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Intestinal human microbiota is a dynamic system that is under the pressures of its host organism and external factors. Microbiota disruption caused by these factors can lead to severe diseases including inflammatory and oncological diseases of the gastrointestinal tract. One of the possible approaches in managing the intestinal microbiota is fecal microbiota transplantation (FT) – transfer of the microbiota from the stool of a healthy donor to the intestinal tract of a recipient patient. Currently, this procedure is recognized as an efficacious method to normalize the intestinal microbiota mainly in inflammatory diseases of the gastrointestinal tract. In Russia, pilot studies of the effectiveness of FT in patients with ulcerative colitis have been conducted for several years, and these studies were started in Novosibirsk. The aim of this study was to assess the change of intestinal microbiome in 20 patients with ulcerative colitis after a single FT procedure. The main method is a comparative analysis of 16S ribosomal RNA sequence libraries constructed using fecal samples obtained from patients with ulcerative colitis before and after FT and sequenced on the Illumina MiSeq platform. The obtained results showed that FT led to an increase in average biodiversity in samples after FT compared to samples before FT; however, the difference was not significant. In the samples studied, the proportion of Firmicutes sequences, the major gastrointestinal microbiota of healthy people, was decreased (~32 % vs. >70 %), while the proportion of Proteobacteria sequences was increased (>9 % vs.

Here, we present the complete mitochondrial DNA sequence of Dermacentor reticulatus. The mitogenome is 14,806 bp and contains 13 protein-coding, 2 rRNA, and 22 tRNA genes, along with 2 control regi...

An analysis of the incidence in the dynamics of years (1998-2018) showed that the leading place among infections transmitted by ixodid ticks in the Chelyabinsk region is occupied by tick-borne tick-borne borreliosis (IKB), tick-borne encephalitis (TBE) is less common. Long-term monitoring of the natural foci of TBE and IKB showed their high epizootological potential. In 2018, febrile forms prevailed in the structure of clinical forms of TBE - 61.9%, meningeal and focal forms were found in 28.5% and 9.4%, respectively. Focal forms were represented by meningoencephalitic and polioencephalomyelitis forms with the same frequency of 4.7%. In the structure of the nosological diagnosis of ICD in the South Urals, erythema forms of the disease prevail (69.5%). The detection frequency of Borrelia DNA of the pathogenic complex B.burgdorferi s.l. in the blood serum and leukocyte fraction of patients was 13%. In 4 patients, for the first time in the Chelyabinsk region, DNA of a new Borrelia miyamotoi Borrelia genotype was detected in whole blood samples and in the samples of the leukocyte fraction using PCR-RV. Phylogenetic analysis of B. miyamotoi was carried out on all sequences of glpQ and 23SrRNA gene fragments, deposited at NCBI and homologous sequences of Chelyabinsk-2018 isolates. The disease proceeded in non-erythema form, intoxication syndrome, myalgia, chills were observed in the clinical picture.

In studied blood serum samples from Russian patients hospitalized with suspected dengue fever, one or more markers of dengue fever have been detected, namely, viral RNA, NS1 antigen, and IgM or IgG antibodies. Moreover, only the combined use of various immunological and genetic methods provided a more effective diagnosis of dengue fever. The detection of IgG to dengue virus in patients with high titers of IgG to tick-borne encephalitis virus (TBEV) and, conversely, the detection of IgG to TBEV virus in patients with high titers of IgG to dengue has been documented. The results confirm the literature data on pronounced antigenic cross-sections between different representatives of flaviviruses, which may complicate the ELISA diagnosis of TBEV and dengue in patients. Genotyping of obtained dengue virus isolates showed that imported cases of dengue fever are caused by subtypes 1–4 of the dengue virus, with the prevalence of infection cases caused by dengue virus 1. Sequencing of these dengue virus isolates, including genome-wide, showed that viral isolates obtained on the territory of Russia are phylogenetically close to modern variants of the dengue virus circulating in the countries of Southeast Asia.

Data obtained from monitoring cases of severe influenza, cases of vaccinated individuals, and unique cases were used to describe influenza viruses that circulated in Russia in the 2018–2019 epidemic season. A high proportion of the mutations D222G/N in A(H1N1)pdm09 HA was detected in fatal cases. Viruses of the B/Victoria lineage with deletions in HA were detected in Russia, and a reassortant seasonal influenza A(H1N2) virus was identified. A C-terminal truncation in the NS1 protein was detected in a substantial proportion of A(H3N2) viruses.

Helicoverpa zea (Boddie, 1850) (Hz) single nucleocapcide nucleopolyhedrovirus (SNPV) was adapted to the cotton bollworm (Helicoverpa armigera, (Hübner, 1805) (Ha)) by five blind passages on larvae. The full genomic sequence of the resulting strain HS-18 has been determined (GenBank acc. №: KJ004000.1). Biological activity of the HS-18 strain is higher than the activity of all other Russian strains of NPV, as far as cotton bollworm strain HearSNPV-G4. HS-18-infected caterpillars at the 3-rd and 4-th ages died much faster than those infected with HearSNPV-G4 strain. A major difference of HS-18 genome is an 18 bp repeat in the RING-finger ORF that confirms high variability of this region. Three other insertions and seven base substitutions were observed earlier, while six base substitutions are new. Mutations are located at ORF42, lef-9, ORF58, VP39, PIF-4, P48, SOD, ORF111, ORF129 and ORF138 genes. Among all nucleotide mutation only one is synonymous. Thus we suppose the selective pressure to the virus. The resulting strain HS-18 is recommended as a biopesticide for controlling the number of cotton bollworm in cotton fields.Вирус одиночно-капсидного ядерного полиэдроза (ВЯП) американской хлопковой совки (АХС) (Helicoverpa zea (Boddie, 1850)) был адаптирован к хлопковой совке Старого Света (ХС) Helicoverpa armigera (Hübner, 1805) с помощью 5 слепых пассажей на личинках. Была определена полная геномная последовательность полученного штамма ХС-18 (GenBank № KJ004000.1). По биологической активности штамм ХС-18 превосходит как все ранее созданные в России варианты ВЯП, так и штамм HearSNPV-G4 на основе ВЯП хлопковой совки. Гусеницы хлопковой совки III и IV возрастов при заражении их штаммом ХС-18 гибнут значительно быстрее, чем при заражении эталонным штаммом HearSNPV-G4. Основным отличием генома ХС-18 от ближайшего родственного штамма ВЯП АХС, использованного в препарате Элькар, является наличие повтора из 18 пар нуклеотидных оснований внутри рамки считывания гена RING-finger, что подтверждает высокую изменчивость этого региона. Три другие вставки и обнаруженные 7 замен нуклеотидных оснований наблюдались ранее, 6 замен ранее не встречались. Мутации расположены в генах ORF42, lef-9, ORF58, VP39, PIF-4, P48, SOD, ORF111, ORF129 и ORF138. Среди всех нуклеотидых замещений только одна является синонимичной, что свидетельствует о присутствии селективного давления на вирус. Полученный штамм ХС-18 рекомендован в качестве биопестицида для контроля численности ХС на полях хлопчатника.

The C11-13 strain from the Siberian subtype of tick-borne encephalitis virus (TBEV) was isolated from human brain using pig embryo kidney (PEK), 293, and Neuro-2a cells. Analysis of the complete viral genome of the C11-13 variants during six passages in these cells revealed that the cell-adapted C11-13 variants had multiple amino acid substitutions as compared to TBEV from human brain. Seven out of eight amino acids substitutions in the high-replicating C11-13(PEK) variant mapped to non-structural proteins; 13 out of 14 substitutions in the well-replicating C11-13(293) variant, and all four substitutions in the low-replicating C11-13(Neuro-2a) variant were also localized in non-structural proteins, predominantly in the NS2a (2), NS3 (6) and NS5 (3) proteins. The substitutions NS2a1067 (Asn → Asp), NS2a1168(Leu → Val) in the N-terminus of NS2a and NS31745(His → Gln) in the helicase domain of NS3 were found in all selected variants. We postulate that multiple substitutions in the NS2a, NS3 and NS5 genes play a key role in adaptation of TBEV to different cells.

This study aimed to assess the antiviral susceptibility of influenza A(H5N8) viruses isolated in Russia in 2014–2018. Genetic analysis of 57 Russian isolates with full genome sequences did not find any markers of reduced susceptibility to baloxavir. Only one strain bore an amino acid substitution associated with adamantane resistance (M2-S31N). The neuraminidase of 1 strain had an NA-N293/294S (N8/N2 numbering) substitution associated with reduced inhibition by oseltamivir and normal inhibition by zanamivir, which was confirmed phenotypically. There were no other strains with reduced inhibition by oseltamivir and zanamivir in the phenotypic analysis. In order to estimate the worldwide prevalence of influenza A(H5N8) viruses bearing genetic markers of antiviral resistance, genome sequences deposited in the GISAID database were analyzed (database access: October 2020). The M2 protein of A(H5N8) viruses from the 2.3.4.4c clade had an M2-S31N substitution associated with reduced susceptibility to adamantanes. On the contrary, the majority (94%) of viruses from the 2.3.4.4b clade had the M2-S31 genotype. Fewer than 1% of analyzed viruses had amino acid substitutions associated with reduced susceptibility to baloxavir (PA-E199G, PA-E199E/G) or reduced or highly reduced inhibition by neuraminidase inhibitors (NA-R150/152K, NA-I221/222M, NA-I221/222I/M, NA-I221/222V, NA-I115/117V, NA-G145/147R, NA-R291/292R/K). An NA-N293/294S substitution was not present in sequences from the GISAID database. To the best of our knowledge, influenza A(H5N8) viruses with reduced inhibition by oseltamivir bearing an NA-N293/294S substitution have not been previously reported in epidemiological surveillance studies.

Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018–2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.

Human carcinoma A431 cells were subcutaneously injected into nude mice at points remote from each other. One of the two xenografts developed afterwards was used for the treatment with a recombinant vaccinia virus, while the other xenograft served as an artificial metastasis. We used the attenuated recombinant vaccinia virus (VACV) VVdGF-GFP2 of the L-IVP strain (GenBank accession number KP233807) with the deletion of two virulence genes, i.e., the genes of the virus growth factor and thymidine kinase, with the gene for the green fluorescent protein (GFP2) inserted in the place of the latter. The treatment was performed by a single intratumoral injection of recombinant VACV at a dose of 107 PFU/mouse. VACV was detected in cells of the artificial metastasis as early as two days after infection. After eight days, the virus concentration was comparable with that in the infected tumor (~109 PFU/mL). Electron microscopy revealed selective replication of the recombinant virus in the tumor cells. The targeted accumulation of GFP2 in both tumor and metastasis was shown in the UV images of the mice obtained using the In-vivo Multispectral Imaging System (Bruker, Germany). The complete destruction of the tumor was detected after 12 days, and that of metastasis, after 20 days after the injection of VVdGF-GFP2. The destruction process was accompanied by pronounced edema and leukocyte infiltration of the tumor tissue. The recombinant virus induced a significant reduction in the sizes of the tumor and metastasis. By the end of the experiment (35 days), the xenografts in the control mice were 10 times larger than those in the treated mice (5000 vs 500 mm3). Our study has shown that the attenuated VACV administered by the peripheral route can not only destroy the primary tumor but also has a distinct antimetastatic effect.

The occurrence of Mediterranean fever with periods of increase and decrease has been recorded in the Crimean peninsula. The city of Sevastopol and its vicinity are known endemic areas for this disease. Some of the most active agents in the spread of this rickettsiosis are feral and abandoned dogs. The aim of this study was to test ticks parasitizing dogs in Sevastopol for the presence of Rickettsia using molecular methods. The testing of ticks was carried out using real-time PCR and the ‘Real Best DNA Rickettsia species’ kit (AO ‘Vector-Best’) followed by sequence identification of the rickettsial DNA detected. The DNA marker for Rickettsia species (a conservative area of citrate synthase gene, gltA) was detected in 16 of 84 (19.1%) samples of Rhipicephalus sanguineus ticks tested. Larger fragments of gltA, ompA and sca4 were amplified and sequenced for 10 of 16 PCR-positive samples. Rickettsia DNA amplified from eight of the samples matched the sequence of Rickettsia conorii conorii Malish, the causative agent of Mediterranean fever. The sequences of Rickettsia DNA from two other ticks had the closest match to homologous fragments of Rickettsia massiliae, a pathogenic spotted fever rickettsia that was identified in the Crimean Peninsula for the first time as part of this study. The detection of two pathogenic species of Rickettsia in the studied ticks suggests the potential for two rickettsial diseases in the region and warrants further epidemiological and clinical studies.

The 2017-2018 influenza epidemic season in Russia was characterized by a relatively low morbidity and mortality. We evaluated herd immunity prior to the 2017-2018 influenza season in hemagglutination inhibition assay, and performed characterization of influenza viruses isolated from severe or fatal influenza cases and from influenza cases in people vaccinated in the fall of 2017. During the 2017-2018 epidemic season, 87 influenza A and B viruses were isolated and viruses of the 75 influenza cases, including selected viral isolates and viruses analyzed directly from the original clinical material, were genetically characterized. The analyzed A(H1N1)pdm09 viruses belonged to clade 6B.1, B/Yamagata-like viruses belonged to clade 3, and B/Victoria-like viruses belonged to clade 1A and they were antigenically similar to the corresponding vaccine strains. A(H3N2) viruses belonged to clade 3C.2a and were difficult to characterize antigenically and the analysis indicated antigenic differences from the corresponding egg-grown vaccine strain. The next generation sequencing revealed the presence of D222/G/N polymorphism in the hemagglutinin gene in 32% of the analyzed A(H1N1)pdm09 lethal cases. This study demonstrated the importance of monitoring D222G/N polymorphism, including detection of minor viral variants with the mutations, in the hemagglutinin gene of A(H1N1)pdm09 for epidemiological surveillance. One strain of influenza virus A(H1N1)pdm09 was resistant to oseltamivir and had the H275Y amino acid substitution in the NA protein. All other isolates were susceptible to NA inhibitors. Prior to the 2017-2018 epidemic season, 67.4 million people were vaccinated, which accounted for 46.6% of the country's population. Just before the epidemic season 33-47% and 24-30% of blood sera samples collected within the territory of Russia showed the presence of protective antibody titers against vaccine strains of influenza A and influenza B/Victoria-like, respectively. Mass vaccination of the population had evidently reduced the severity of the flu epidemic during the 2017-2018 influenza epidemic season in Russia.

Most of the live vaccine doses of vaccinia virus donated to the Intensified Smallpox Eradication Programme after 1971 were prepared using the L-IVP strain. A mixture of three clones of the L-IVP strain was sequenced using MySEQ. Consensus sequence similarity with the vaccinia virus Lister strain is 99.5%.