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2. Soil Giant Phage: Genome and Biological Characteristics of Sinorhizobium Jumbo Phage.

Author

Kozlova, Alexandra P., Muntyan, Victoria S., Vladimirova, Maria E., Saksaganskaia, Alla S., Kabilov, Marsel R., Gorbunova, Maria K., Gorshkov, Andrey N., Grudinin, Mikhail P., Simarov, Boris V., and Roumiantseva, Marina L.

Subjects
AMINO acid sequence, NITROGEN-fixing bacteria, BACTERIOPHAGE T4, BACTERIOPHAGES, NITROGEN-fixing microorganisms
Abstract

This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage–microbe interactions with nitrogen-fixing symbiotic microorganisms. [ABSTRACT FROM AUTHOR]

Published
2024
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3. CRISPR-Cas9 mediated knockout of AnxA6 gene enhances influenza A virus replication in low-permissive HEK293FT cell line

Author

Komissarov, Andrey, primary, Sergeeva, Mariia, additional, Zhuravlev, Evgenii, additional, Medvedev, Sergey, additional, Malakhova, Anastasia, additional, Andreeva, Evgeniya, additional, Shurygina, Anna-Polina, additional, Gorshkov, Andrey, additional, Timofeeva, Mariia, additional, Balakhonova, Evgenia, additional, Grudinin, Mikhail, additional, Zakian, Suren, additional, Richter, Vladimir, additional, and Stepanov, Grigory, additional

Published
2022
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8. COMPARATIVE GENOMICS OF THE SINORHIZOBIAL PHILM21-LIKE INTACT PROPHAGESON COMPLETE CHROMOSOMES.

Author

Kozlova, Alexandra P., Muntyan, Victoria S., Vladimirova, Maria E., Grudinin, Mikhail P., and Roumiantseva, Marina L.

Subjects
ROOT-tubercles, CHROMOSOMES, BACTERIAL chromosomes, HORIZONTAL gene transfer, COMPARATIVE genomics, AMINO acid sequence, INTEGRASES, ALFALFA
Abstract

Soil saprophytic nitrogen-fixing nodule bacteria (rhizobia) of the Sinorhizobium meliloti species are formed symbiosis with alfalfa and can also be a host of bacteriophages. Rhizobia have a symbiotic and saprophytic life phase’s cycle. Nodules formed by rhizobia on alfalfa roots are destroyed at the end of the growing season and bacteria surviving in nodule threads and did not transformed into bacteroids are released into the soil microbiome. The last is enriched in bacteriophages, which can significantly decrease viability and population density of rhizobia. Bacteriophages can cause lytic infection, accompanied by reprogramming of the host metabolism, destruction of the host cell, or can integrate into the bacterial chromosome as prophages in the result of lysogenic infection that and transmitted to future generations. In this work, sequences of chromosomes of 22 S. meliloti strains deposited in GenBank with additional two strains the AK555 and CXM1-105 strains (sequenced in the framework of the RSF17-16-01095 project) were evaluated for prophages by PHASTER web server. ORFs and protein sequences were analyzed by BLASTn and BLASTp, respectively. Phylogenetic analysis was performed by IQTree (ML). The 18 sequences of intact phiLM21-like (phiLM21, NC_029046) prophages were detected in the chromosomes of the 14 different S. meliloti strains. The sizes of phiLM21-like prophages ranged from 50.8 to 69kb in length. The GC-content (%) of prophages varied from 59.2 to 60.8 and contained from 55 to 90 ORFs. Prophages were integrated into different tRNA genes located in the second and third quarters of the chromosome counting from the oriC. Revealed phiLM21-like prophages contained 3 types of integrases. The 11 out of 16 integrases were homologous on 26% to integrase from Azospirillum phage Cd (YP_001686913.1), the other 4 showed homology (37%) to integrase from Caulobacter phage Cr30 (YP_009098910.1) and the last one was on 81.6% identical to the integrase of the phiLM21 bacteriophage (YP_009221472.1). It was established that more than 50% of all ORFs encoded genes were homologous to phage genes, among which were ORFs encoding head and tail of the virion. Obtained data strongly evident that a high recombination activity is occurred between phages, as well as prophages are actively participated in horizontal gene transfer in a phage-bacteria-phage interaction frame. This work was financially supported by RSF 20-16-00105. [ABSTRACT FROM AUTHOR]

Published
2020
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10. Safety and efficacy of p62 DNA vaccine ELENAGEN in a first-in-human trial in patients with advanced solid tumors

Author

Ponomarenko, Dmitry M., primary, Klimova, Irina D., additional, Chapygina, Yulia A., additional, Dvornichenko, Viktoria V., additional, Zhukova, Natalia V., additional, Orlova, Rashida V., additional, Manikhas, Georgy M., additional, Zyryanov, Alexandr V., additional, Burkhanova, Lilya A., additional, Badrtdinova, Irina I., additional, Oshchepkov, Basile N., additional, Filippova, Elena V., additional, Orlov, Sergei V., additional, Kolesnikov, Sergei I., additional, Sufianov, Albert A., additional, Baum, Svetlana R., additional, Zaitzeva, Olga Y., additional, Komissarov, Andrey B., additional, Grudinin, Mikhail P., additional, Kiselev, Oleg I., additional, Tsyb, Anatoly F., additional, Venanzi, Franco, additional, Shcherbinina, Vita, additional, Chursov, Andrey, additional, Gabai, Vladimir L., additional, and Shneider, Alexander M., additional

Published
2017
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11. Changes in the antigenic and genetic structure of influenza viruses: analysis of surveillance data of influenza A and B in Russia in 2006-2013

Author

Grudinin Mikhail P., Pisareva Maria M., Komissarov Andrey B., Kosheleva Anna A., Buzitskaya Janna V., Stukova Marina A., Prokopetz Alexandra V., Danilenko Daria M., Konovalova Nadezhda I., Lobova Tamara G., Sominina Anna A., and Kiselev Oleg I.

Subjects
influenza virus, hemagglutinin, antigenic properties, phylogenetic structure, viruses, virus diseases
Abstract

The goal of this research project was to study the natural variability of human influenza A and B viruses based on the analysis of the population structure of influenza viruses, circulating in Russia in 2006-2013, in order to determine the direction of their genetic and antigenic drift by comparison to the WHO reference strains. Our results proved that during that period significant changes occurred in the genetic structure of influenza viruses, their phylogenetic affiliation, as well as their sensitivity to antiviral drugs. According to the surveillance data, the percentage of influenza A(H1N1) viruses among patients with influenza-like illness or acute respiratory infection gradually decreased from 42% of the total number of influenza viruses in 2006-2007 to 19% in 2008- 2009. Influenza A(H1N1) viruses are characterized by «silent» variability that manifests in the gradual accumulation of amino acid substitutions in the minor undetectable group of viruses. The share of influenza A(H3N2) viruses varied from 10% in the 1st post pandemic year to approx. 60% in 2008-2009 and 2011- 2012 epidemic seasons. All of the influenza A strains isolated during the last years of the period, covered in this study, were found to be susceptible to neuraminidase inhibitors and resistant to adamantane antivirals. Influenza B viruses of both Yamagata and Victoria lineages circulated in Russia in the period from 2006 to 2013. The vast majority of these influenza B viruses belonged to the Victoria lineage. Phylogenetic and antigenic analyses of influenza B viruses have demonstrated a gradual drift of Russian isolates from the reference strains. No changes leading to resistance to oseltamivir or zanamivir were found in influenza B strains isolated until 2013.

Published
2015

12. Genetic characterization of influenza viruses from influenza-related hospital admissions in the St. Petersburg and Valencia sites of the Global Influenza Hospital Surveillance Network during the 2013/14 influenza season

Author

López-Labrador, F. Xavier, primary, Natividad-Sancho, Angels, additional, Pisareva, Maria, additional, Komissarov, Andrey, additional, Salvatierra, Karina, additional, Fadeev, Artem, additional, Moya, Andrés, additional, Grudinin, Mikhail, additional, Díez-Domingo, Javier, additional, Afanasieva, Olga, additional, Konovalova, Nadezhda, additional, Sominina, Anna, additional, and Puig-Barberà, Joan, additional

Published
2016
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13. Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation)

Author

Komissarov, Andrey, primary, Fadeev, Artem, additional, Sergeeva, Maria, additional, Petrov, Sergey, additional, Sintsova, Kseniya, additional, Egorova, Anna, additional, Pisareva, Maria, additional, Buzitskaya, Zhanna, additional, Musaeva, Tamila, additional, Danilenko, Daria, additional, Konovalova, Nadezhda, additional, Petrova, Polina, additional, Stolyarov, Kirill, additional, Smorodintseva, Elizaveta, additional, Burtseva, Elena, additional, Krasnoslobodtsev, Kirill, additional, Kirillova, Elena, additional, Karpova, Lyudmila, additional, Eropkin, Mikhail, additional, Sominina, Anna, additional, and Grudinin, Mikhail, additional

Published
2016
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14. Changes in the antigenic and genetic structure of influenza viruses: analysis of surveillance data of influenza A and B in Russia in 2006-2013

Author

Grudinin, Mikhail P., primary, Pisareva, Maria M., additional, Komissarov, Andrey B., additional, Kosheleva, Anna A., additional, Buzitskaya, Janna V., additional, Stukova, Marina A., additional, Prokopetz, Alexandra V., additional, Danilenko, Daria M., additional, Konovalova, Nadezhda I., additional, Lobova, Tamara G., additional, Sominina, Anna A., additional, and Kiselev, Oleg I., additional

Published
2015
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15. Two years of experience in hospital surveillance for the severe influenza like illnesses in St. Petersburg: etiology, clinical characterization of diseases, antigenic and genetic properties of isolated influenza viruses

Author

Sominina, Anna A., primary, Pisareva, Maria M., additional, Grudinin, Mikhail P., additional, Eropkin, Mikhail Yu., additional, Konovalova, Nadezhda I., additional, Sukhovetskaya, Vera F., additional, Afanasieva, Olga I., additional, Voloshuk, Lubov V., additional, Komissarov, Andrey B., additional, Buzitskaya, Zhanna V., additional, Fadeev, Artem V., additional, Stolyarov, Kirill A., additional, Smorodintseva, Elizaveta A., additional, Afanasieva, Veronika S., additional, Yanina, Marina A., additional, Gonchar, Vitalii V., additional, Osidak, Ludmila V., additional, and Go, Alexey A., additional

Published
2015
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18. Broad-spectrum anti-tumor and anti-metastatic DNA vaccine based on p62-encoding vector

Author

Venanzi, Franco, primary, Shifrin, Victor, additional, Sherman, Michael Y., additional, Gabai, Vladimir, additional, Kiselev, Oleg, additional, Komissarov, Andrey, additional, Grudinin, Mikhail, additional, Shartukova, Maria, additional, Romanovskaya-Romanko, Ekaterina A., additional, Kudryavets, Yuri, additional, Bezdenezhnykh, Natalya, additional, Lykhova, Oleksandra, additional, Semesyuk, Nadiia, additional, Concetti, Antonio, additional, Tsyb, Anatoly, additional, Filimonova, Marina, additional, Makarchuk, Victoria, additional, Yakubovsky, Raisa, additional, Chursov, Andrey, additional, Shcherbinina, Vita, additional, and Shneider, Alexander, additional

Published
2013
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20. INFLUENZA SURVEILLANCE IN RUSSIA BASED ON EPIDEMIOLOGICAL AND LABORATORY DATA FOR THE PERIOD FROM 2005 TO 2012.

Author

Anna S, Burtseva E, Eropkin M, Karpova L, Zarubaev V, Smorodintseva E, Konovalova N, Danilenko D, Prokopetz A, Grudinin M, Pisareva M, Anfimov P, Stolyarov K, Kiselev O, Shevchenko E, Ivanova V, Trushakova S, Breslav N, Lvov D, Klimov A, Moen A, and Cox N

Abstract

Exchange of information on and sharing of influenza viruses through the GISRS network has great significance for understanding influenza virus evolution, recognition of a new pandemic virus emergence and for preparing annual WHO recommendations on influenza vaccine strain composition. Influenza surveillance in Russia is based on collaboration of two NICs with 59 Regional Bases. Most epidemiological and laboratory data are entered through the internet into the electronic database at the Research Institute of Influenza (RII), where they are analyzed and then reported to the Ministry of Public Health of Russia. Simultaneously, data are introduced into WHO's Flu Net and Euro Flu, both electronic databases. Annual influenza epidemics of moderate intensity were registered during four pre-pandemic seasons. Children aged 0-2 and 3-6 years were the most affected groups of the population. Influenza registered clinically among hospitalized patients with respiratory infections for the whole epidemic period varied between 1.3 and 5.4% and up but to 18.5-23.0% during the peak of the two pandemic waves caused by influenza A(H1N1) pdm 09 virus and to lesser extent (2.9 to 8.5%) during usual seasonal epidemics. Most epidemics were associated with influenza A(H1N1), A(H3N2) and B co-circulation. During the two pandemic waves (in 2009-2010 and 2010-2011) influenza A(H1N1) pdm 09 predominated. It was accompanied by a rapid growth of influenza morbidity with a significant increase of both hospitalization and mortality. The new pandemic virus displaced the previous seasonal A(H1N1) virus completely. As a rule, most of the influenza viruses circulating in Russia were antigenic ally related to the strains recommended by WHO for vaccine composition for the Northern hemisphere with the exception of two seasons when an unexpected replacement of the influenza B Victoria lineage by Yamagata lineage (2007-2008) and the following return of Victoria lineage viruses (2008-2009) was registered. Influenza surveillance in Russia was improved as a result of enhancing capacity to international standards and the introduction of new methods in NICs such as rRT-PCR diagnosis, regular testing of influenza viruses for susceptibility to antivirals, phylogenetic analysis as well as organization of sentinel surveillance in a number of Regional Base Laboratories. Improvements promoted rapid recognition of the appearance a new pandemic virus in the country and enhancement of confirmation tests in investigation of influenza related death cases.

Published
2013
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