Kirill Sharshov

Kirill Sharshov
Federal Research Center of Fundamental and Translational Medicine · Laboratory of Molecular epidemiology and biodiversity of viruses

PhD

About

164
Publications
10,824
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896
Citations
Additional affiliations
May 2010 - present
Novosibirsk State University
Position
  • Senior Researcher
July 2005 - July 2013
State Research Center of Virology and Biotechnology VECTOR
Position
  • Head of Laboratory of Influenza Virus Ecology

Publications

Publications (164)
Article
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In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total n...
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In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica...
Article
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Antibodies to several pathogens were detected in the serum samples of nine polar bears (Ursus maritimus, Phipps, 1774) from areas of the Russian Arctic. Plasma was studied for antibodies to sixteen infectious and parasitic diseases using indirect Protein-A ELISA. It is known that when using ELISA, the interaction of antibodies with a heterologous a...
Article
In winter 2020–2021, Japan experienced multiple serious outbreaks of H5N8 high pathogenicity avian influenza (HPAI)—52 outbreaks at poultry farms and 58 cases in wild birds or the environment—that occurred simultaneously with outbreaks in Europe. Here, we examined how the H5N8 HPAI viruses (HPAIVs) emerged and spread through Japan and across the Eu...
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In the last ten years, humanity has faced new challenges in the field of human and animal health, including emerging viral infections. The widespread occurrence of emerging and re-emerging pathogens (e.g., highly pathogenic avian influenza virus (HPAIV), the new COVID-2019 of zoonotic nature, coronaviruses that cause severe acute respiratory syndro...
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To discover sources for novel anti-influenza drugs, we evaluated the antiviral potential of nine extracts from eight medicinal plants and one mushroom (Avena sativa L., Hordeum vulgare Linn. var. nudum Hook. f., Hippophae rhamnoides Linn., Lycium ruthenicum Murr., Nitraria tangutorum Bobr., Nitraria tangutorum Bobr. by-products, Potentilla anserina...
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Background Himalayan Griffons ( Gyps himalayensis ), large scavenging raptors widely distributed in Qinghai-Tibetan Plateau, have evolved a remarkable ability to feed on carcasses without suffering any adverse effects. The gut microbiome plays an important role in animal physiological and pathological processes, and has also been found to play a he...
Article
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Different methods for producing bulk quantities of concentrated and purified SARS-CoV-2 for the use as antigens and for the research into COVID-19 biology were tested.
Article
Aim. The work is aimed at exploring the molecular and genetic properties of avian paramyxovirus 4 (APMV‐4) isolated from the mallard duck. Material and Methods. In 2018, as a part of an influenza A virus surveillance programme, biological samples were collected from wild birds on Lake Adzhi (Papas) in the Republic of Dagestan. The isolation of viru...
Article
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Influenza and other acute respiratory viral infections lead to a substantial incidence of severe cases and hospitalizations and so remain a global health problem. Within the frame of the Global Influenza Hospital Surveillance Network (GIHSN), we assessed the contribution of influenza and other respiratory viruses to severe cases of influenzalike di...
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We investigated the incidence of 15 respiratory viruses among 2991 children with acute respiratory infections in Novosibirsk city, Russia, prior to the COVID-19 pandemic (2013–2020). Viral infections were detected in 72.5% cases. The incidence of human coronavirus was 2% (Alphacoronaviruses, 63%; Betacoronaviruses, 37%).
Article
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Two variants of highly pathogenic avian influenza A(H5N8) virus were detected in dead poultry in Western Siberia, Russia, during August and September 2020. One variant was represented by viruses of clade 2.3.4.4b and the other by a novel reassortant between clade 2.3.4.4b and Eurasian low pathogenicity avian influenza viruses circulating in wild bi...
Article
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Avian influenza viruses (AIVs) are maintained in wild bird reservoirs, particularly in mallard ducks and other waterfowl. Novel evolutionary lineages of AIV that arise through genetic drift or reassortment can spread with wild bird migrations to new regions, infect a wide variety of resident bird species, and spillover to domestic poultry. The vast...
Article
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Aim. The aim is to explore the molecular and biological characteristics of influenza virus subtype H6N8. Material and Methods. Regular collecting of biological samples from wild birds was carried out in 2016 in the south of Western Siberia. Isolation of avian influenza virus strains from birds’ cloacal swabs was performed using three passages in em...
Article
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Photodynamic inactivation of pathogenic microorganisms can be successfully used to eradicate pathogens in localized lesions, infected liquid media, and on various surfaces. This technique utilizes the photosensitizer (PS), light, and molecular oxygen to produce reactive oxygen species that kill pathogens. Here, we used the PS, water soluble octakis...
Article
WLEDs have lately been the preferred lighting device based on properties such as energy saving, high efficiency, longevity, and environmental protection. However, studies on the safety of white light-emitting diode (WLED) are limited. In our previous study, we found that WLED light (4000 K ± 500 K color temperature, 250 lx, and 20 min exposure) is...
Article
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We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIVpositive samples and perform next generation sequencing. AIV-positive rates (12.73%) fro...
Article
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Objective: isolation of coronavirus SARS-CoV-2 from clinical sample of patient with COVID-19 in Novosibirsk; obtaining a purified and inactivated viral antigen and study of its antigenic properties. Materials and methods: virus isolation was carried out in Vero cell culture from nasopharyngeal swab positive on SARS-CoV-2 RNA. The efficiency of SARS...
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The black-necked crane (Grus nigricollis) is a vulnerable species, breeding exclusively on the high-altitude wetlands of the Qinghai–Tibet Plateau. Bird species harbor diverse communities of microorganisms within their gastrointestinal tracts, which have important roles in the health, nutrition, and physiology of birds. Hitherto, virtually nothing...
Article
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Every year, influenza B viruses (IBVs) contribute to annual illness, and infection can lead to serious respiratory disease among humans. More attention is needed in several areas, such as increasing virulence or pathogenicity of circulating B viruses and developing vaccines against current influenza. Since preclinical trials of anti-influenza drugs...
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Background The bar-headed goose ( Anser indicus ) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-heade...
Preprint
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Over the years influenza B virus (IBV) contribute annual disease and can lead to serious respiratory disease among humans. More attention should be paid to the mammalian adaptive processes of B viruses and development of vaccines against current influenza. Because of preclinical trials of anti-influenza drugs are conducted mainly on mice, we develo...
Article
Ma-Nuo-Xi Decoction (MNXD) is well-known in Tibetan medicine to be in line with the theory of treatment determination based on syndrome differentiation. However, the components responsible for its immunomodulating effect are unknown. In this study, three polysaccharide components-MNXD-P, MNXD-BD-P, and MNXD-AD-P-were isolated from MNXD and its basi...
Article
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Objective: to develop a new antigenic relevance influenza B virus suitable for modeling influenza infection in mice to assess of in vivo and in vitro therapeutic and preventive efficacy of antiviral drugs.Materials and methods: was carried out an adaptation of influenza B virus in BALB/c mice. Was performed, comparative assessment of in vivo and in...
Article
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Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Nor...
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Hitherto, virtually nothing is known about the microbial communities related to the bird species in the family Corvidae. To fill this gap, the present study was conducted to provide a baseline description of the gut microbiota of wild red-billed choughs (Pyrrhocorax pyrrhocorax). In this study, microbiota from four gastrointestinal locations (oroph...
Article
As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, composition...
Article
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We isolated Tamdy virus (TAMV; strain XJ01/TAMV/China/2018) from Hyalomma asiaticum ticks infesting Bactrian camels in Xinjiang, China, in 2018. The genome of the strain showed high nucleotide similarity with previously described TAMV strains from Asia. Our study highlights the potential threat of TAMV to public health in China.
Article
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Ultrastructural studies revealing morphological differences between intact and photodynamically inactivated virions can point to inactivation mechanisms and molecular targets. Using influenza as a model system, we show that photodynamic virus inactivation is possible without total virion destruction. Indeed, irradiation with a relatively low concen...
Article
Since 2013, H5N6 highly pathogenic avian influenza viruses (HPAIVs) have been responsible for outbreaks in poultry and wild birds around Asia. H5N6 HPAIV is also a public concern due to sporadic human infections being reported in China. In the current study, we isolated an H5N6 HPAIV strain (A/Muscovy duck/Long An/AI470/2018; AI470) from an outbrea...
Article
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Avian orthoavulavirus 13 (AOAV­13), also named avian paramyxovirus 13 (APMV­13), has been found sporadically in wild birds around the world ever since the discovery of AOAV­13 (AOAV­13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV­13 in China. In the present study, a novel AOAV­13 virus (AOAV­...
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Aim. To evaluate the possibility of herpes viruses circulation and possible routes of transmission in population of Steller sea lions of the Sea of Okhotsk by combining a thorough literature study with screening of blood sera samples of Steller sea lion puppies of the Sea of Okhotsk obtained in 2008‐2012. Methods . We investigated 370 blood sera of...
Article
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The emergence of novel highly pathogenic avian influenza viruses (HPAIVs) in migratory birds raises serious concerns as these viruses have the potential to spread during fall migration. We report the identification of novel HPAIV A(H5N8) clade 2.3.4.4 virus that was isolated from sick domestic duck at commercial farm during the second wave of sprea...
Article
The gastrointestinal microbiota played an important role in animal health by acting as a barrier against pathogens, exerting multiple metabolic functions and stimulating the development of the host immune system. To better understand the age-related dynamic changes in gut microbiota, we used 16S rRNA genes sequencing to investigate the cloacal micr...
Article
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Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe-geographically distinct regions-during winter 2017-2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues fo...
Article
An H5N6 highly pathogenic avian influenza virus (HPAIV) outbreak occurred in poultry in Japan during January 2018, and H5N6 HPAIVs killed several wild birds in 3 prefectures during Winter 2017-2018. Time-measured phylogenetic analyses demonstrated that the Hemagglutinin (HA) and internal genes of these isolates were genetically similar to clade 2.3...
Article
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Aim. The aim of the work is to carry out an analysis of the wetlands of the Republic of Dagestan in order to justify the selection of the collecting sites for material from migratory aquatic and semi aquatic birds in order to monitor the influenza A virus. Material and methods. Studying scientific publications of different years and available infor...
Article
Pilot testing of a microbiological method for disposal of spent hydrocarbon oils (HO) by a previously developed consortium of hydrocarbon oxidizing microorganisms (HOM): Aquamicrobium lusatiense strain 854/1 (AM884147); Pseudomonas aeruginosa strain HNYM10 (JN 999888), Paracoccus aminophilus strain ATCC 7061 (NR_043242), Gordonia hydrophobica strai...
Article
Pilot testing of a microbiological method for disposal of spent hydrocarbon oils (HO) by a previously developed consortium of hydrocarbon oxidizing microorganisms (HOM): Aquamicrobium lusatiense strain 854/1 (AM884147); Pseudomonas aeruginosa strain HNYM10 (JN 999888), Paracoccus aminophilus strain ATCC 7061 (NR_043242), Gordonia hydrophobica strai...
Article
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Pigs play an important role in interspecies transmission of the influenza virus, particularly as “mixing vessels” for reassortment. Two influenza A/H1N1 virus strains, A/swine/Siberia/1sw/2016 and A/swine/Siberia/4sw/2017, were isolated during a surveillance of pigs from private farms in Russia from 2016 to 2017. There was a 10% identity difference...
Article
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In the present study, 27 Caspian seals of 18–20 months age (17 female and 10 male) were captured during an integrated research on AIV at Zhemchuzhny island (Astrakhan Region, Russia) in 2012. Sera samples were collected from the captured seals and tested for H1, H3, H5 and H7 specific antibodies. All animals were sera negative for these subtypes. Na...
Article
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Aim. In the present work we investigated the circulation of AIV in wild bird populations and studied the sorption of the influenza virus in the feathers of wild waterfowl nesting on reservoirs during the autumn mass migration. Material and methods. Sampling was carried out on the territory of the Novosibirsk region on Lake Chany during the period f...
Article
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Background Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 201...
Article
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Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industri...
Preprint
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Background Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0-15 years old) admitted to Novosibirsk Children's Municipal Clinical Hospital in 201...
Article
Antiviral efficiency of oxidized dextrans (OD) with different molecular weights and oxidation degree (OD40min, OD70min, OD40max, and OD70 max) was studied in vitro and in vivo. Dextrans OD40max and OD70max prevented the development of the cytopathic effect of influenza A(H1N1)pdm09 virus in more than 50% MDCK cells vs. control (no OD). Four intrana...
Article
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Aim. Compare the degree of pathogenicity of newly emerging influenza virus strains with pandemic potential by experimental infection of BALB/c mice with highly pathogenic avian influenza A(H5N1) virus and mouse adapted pandemic influenza A(H1N1)pdm09 virus. Materials and methods. The first group of BALB/c mice (n=24) were infected with highly patho...
Article
In this study, we characterized for the first time the gut microbiota of Greylag geese (Anser anser) using high-throughput 16S rRNA gene sequencing technology. The results showed that the phyla Firmicutes (78.55%), Fusobacteria (9.38%), Proteobacteria (7.55%), Bacteroidetes (1.82%), Cyanobacteria (1.44%), and Actinobacteria (0.61%) dominated the gu...
Article
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Aim. Marine mammals play the role of "sentries", standing guard over the health and functioning of marine ecosystems. The analysis of data reported in literature was carried out to understand and to evaluate a circulation of representatives of the Orthomyxoviridae and Paramyxoviridae, dangerous pathogens capable to cause morbidity and mortality in...
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Aim: To determine the molecular basis of A(H1N1)pdm09 virus adaptation to a new host. Methods: The pandemic virus A/Russia/01/2009 was adapted to mice by serial lung-to-lung passages. The growth prop- erties, pathogenicity and genome sequences of the mouse-adapted virus were compared with those of the parental strain. Results: The A(H1N1)pdm09 viru...
Article
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To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016-2017 and 117 AIV/HPAIVs isolated in Japan and Russia. Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that per...
Article
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We report here the genome sequence of the influenza A virus strain A/swine/Siberia/1sw/2016, isolated from a swine in Russia. On the basis of sequence analysis, A/swine/Siberia/1sw/2016 is characterized by unusual surface glycoproteins phylogenetically distinct from those of swine A(H1N1)pdm09 influenza virus.
Article
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Thirty-two muskrats (Ondatra zibethicus) were captured for surveillance of avian influenza virus in wild waterfowl and mammals near Lake Chany, Western Siberia, Russia. A/muskrat/Russia/63/2014 (H2N2) was isolated from an apparently healthy muskrat using chicken embryos. Based on phylogenetic analysis, the hemagglutinin and neuraminidase genes of t...
Article
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Background The aim of the study was to explore the ecological diversity of wild birds in Siberia, which are the natural reservoir of avian influenza virus (AIV). Methods Cloacal swabs and intestinal fragments were collected from wild migratory birds from 2007‒2014. Isolated viruses were grown in the allantoic cavity of embryonated chicken eggs. The...
Article
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Staphylococcus hominis belongs to a group of coagulase-negative staphylococci and is an opportunistic pathogen, usually found on the skin and mucous membranes. Studies involving S. hominis isolated from wild birds are scarce. Here, we report a 2.365-Mb draft genome sequence of S. hominis BHG17, isolated from the feces of a bar-headed goose.