#Genetic Characterization of #Avian #Influenza A(#H5N6) Virus Clade 2.3.4.4, #Russia, 2018 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 12—December 2019 / Research Letter

Genetic Characterization of Avian Influenza A(H5N6) Virus Clade 2.3.4.4, Russia, 2018

Ivan Susloparov  , Natalia Goncharova, Natalia Kolosova, Alexey Danilenko, Vasiliy Marchenko, Galina Onkhonova, Vasiliy Evseenko, Elena Gavrilova, Rinat A. Maksutov, and Alexander Ryzhikov

Author affiliations: State Research Center of Virology and Biotechnology Vector, Koltsovo, Russia

 

Abstract

Timely identification of pandemic influenza threats depends on monitoring for highly pathogenic avian influenza viruses. We isolated highly pathogenic avian influenza A(H5N6) virus clade 2.3.4.4, genotype G1.1, in samples from a bird in southwest Russia. The virus has high homology to human H5N6 influenza strains isolated from southeast China.

Keywords: Avian Influenza; H5N6; Wild Birds; Russia; China.

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#Evolution of #pandemic #influenza virus A #H1N1pdm09 in 2009-2016: dynamics of #receptor specificity of the first #hemagglutinin subunit (HA1) (Vopr Virusol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Vopr Virusol. 2019;64(2):63-72. doi: 10.18821/0507-4088-2019-64-2-63-72.

[Evolution of pandemic influenza virus A(H1N1)pdm09 in 2009-2016: dynamics of receptor specificity of the first hemagglutinin subunit (HA1).]

[Article in Russian]

Lvov DK1, Bogdanova VS1, Kirillov IM1, Shchelkanov MY2, Burtseva EI1, Bovin NV3, Fedyakina IT1, Prilipov AG1, Alhovsky SV1, Samokhvalov EI1, Proshina ES1, Kirillova ES1, Syroeshkin AV4.

Author information: 1 Ivanovsky Institute of Virology «National Research Centre for Epidemiology and Microbiology named honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation. 2 Far Eastern Federal University, Vladivostok, 690950, Primorsky Krai, Russian Federation. 3 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russian Federation. 4 Peoples Frendship University of Russia (RUDN), Moscow, 117198, Russian Federation.

 

Abstract

INTRODUCTION:

The new reassortant of the swine flu virus A(H1N1)pdm09, which emerged in 2009, overcame the species barrier and caused the 2009-2010 pandemic. One of the key points required for the influenza virus to overcome the species barrier and adapt it to humans is its specific binding to the receptors on the epithelium of the human respiratory tract.

PURPOSE:

Studying the dynamics of changes in receptor specificity (RS) of the HA1 subunit of the hemagglutinin of the influenza A(H1N1)pdm09 virus strains isolated during the period 2009-2016 on the territory of the Russian Federation, and an analysis of the possible impact of these changes on the incidence rates of the population of the Russian Federation of pandemic influenza in certain epidemic seasons.

MATERIAL AND METHODS:

Standard methods of collecting clinical materials, isolation of influenza viruses, their typing and genome sequencing were used. For the study of RS of influenza A virus (H1N1)pdm09, the method of solid phase sialosidenzyme analysis was used.

RESULTS:

It is shown that the change in the parameter W3/6 , which characterizes the degree of a2-3 receptor specificity (a2-3-RS) of the influenza virus A(H1N1) pdm09 over a2-6-RS, coincides with the change in the incidence rates of the Russian Federation’s pandemic flu in separate epidemic seasons. There is a tendency to increase the affinity of the virus A(H1N1)pdm09 to α2-3 analogs of the sialyl-glycan receptors of the human respiratory tract epithelium – α2-3-sialoglycopolymers (α2-3-SGP), and falls to α2-6-SGP, with the virus showing the greatest affinity for sulfated sialoglycopolymers.

DISCUSSION:

Screening for RS strains of influenza A (H1N1)pdm09 virus isolated on the territory of the Russian Federation in 2009-2016 revealed a decrease in the affinity of viruses for a2-6-sialosides, especially for 6’SL-SGP, which is probably due to the presence of amino acid substitutions in the 222 and 223 positions of RBS HA1 viruses. Previous studies have shown that the presence of such substitutions correlates with an increase in the virulence of the influenza A virus (H1N1)pdm09 [16, 23]. Probably, the pandemic virus has evolved towards the selection of more virulent pneumotropic variants.

CONCLUSION:

Monitoring of the receptor specificity of a pandemic influenza virus makes it possible to identify strains with altered RS to the epithelium of the human respiratory tract and an increased ability to transfer from person to person. Change in the period 2009-2016 the W3/6parameter characterizing the degree of α2-3-RS excess of the influenza A(H1N1)pdm09 virus over α2-6-RS, coincides with the change in the incidence rates of the pandemic influenza population of the Russian Federation in certain epidemic seasons.

KEYWORDS: epidemic season; hemagglutinin (HA); influenza; influenza virus A(H1N1)pdm09; receptor specificity; sialoglycopolymer (SGP); sialyl-glycan receptor

PMID: 31412172 DOI: 10.18821/0507-4088-2019-64-2-63-72

Keywords: Seasonal Influenza; H1N1pdm09; Russia.

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#Severe cases of seasonal #influenza in #Russia in 2017-2018 (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Severe cases of seasonal influenza in Russia in 2017-2018

Natalia P. Kolosova  , Tatyana N. Ilyicheva , Alexey V. Danilenko, Julia A. Bulanovich, Svetlana V. Svyatchenko, Alexander G. Durymanov, Natalia I. Goncharova, Andrei S. Gudymo, Alexander N. Shvalov, Ivan M. Susloparov, Vasiliy Y. Marchenko, Tatyana V. Tregubchak, Elena V. Gavrilova, Rinat A. Maksyutov, Alexander B. Ryzhikov

Published: July 29, 2019 / DOI: https://doi.org/10.1371/journal.pone.0220401

 

Abstract

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.

___

Citation: Kolosova NP, Ilyicheva TN, Danilenko AV, Bulanovich JA, Svyatchenko SV, Durymanov AG, et al. (2019) Severe cases of seasonal influenza in Russia in 2017-2018. PLoS ONE 14(7): e0220401. https://doi.org/10.1371/journal.pone.0220401

Editor: Florian Krammer, Icahn School of Medicine at Mount Sinai, UNITED STATES

Received: March 14, 2019; Accepted: July 14, 2019; Published: July 29, 2019

Copyright: © 2019 Kolosova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: This work was supported by State Assignments no. 1/16 and 2/18 (FBRI SRC VB VECTOR, Rospotrebnadzor), http://www.vector.nsc.ru/. The funders supported obtaining a number of reagents, funded sequencing and HI tests, data analysis and covered publication fees.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Seasonal Influenza; Russia.

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#Airborne concentrations and chemical considerations of #radioactive #ruthenium from an undeclared major nuclear release in 2017 (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Airborne concentrations and chemical considerations of radioactive ruthenium from an undeclared major nuclear release in 2017

O. Masson, G. Steinhauser, D. Zok, O. Saunier, H. Angelov, D. Babić, V. Bečková, J. Bieringer, M. Bruggeman, C. I. Burbidge, S. Conil, A. Dalheimer, L.-E. De Geer, A. de Vismes Ott, K. Eleftheriadis, S. Estier, H. Fischer, M. G. Garavaglia, C. Gasco Leonarte, K. Gorzkiewicz, D. Hainz, I. Hoffman, M. Hýža, K. Isajenko, T. Karhunen, J. Kastlander, C. Katzlberger, R. Kierepko, G.-J. Knetsch, J. Kövendiné Kónyi, M. Lecomte, J. W. Mietelski, P. Min, B. Møller, S. P. Nielsen, J. Nikolic, L. Nikolovska, I. Penev, B. Petrinec, P. P. Povinec, R. Querfeld, O. Raimondi, D. Ransby, W. Ringer, O. Romanenko, R. Rusconi, P. R. J. Saey, V. Samsonov, B. Šilobritienė, E. Simion, C. Söderström, M. Šoštarić, T. Steinkopff, P. Steinmann, I. Sýkora, L. Tabachnyi, D. Todorovic, E. Tomankiewicz, J. Tschiersch, R. Tsibranski, M. Tzortzis, K. Ungar, A. Vidic, A. Weller, H. Wershofen, P. Zagyvai, T. Zalewska, D. Zapata García, and B. Zorko

PNAS first published July 26, 2019 / DOI: https://doi.org/10.1073/pnas.1907571116

Edited by John H. Seinfeld, California Institute of Technology, Pasadena, CA, and approved June 21, 2019 (received for review May 2, 2019)

 

Significance

A massive atmospheric release of radioactive 106Ru occurred in Eurasia in 2017, which must have been caused by a sizeable, yet undeclared nuclear accident. This work presents the most compelling monitoring dataset of this release, comprising 1,100 atmospheric and 200 deposition data points from the Eurasian region. The data suggest a release from a nuclear reprocessing facility located in the Southern Urals, possibly from the Mayak nuclear complex. A release from a crashed satellite as well as a release on Romanian territory (despite high activity concentrations) can be excluded. The model age of the radioruthenium supports the hypothesis that fuel was reprocessed ≤2 years after discharge, possibly for the production of a high-specific activity 144Ce source for a neutrino experiment in Italy.

 

Abstract

In October 2017, most European countries reported unique atmospheric detections of aerosol-bound radioruthenium (106Ru). The range of concentrations varied from some tenths of µBq·m−3 to more than 150 mBq·m−3. The widespread detection at such considerable (yet innocuous) levels suggested a considerable release. To compare activity reports of airborne 106Ru with different sampling periods, concentrations were reconstructed based on the most probable plume presence duration at each location. Based on airborne concentration spreading and chemical considerations, it is possible to assume that the release occurred in the Southern Urals region (Russian Federation). The 106Ru age was estimated to be about 2 years. It exhibited highly soluble and less soluble fractions in aqueous media, high radiopurity (lack of concomitant radionuclides), and volatility between 700 and 1,000 °C, thus suggesting a release at an advanced stage in the reprocessing of nuclear fuel. The amount and isotopic characteristics of the radioruthenium release may indicate a context with the production of a large 144Ce source for a neutrino experiment.

environmental radioactivity – ruthenium – nuclear forensics – environmental release – accidental release

Keywords: Environmental Pollution; Radiations; Radionuclides; Italy; Russia.

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#Plasmid-Mediated #mcr-1 #Colistin #Resistance in #Escherichia coli from a Black Kite in #Russia (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Plasmid-Mediated mcr-1 Colistin Resistance in Escherichia coli from a Black Kite in Russia

Hassan Tarabai, Adam Valcek, Ivana Jamborova, Sergey V. Vazhov, Igor V. Karyakin, Rainer Raab, Ivan Literak, Monika Dolejska

DOI: 10.1128/AAC.01266-19

 

ABSTRACT

The gene mcr-1 conferring resistance to last-line antibiotic colistin has been reported globally. Here we describe the first detection of plasmid-mediated colistin resistance in Russian wildlife, an isolate of Escherichia coli sequence type 2280 from a black kite (Milvus migrans), scavenging raptor. Whole genome sequencing and plasmid transferability experiments revealed that mcr-1.1 was located on a conjugative IncI2 plasmid pDR164 (59891 bp). Migratory Black Kites may contribute to the global spread of mobile colistin resistance.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Colistin; MCR1; E. Coli; Wild Birds; Russia.

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#Rivers across the #Siberian #Arctic unearth the #patterns of #carbon #release from thawing #permafrost (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Rivers across the Siberian Arctic unearth the patterns of carbon release from thawing permafrost

Birgit Wild, August Andersson, Lisa Bröder, Jorien Vonk, Gustaf Hugelius, James W. McClelland, Wenjun Song, Peter A. Raymond, and Örjan Gustafsson

PNAS first published May 6, 2019 / DOI: https://doi.org/10.1073/pnas.1811797116

Edited by Mark H. Thiemens, University of California, San Diego, La Jolla, CA, and approved March 26, 2019 (received for review July 9, 2018)

 

Significance

High-latitude permafrost and peat deposits contain a large reservoir of dormant carbon that, upon warming, may partly degrade to CO2 and CH4 at site and may partly enter rivers. Given the scale and heterogeneity of the Siberian Arctic, continent-wide patterns of thaw and remobilization have been challenging to constrain. This study combines a decade-long observational record of 14C in organic carbon of four large Siberian rivers with an extensive 14C source fingerprint database into a statistical model to provide a quantitative partitioning of the fraction of fluvially mobilized organic carbon that specifically stems from permafrost and peat deposits, and separately for dissolved and particulate vectors, across the Siberian Arctic, revealing distinct spatial and seasonal system patterns in carbon remobilization.

 

Abstract

Climate warming is expected to mobilize northern permafrost and peat organic carbon (PP-C), yet magnitudes and system specifics of even current releases are poorly constrained. While part of the PP-C will degrade at point of thaw to CO2 and CH4 to directly amplify global warming, another part will enter the fluvial network, potentially providing a window to observe large-scale PP-C remobilization patterns. Here, we employ a decade-long, high-temporal resolution record of 14C in dissolved and particulate organic carbon (DOC and POC, respectively) to deconvolute PP-C release in the large drainage basins of rivers across Siberia: Ob, Yenisey, Lena, and Kolyma. The 14C-constrained estimate of export specifically from PP-C corresponds to only 17 ± 8% of total fluvial organic carbon and serves as a benchmark for monitoring changes to fluvial PP-C remobilization in a warming Arctic. Whereas DOC was dominated by recent organic carbon and poorly traced PP-C (12 ± 8%), POC carried a much stronger signature of PP-C (63 ± 10%) and represents the best window to detect spatial and temporal dynamics of PP-C release. Distinct seasonal patterns suggest that while DOC primarily stems from gradual leaching of surface soils, POC reflects abrupt collapse of deeper deposits. Higher dissolved PP-C export by Ob and Yenisey aligns with discontinuous permafrost that facilitates leaching, whereas higher particulate PP-C export by Lena and Kolyma likely echoes the thermokarst-induced collapse of Pleistocene deposits. Quantitative 14C-based fingerprinting of fluvial organic carbon thus provides an opportunity to elucidate large-scale dynamics of PP-C remobilization in response to Arctic warming.

carbon cycle – climate change – radiocarbon – peat – leaching

Keywords: Climate change; Global Warming; Permafrost; Russia.

——

#Rivers across the #Siberian #Arctic unearth the #patterns of #carbon #release from thawing #permafrost (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Rivers across the Siberian Arctic unearth the patterns of carbon release from thawing permafrost

Birgit Wild, August Andersson, Lisa Bröder, Jorien Vonk, Gustaf Hugelius, James W. McClelland, Wenjun Song, Peter A. Raymond, and Örjan Gustafsson

PNAS first published May 6, 2019 / DOI: https://doi.org/10.1073/pnas.1811797116

Edited by Mark H. Thiemens, University of California, San Diego, La Jolla, CA, and approved March 26, 2019 (received for review July 9, 2018)

 

Significance

High-latitude permafrost and peat deposits contain a large reservoir of dormant carbon that, upon warming, may partly degrade to CO2 and CH4 at site and may partly enter rivers. Given the scale and heterogeneity of the Siberian Arctic, continent-wide patterns of thaw and remobilization have been challenging to constrain. This study combines a decade-long observational record of 14C in organic carbon of four large Siberian rivers with an extensive 14C source fingerprint database into a statistical model to provide a quantitative partitioning of the fraction of fluvially mobilized organic carbon that specifically stems from permafrost and peat deposits, and separately for dissolved and particulate vectors, across the Siberian Arctic, revealing distinct spatial and seasonal system patterns in carbon remobilization.

 

Abstract

Climate warming is expected to mobilize northern permafrost and peat organic carbon (PP-C), yet magnitudes and system specifics of even current releases are poorly constrained. While part of the PP-C will degrade at point of thaw to CO2 and CH4 to directly amplify global warming, another part will enter the fluvial network, potentially providing a window to observe large-scale PP-C remobilization patterns. Here, we employ a decade-long, high-temporal resolution record of 14C in dissolved and particulate organic carbon (DOC and POC, respectively) to deconvolute PP-C release in the large drainage basins of rivers across Siberia: Ob, Yenisey, Lena, and Kolyma. The 14C-constrained estimate of export specifically from PP-C corresponds to only 17 ± 8% of total fluvial organic carbon and serves as a benchmark for monitoring changes to fluvial PP-C remobilization in a warming Arctic. Whereas DOC was dominated by recent organic carbon and poorly traced PP-C (12 ± 8%), POC carried a much stronger signature of PP-C (63 ± 10%) and represents the best window to detect spatial and temporal dynamics of PP-C release. Distinct seasonal patterns suggest that while DOC primarily stems from gradual leaching of surface soils, POC reflects abrupt collapse of deeper deposits. Higher dissolved PP-C export by Ob and Yenisey aligns with discontinuous permafrost that facilitates leaching, whereas higher particulate PP-C export by Lena and Kolyma likely echoes the thermokarst-induced collapse of Pleistocene deposits. Quantitative 14C-based fingerprinting of fluvial organic carbon thus provides an opportunity to elucidate large-scale dynamics of PP-C remobilization in response to Arctic warming.

carbon cycle – climate change – radiocarbon – peat – leaching

Keywords: Climate Change; Global Warming; Permafrost; Russia.

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