This page has only limited features, please log in for full access.

Dr. Andrei Deviatkin
Sechenov First Moscow State Medical University

Basic Info


Research Keywords & Expertise

0 Diagnostics
0 Evolution
0 Taxonomy
0 phylogeny
0 Rabies Virus

Fingerprints

Evolution
Rabies Virus
tick-borne encephalitis virus
Diagnostics

Honors and Awards

The user has no records in this section


Career Timeline

The user has no records in this section.


Short Biography

The user biography is not available.
Following
Followers
Co Authors
The list of users this user is following is empty.
Following: 0 users

Feed

Journal article
Published: 29 June 2021 in Viruses
Reads 0
Downloads 0

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.

ACS Style

Yulia Vakulenko; Andrei Deviatkin; Jan Drexler; Alexander Lukashev. Modular Evolution of Coronavirus Genomes. Viruses 2021, 13, 1270 .

AMA Style

Yulia Vakulenko, Andrei Deviatkin, Jan Drexler, Alexander Lukashev. Modular Evolution of Coronavirus Genomes. Viruses. 2021; 13 (7):1270.

Chicago/Turabian Style

Yulia Vakulenko; Andrei Deviatkin; Jan Drexler; Alexander Lukashev. 2021. "Modular Evolution of Coronavirus Genomes." Viruses 13, no. 7: 1270.

English abstract
Published: 07 March 2021 in Problems of Virology
Reads 0
Downloads 0

Введение. Геморрагическая лихорадка с почечным синдромом (ГЛПС) занимает ведущее место среди природно-очаговых болезней человека в Российской Федерации. Этиотропная терапия заболевания в настоящее время отсутствует. Наиболее действенным методом контроля этой инфекции может стать вакцинопрофилактика. Основными критериями оценки инактивированной вакцины являются её иммуногенность и специфическая активность.Цель исследования - разработка чувствительной и специфичной методики проведения ПЦР в реальном времени с целью количественного определения вирусной РНК в инактивированной вакцине, а также установление корреляции между содержанием генетического материала вируса и выраженностью иммуногенности. Материал и методы. В качестве диагностической мишени для олигонуклеотидов и флуоресцентных зондов выбраны фрагменты L-сегмента вакцинных штаммов вирусов ГЛПС Пуумала, Хантаан, Сочи. Иммуногенность экспериментальных вакцин контролировали по индукции нейтрализующих антител (нАТ) в ответ на иммунизацию мышей линии BALB/c.Результаты. Разработана высокоспецифичная, чувствительная методика проведения ПЦР в реальном времени, имеющая высокий показатель воспроизводимости. Аналитическая чувствительность составила для вирусов Пуумала 1,24 ± 1,5 х 102 копий/мл, Хантаан - 1,16 ± 1,4 х 102 копий/мл, Сочи - 1,32 ± 1,8 х 102 копий/мл при содержании вируса 1,5 ± 0,5, 1,8 ± 0,5 и 2,2 ± 0,5 lg ФОЕ/мл соответственно. Показано, что количество вирусной РНК в составе экспериментальных вакцинных препаратов, инактивированных β-про-пиолактоном (β-ПЛ), пропорционально титру нАТ в ответ на иммунизацию.Обсуждение. Установлено, что способ инактивирования вируса влияет на выявляемое количество копий РНК, не оказывая при этом воздействия на иммуногенность, что указывает на равнозначное повреждение белков-иммуногенов при разной степени повреждения вирусной РНК. Прямая зависимость между содержанием копий нуклеиновой кислоты вируса и иммуногенностью позволяет использовать этот критерий для дозирования вакцинного препарата.Заключение. Разработанная система оценки количественного содержания вирусной РНК делает перспективным её применение для контроля специфической активности вакцины против ГЛПС.

ACS Style

M. S. Egorova; S. S. Kurashova; A. A. Ishmukhametov; M. V. Balovneva; A. A. Deviatkin; M. V. Safonova; S. V. Ozherelkov; Yu. Kh. Khapchaev; A. S. Balkina; A. V. Belyakova; T. K. Dzagurova; E A. Tkachenko. Real-time PCR assay development for the control of vaccine against hemorrhagic fever with renal syndrome. Problems of Virology 2021, 66, 65 -73.

AMA Style

M. S. Egorova, S. S. Kurashova, A. A. Ishmukhametov, M. V. Balovneva, A. A. Deviatkin, M. V. Safonova, S. V. Ozherelkov, Yu. Kh. Khapchaev, A. S. Balkina, A. V. Belyakova, T. K. Dzagurova, E A. Tkachenko. Real-time PCR assay development for the control of vaccine against hemorrhagic fever with renal syndrome. Problems of Virology. 2021; 66 (1):65-73.

Chicago/Turabian Style

M. S. Egorova; S. S. Kurashova; A. A. Ishmukhametov; M. V. Balovneva; A. A. Deviatkin; M. V. Safonova; S. V. Ozherelkov; Yu. Kh. Khapchaev; A. S. Balkina; A. V. Belyakova; T. K. Dzagurova; E A. Tkachenko. 2021. "Real-time PCR assay development for the control of vaccine against hemorrhagic fever with renal syndrome." Problems of Virology 66, no. 1: 65-73.

Journal article
Published: 28 February 2021 in Russian Journal of Infection and Immunity
Reads 0
Downloads 0

Molecular phylogenetics, particularly statistical phylogenetics, is widely used to solve the fundamental and applied problems in virology. Bayesian, or statistical, phylogenetic methods, which came into practice 10—15 years ago, markedly expanded the range of questions that can be answered based on analyzing nucleotide and amino acid sequences. An opportunity of using various evolution models allows inferring the chronology, geography and dynamics of the infection spreading. For example, analysis of globally distributed HIV group M by Bayesian methods demonstrated with a probability of 99% that the most recent common ancestor of these viruses existed in the surroundings of the city of Kinshasa (Democratic Republic of the Congo) in the early 1920s. Another study showed that H9N2 influenza virus most likely passed on to humans from wild ducks in Hong Kong in the late 1960s. In addition, using of the Bayesian analysis allows to evaluating the effect of measures taken on the development of the epidemic process. For example, it was shown retrospectively that the rate of hepatitis C virus infection cases in Egypt increased by several orders of magnitude in the mid-20th century. A sharp rise in new case rate is associated with the treatment for schistosomiasis by using non-sterile repeatedly used syringes. A set of Bayesian analysis methods has been applied in tens of thousands of researches describing various aspects of the occurrence and spread of infectious diseases in humans and animals. This was facilitated by the development and accessibility of software that implements these methods. The complexity of Bayesian phylogenetic methods imposes strict requirements on the data being analyzed. The correctness of the phylogenetic analysis data depends on various factors. For example, it is necessary to choose an evolutionary model that most adequately describes the studied objects. A mandatory step in formulating the results is the justification of the selected model. For viruses, the acquisition of genetic elements from other organisms is typical, therefore, the genomes even from closely related viruses may have non-homologous regions unsuitable for phylogenetic analysis. Another aspect is the creation of a representative dataset. Sometimes, all stages of the analysis are not indicated in publications, so that the data obtained can be interpreted ambiguously. The correct use of statistical phylogenetics methods in virology is possible only upon understanding their principles, proper methods of data preparation and evolutionary model selection criteria.

ACS Style

Yu. A. Vakulenko; A. N. Lukashev; A. A. Deviatkin. The use of statistical phylogenetics in virology. Russian Journal of Infection and Immunity 2021, 11, 42 -56.

AMA Style

Yu. A. Vakulenko, A. N. Lukashev, A. A. Deviatkin. The use of statistical phylogenetics in virology. Russian Journal of Infection and Immunity. 2021; 11 (1):42-56.

Chicago/Turabian Style

Yu. A. Vakulenko; A. N. Lukashev; A. A. Deviatkin. 2021. "The use of statistical phylogenetics in virology." Russian Journal of Infection and Immunity 11, no. 1: 42-56.

Journal article
Published: 31 October 2020 in Viruses
Reads 0
Downloads 0

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).

ACS Style

Andrei Deviatkin; Galina Karganova; Yulia Vakulenko; Alexander Lukashev. TBEV Subtyping in Terms of Genetic Distance. Viruses 2020, 12, 1240 .

AMA Style

Andrei Deviatkin, Galina Karganova, Yulia Vakulenko, Alexander Lukashev. TBEV Subtyping in Terms of Genetic Distance. Viruses. 2020; 12 (11):1240.

Chicago/Turabian Style

Andrei Deviatkin; Galina Karganova; Yulia Vakulenko; Alexander Lukashev. 2020. "TBEV Subtyping in Terms of Genetic Distance." Viruses 12, no. 11: 1240.

Journal article
Published: 15 October 2020 in Microorganisms
Reads 0
Downloads 0

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.

ACS Style

Andrei A. Deviatkin; Ivan S. Kholodilov; Oxana A. Belova; Sergey V. Bugmyrin; Lubov A. Bespyatova; Anna Y. Ivannikova; Yulia A. Vakulenko; Alexander N. Lukashev; Galina G. Karganova. Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances. Microorganisms 2020, 8, 1589 .

AMA Style

Andrei A. Deviatkin, Ivan S. Kholodilov, Oxana A. Belova, Sergey V. Bugmyrin, Lubov A. Bespyatova, Anna Y. Ivannikova, Yulia A. Vakulenko, Alexander N. Lukashev, Galina G. Karganova. Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances. Microorganisms. 2020; 8 (10):1589.

Chicago/Turabian Style

Andrei A. Deviatkin; Ivan S. Kholodilov; Oxana A. Belova; Sergey V. Bugmyrin; Lubov A. Bespyatova; Anna Y. Ivannikova; Yulia A. Vakulenko; Alexander N. Lukashev; Galina G. Karganova. 2020. "Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances." Microorganisms 8, no. 10: 1589.

Review
Published: 11 July 2020 in International Journal of Molecular Sciences
Reads 0
Downloads 0

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.

ACS Style

Dmitry S. Mikhaylenko; Marina V. Nemtsova; Irina V. Bure; Ekaterina B. Kuznetsova; Ekaterina A. Alekseeva; Vadim V. Tarasov; Alexander N. Lukashev; Marina I. Beloukhova; Andrei A. Deviatkin; Jr. Andrey A. Zamyatnin. Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response. International Journal of Molecular Sciences 2020, 21, 4911 .

AMA Style

Dmitry S. Mikhaylenko, Marina V. Nemtsova, Irina V. Bure, Ekaterina B. Kuznetsova, Ekaterina A. Alekseeva, Vadim V. Tarasov, Alexander N. Lukashev, Marina I. Beloukhova, Andrei A. Deviatkin, Jr. Andrey A. Zamyatnin. Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response. International Journal of Molecular Sciences. 2020; 21 (14):4911.

Chicago/Turabian Style

Dmitry S. Mikhaylenko; Marina V. Nemtsova; Irina V. Bure; Ekaterina B. Kuznetsova; Ekaterina A. Alekseeva; Vadim V. Tarasov; Alexander N. Lukashev; Marina I. Beloukhova; Andrei A. Deviatkin; Jr. Andrey A. Zamyatnin. 2020. "Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response." International Journal of Molecular Sciences 21, no. 14: 4911.

Journal article
Published: 23 February 2020 in Viruses
Reads 0
Downloads 0

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.

ACS Style

Andrei A. Deviatkin; Ivan S. Kholodilov; Yulia A. Vakulenko; Galina G. Karganova; Alexander N. Lukashev. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses 2020, 12, 247 .

AMA Style

Andrei A. Deviatkin, Ivan S. Kholodilov, Yulia A. Vakulenko, Galina G. Karganova, Alexander N. Lukashev. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses. 2020; 12 (2):247.

Chicago/Turabian Style

Andrei A. Deviatkin; Ivan S. Kholodilov; Yulia A. Vakulenko; Galina G. Karganova; Alexander N. Lukashev. 2020. "Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis?" Viruses 12, no. 2: 247.

Review
Published: 09 January 2020 in Biomedicines
Reads 0
Downloads 0

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.

ACS Style

Andrei A. Deviatkin; Yulia A. Vakulenko; Ludmila V. Akhmadishina; Vadim V. Tarasov; Marina Beloukhova; Andrey A. Zamyatnin Jr.; Alexander N. Lukashev. Emerging Concepts and Challenges in Rheumatoid Arthritis Gene Therapy. Biomedicines 2020, 8, 9 .

AMA Style

Andrei A. Deviatkin, Yulia A. Vakulenko, Ludmila V. Akhmadishina, Vadim V. Tarasov, Marina Beloukhova, Andrey A. Zamyatnin Jr., Alexander N. Lukashev. Emerging Concepts and Challenges in Rheumatoid Arthritis Gene Therapy. Biomedicines. 2020; 8 (1):9.

Chicago/Turabian Style

Andrei A. Deviatkin; Yulia A. Vakulenko; Ludmila V. Akhmadishina; Vadim V. Tarasov; Marina Beloukhova; Andrey A. Zamyatnin Jr.; Alexander N. Lukashev. 2020. "Emerging Concepts and Challenges in Rheumatoid Arthritis Gene Therapy." Biomedicines 8, no. 1: 9.

Journal article
Published: 06 November 2019 in Viruses
Reads 0
Downloads 0

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

ACS Style

Yulia Vakulenko; Andrei Deviatkin; Alexander Lukashev. The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019, 11, 1032 .

AMA Style

Yulia Vakulenko, Andrei Deviatkin, Alexander Lukashev. The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses. 2019; 11 (11):1032.

Chicago/Turabian Style

Yulia Vakulenko; Andrei Deviatkin; Alexander Lukashev. 2019. "The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses." Viruses 11, no. 11: 1032.

Journal article
Published: 25 September 2019 in Viruses
Reads 0
Downloads 0

Neurovirulent enterovirus 71 (EV-A71) caused a massive epidemic in China in 2008–2011. While subgenotype C4 was the major causative agent, a few isolates were almost identical to the prototype EV-A71 strain and belonged to genotype A. This variant was allegedly extinct since 1970, and its identification in this epidemic suggests reintroduction of the archive virus. Regression analysis of genetic distances (TempEst software) was of moderate utility due to the low resolution of classical phylogenetic methods. Bayesian phylogenetic analysis (BEAST software) suggested artificial introduction event based on highly aberrant phylogenetic tree branch rates that differed by over three standard deviations from the mean substitution rate for EV71. Manual nucleotide-level analysis was used to further explore the virus spread pattern after introduction into circulation. Upon reintroduction, the virus accumulated up to seven substitutions in VP1, most of them non-synonymous and located within the capsid’s canyon or at its rims, compatible with readaptation of a lab strain to natural circulation.

ACS Style

Yulia Vakulenko; Andrei Deviatkin; Alexander Lukashev. Using Statistical Phylogenetics for Investigation of Enterovirus 71 Genotype A Reintroduction into Circulation. Viruses 2019, 11, 895 .

AMA Style

Yulia Vakulenko, Andrei Deviatkin, Alexander Lukashev. Using Statistical Phylogenetics for Investigation of Enterovirus 71 Genotype A Reintroduction into Circulation. Viruses. 2019; 11 (10):895.

Chicago/Turabian Style

Yulia Vakulenko; Andrei Deviatkin; Alexander Lukashev. 2019. "Using Statistical Phylogenetics for Investigation of Enterovirus 71 Genotype A Reintroduction into Circulation." Viruses 11, no. 10: 895.

Review
Published: 24 May 2019 in Pharmaceutics
Reads 0
Downloads 0

Brain tumors are characterized by very high mortality and, despite the continuous research on new pharmacological interventions, little therapeutic progress has been made. One of the main obstacles to improve current treatments is represented by the impermeability of the blood vessels residing within nervous tissue as well as of the new vascular net generating from the tumor, commonly referred to as blood-brain barrier (BBB) and blood-brain tumor barrier (BBTB), respectively. In this review, we focused on established and emerging strategies to overcome the blood-brain barrier to increase drug delivery for brain cancer. To date, there are three broad strategies being investigated to cross the brain vascular wall and they are conceived to breach, bypass, and negotiate the access to the nervous tissue. In this paper, we summarized these approaches highlighting their working mechanism and their potential impact on the quality of life of the patients as well as their current status of development.

ACS Style

Alessandro Parodi; Magdalena Rudzińska; Andrei A. Deviatkin; Surinder M. Soond; Alexey V. Baldin; Andrey A. Zamyatnin. Established and Emerging Strategies for Drug Delivery Across the Blood-Brain Barrier in Brain Cancer. Pharmaceutics 2019, 11, 245 .

AMA Style

Alessandro Parodi, Magdalena Rudzińska, Andrei A. Deviatkin, Surinder M. Soond, Alexey V. Baldin, Andrey A. Zamyatnin. Established and Emerging Strategies for Drug Delivery Across the Blood-Brain Barrier in Brain Cancer. Pharmaceutics. 2019; 11 (5):245.

Chicago/Turabian Style

Alessandro Parodi; Magdalena Rudzińska; Andrei A. Deviatkin; Surinder M. Soond; Alexey V. Baldin; Andrey A. Zamyatnin. 2019. "Established and Emerging Strategies for Drug Delivery Across the Blood-Brain Barrier in Brain Cancer." Pharmaceutics 11, no. 5: 245.

Journal article
Published: 11 December 2018 in International Journal of Molecular Sciences
Reads 0
Downloads 0

Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model (HMMer) algorithm and Pfam database, comprehensive analysis of the T. aestivum genome revealed a large number of proteases (1544 in total) belonging to the five major protease families: serine, cysteine, threonine, aspartic, and metallo-proteases. Mass-spectrometry analysis revealed a 30% difference between degradomes of distinct wheat cultivars (Khakasskaya and Darya), and infection by biotrophic (Puccinia recondita Rob. ex Desm f. sp. tritici) or necrotrophic (Stagonospora nodorum) pathogens induced drastic changes in the presence of proteolytic enzymes. This study shows that an early immune response to biotic stress is associated with the same core of proteases from the C1, C48, C65, M24, M41, S10, S9, S8, and A1 families. Further liquid chromatography-mass spectrometry (LC-MS) analysis of the detected protease-derived peptides revealed that infection by both pathogens enhances overall proteolytic activity in wheat cells and leads to activation of proteolytic cascades. Moreover, sites of proteolysis were identified within the proteases, which probably represent targets of autocatalytic activation, or hydrolysis by another protease within the proteolytic cascades. Although predicted substrates of metacaspase-like and caspase-like proteases were similar in biotrophic and necrotrophic infections, proteolytic activation of proteases was not found to be associated with metacaspase-like and caspase-like activities. These findings indicate that the response of T. aestivum to biotic stress is regulated by unique mechanisms.

ACS Style

Anastasia V. Balakireva; Andrei A. Deviatkin; Victor G. Zgoda; Maxim I. Kartashov; Natalia S. Zhemchuzhina; Vitaly G. Dzhavakhiya; Andrey V. Golovin; Jr. Andrey A. Zamyatnin. Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L. International Journal of Molecular Sciences 2018, 19, 3991 .

AMA Style

Anastasia V. Balakireva, Andrei A. Deviatkin, Victor G. Zgoda, Maxim I. Kartashov, Natalia S. Zhemchuzhina, Vitaly G. Dzhavakhiya, Andrey V. Golovin, Jr. Andrey A. Zamyatnin. Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L. International Journal of Molecular Sciences. 2018; 19 (12):3991.

Chicago/Turabian Style

Anastasia V. Balakireva; Andrei A. Deviatkin; Victor G. Zgoda; Maxim I. Kartashov; Natalia S. Zhemchuzhina; Vitaly G. Dzhavakhiya; Andrey V. Golovin; Jr. Andrey A. Zamyatnin. 2018. "Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L." International Journal of Molecular Sciences 19, no. 12: 3991.

Review
Published: 03 August 2018 in Reviews in Medical Virology
Reads 0
Downloads 0

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.

ACS Style

Alexander N. Lukashev; Yulia A. Vakulenko; Natalia A. Turbabina; Andrei Deviatkin; Jan Felix Drexler. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Reviews in Medical Virology 2018, 28, e2002 .

AMA Style

Alexander N. Lukashev, Yulia A. Vakulenko, Natalia A. Turbabina, Andrei Deviatkin, Jan Felix Drexler. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Reviews in Medical Virology. 2018; 28 (6):e2002.

Chicago/Turabian Style

Alexander N. Lukashev; Yulia A. Vakulenko; Natalia A. Turbabina; Andrei Deviatkin; Jan Felix Drexler. 2018. "Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?" Reviews in Medical Virology 28, no. 6: e2002.

Journal article
Published: 01 June 2018 in Infection, Genetics and Evolution
Reads 0
Downloads 0

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).

ACS Style

Andrei A. Deviatkin; Alexander N. Lukashev. Recombination in the rabies virus and other lyssaviruses. Infection, Genetics and Evolution 2018, 60, 97 -102.

AMA Style

Andrei A. Deviatkin, Alexander N. Lukashev. Recombination in the rabies virus and other lyssaviruses. Infection, Genetics and Evolution. 2018; 60 ():97-102.

Chicago/Turabian Style

Andrei A. Deviatkin; Alexander N. Lukashev. 2018. "Recombination in the rabies virus and other lyssaviruses." Infection, Genetics and Evolution 60, no. : 97-102.

Journal article
Published: 01 April 2018 in Infection, Genetics and Evolution
Reads 0
Downloads 0
ACS Style

A.N. Lukashev; A.A. Deviatkin. Phylodynamics of Crimean Congo hemorrhagic fever virus in South Russia. Infection, Genetics and Evolution 2018, 59, 23 -27.

AMA Style

A.N. Lukashev, A.A. Deviatkin. Phylodynamics of Crimean Congo hemorrhagic fever virus in South Russia. Infection, Genetics and Evolution. 2018; 59 ():23-27.

Chicago/Turabian Style

A.N. Lukashev; A.A. Deviatkin. 2018. "Phylodynamics of Crimean Congo hemorrhagic fever virus in South Russia." Infection, Genetics and Evolution 59, no. : 23-27.

Journal article
Published: 01 February 2018 in Journal of General Virology
Reads 0
Downloads 0

We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.

ACS Style

Alexander G. Litov; Andrei Deviatkin; Irina A. Goptar; Vladimir G. Dedkov; Anatoly P. Gmyl; Mikhail L. Markelov; German A. Shipulin; Galina G. Karganova. Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing. Journal of General Virology 2018, 99, 240 -245.

AMA Style

Alexander G. Litov, Andrei Deviatkin, Irina A. Goptar, Vladimir G. Dedkov, Anatoly P. Gmyl, Mikhail L. Markelov, German A. Shipulin, Galina G. Karganova. Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing. Journal of General Virology. 2018; 99 (2):240-245.

Chicago/Turabian Style

Alexander G. Litov; Andrei Deviatkin; Irina A. Goptar; Vladimir G. Dedkov; Anatoly P. Gmyl; Mikhail L. Markelov; German A. Shipulin; Galina G. Karganova. 2018. "Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing." Journal of General Virology 99, no. 2: 240-245.

Evaluation study
Published: 01 January 2018 in Diagnostic Microbiology and Infectious Disease
Reads 0
Downloads 0

Rabies virus is endemic to Russia, among other countries. It is therefore critical to develop a high-quality and high-precision diagnostic procedure for the control and prevention of infection. The main objective of the research presented here was to develop a reliable RT-qPCR assay for rabies diagnostics. For this purpose, a RABV strains from various biological and geographical origins were used. In addition, rabies-positive and rabies-negative samples, as well as nucleic acids from other viruses and DNA extracted from the brain tissues of mice, dogs, cats, bats and humans, were studied using the developed assay. The analytical sensitivity of the assay, as assessed using armored recombinant positive control dilutions, was 103 copies/ml, and the sensitivity measured using characterized strains was between 0.1 LD50/ml and 1.0 LD50/ml. A broad range of RNA from RABV strains circulating in different regions of Russia, as well as RNA from RABV-positive primary brain samples from 81 animals and two humans, was detected using the developed assay. No false-positive or false-negative results were obtained. Given that high analytical and diagnostic sensitivities and a high specificity were verified for this assay, it has high potential as a screening test that may be suitable for the epizootiological monitoring of animals and for the fast postmortem diagnosis of rabies.

ACS Style

V.G. Dedkov; A.A. Deviatkin; Е.м. Poleshchuk; M.V. Safonova; E.A. Blinova; M. Yu Shchelkanov; G.N. Sidorov; E.G. Simonova; German Shipulin. Development and evaluation of a RT-qPCR assay for fast and sensitive rabies diagnosis. Diagnostic Microbiology and Infectious Disease 2018, 90, 18 -25.

AMA Style

V.G. Dedkov, A.A. Deviatkin, Е.м. Poleshchuk, M.V. Safonova, E.A. Blinova, M. Yu Shchelkanov, G.N. Sidorov, E.G. Simonova, German Shipulin. Development and evaluation of a RT-qPCR assay for fast and sensitive rabies diagnosis. Diagnostic Microbiology and Infectious Disease. 2018; 90 (1):18-25.

Chicago/Turabian Style

V.G. Dedkov; A.A. Deviatkin; Е.м. Poleshchuk; M.V. Safonova; E.A. Blinova; M. Yu Shchelkanov; G.N. Sidorov; E.G. Simonova; German Shipulin. 2018. "Development and evaluation of a RT-qPCR assay for fast and sensitive rabies diagnosis." Diagnostic Microbiology and Infectious Disease 90, no. 1: 18-25.

Journal article
Published: 06 October 2017 in PeerJ
Reads 0
Downloads 0

BackgroundEnteroviruses 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.MethodsTo 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.ResultsA 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 C3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.DiscussionDespite 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.

ACS Style

Maria Prostova; Andrei Deviatkin; Irina O. Tcelykh; Alexander N. Lukashev; Anatoly P. Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C. PeerJ 2017, 5, e3896 .

AMA Style

Maria Prostova, Andrei Deviatkin, Irina O. Tcelykh, Alexander N. Lukashev, Anatoly P. Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C. PeerJ. 2017; 5 ():e3896.

Chicago/Turabian Style

Maria Prostova; Andrei Deviatkin; Irina O. Tcelykh; Alexander N. Lukashev; Anatoly P. Gmyl. 2017. "Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C." PeerJ 5, no. : e3896.

Preprint
Published: 12 September 2017
Reads 0
Downloads 0

Background. Enteroviruses are small non-enveloped viruses with (+) 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 low fidelity, 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 (>6400 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.

ACS Style

Maria A Prostova; Andrei A Deviatkin; Irina O Tcelykh; Alexander N Lukashev; Anatoly P Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C. 2017, 1 .

AMA Style

Maria A Prostova, Andrei A Deviatkin, Irina O Tcelykh, Alexander N Lukashev, Anatoly P Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C. . 2017; ():1.

Chicago/Turabian Style

Maria A Prostova; Andrei A Deviatkin; Irina O Tcelykh; Alexander N Lukashev; Anatoly P Gmyl. 2017. "Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C." , no. : 1.

Preprint content
Published: 12 September 2017
Reads 0
Downloads 0

Background. Enteroviruses are small non-enveloped viruses with (+) 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 low fidelity, 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 (>6400 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.

ACS Style

Maria A Prostova; Andrei A Deviatkin; Irina O Tcelykh; Alexander N Lukashev; Anatoly P Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C. 2017, 1 .

AMA Style

Maria A Prostova, Andrei A Deviatkin, Irina O Tcelykh, Alexander N Lukashev, Anatoly P Gmyl. Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C. . 2017; ():1.

Chicago/Turabian Style

Maria A Prostova; Andrei A Deviatkin; Irina O Tcelykh; Alexander N Lukashev; Anatoly P Gmyl. 2017. "Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C." , no. : 1.