovsk, Russia
| | - Elena N Amjaga
- Khabarovsk Institute of Epidemiology and Microbiology, Khabarovsk, Russia
| | - Vadim I Reznik
- Center of Hygiene and Epidemiology in Khabarovsk Region, Khabarovsk, Russia
| | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Gilda Grard
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Raphael Taty Taty
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Olga E Trotsenko
- Khabarovsk Institute of Epidemiology and Microbiology, Khabarovsk, Russia
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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