Detection of tick-borne pathogens in wild birds and their ticks in Western Siberia and high level of their mismatch

Abstract: The Tomsk region located in the south of Western Siberia is one of the most high-risk areas for tick-borne diseases due to elevated incidence of tick-borne encephalitis and Lyme disease in humans. Wild birds may be considered as one of the reservoirs for tick-borne pathogens and hosts for infected ticks. A high mobility of wild birds leads to unpredictable possibilities for the dissemination of tick-borne pathogens into new geographical regions. The primary goal of this study was to evaluate the prevalence of tick-borne pathogens in wild birds and ticks that feed on them as well as to determine the role of different species of birds in maintaining the tickborne infectious foci. We analysed the samples of 443 wild birds (60 species) and 378 ticks belonging to the genus Ixodes Latraille, 1795 collected from the wild birds, for detecting occurrence of eight tick-borne pathogens, the namely tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and species of Borrelia, Rickettsia, Ehrlichia, Anaplasma, Bartonella and Babesia Starcovici, 1893, using RT-PCR/or PCR and enzyme immunoassay. One or more tick-borne infection markers were detected in 43 species of birds. All markers were detected in samples collected from fieldfare Turdus pilaris Linnaeus, Blyth’s reed warbler Acrocephalus dumetorum Blyth, common redstart Phoenicurus phoenicurus (Linnaeus), and common chaffinch Fringilla coelebs Linnaeus. Although all pathogens have been identified in birds and ticks, we found that in the majority of cases (75.5%), there were mismatches of pathogens in birds and ticks collected from them. Wild birds and their ticks may play an extremely important role in the dissemination of tick-borne pathogens into different geographical regions

PCR Results of Vector and Carrier Investigations for the Presence of Tick-Borne Borreliosis, Human Monocytic Ehrlichiosis, and Human Granulocytic Anaplasmosis Agents in Natural Foci of the Rostov Region

Objective of the study is to detect the circulation of the agents of ixodic tick-borne borreliosis (ITB), human monocytic ehrlichiosis (HME), and human granulocytic anaplasmosis (HGA) in samples collected from carriers and vectors of transmissible tick-borne infections using PCR-assay. Materials and methods. Field material was studied in PCR for evaluating the rate of infection by causative agents of tick-borne infections (tick-borne borrelioses, ehrlichioses, anaplasmosis) in combined natural foci on the territory of the Rostov Region. Results and conclusions. The data obtained during epizootiological investigations carried out in 21 administrative districts and 10 cities of the Rostov Region between 2014 and 2016 were used in the study. The results were indicative of spontaneous infection in ixodic ticks by ITB causative agent on the territory of the Rostov Region, as well as of presence of corresponding natural focus. Since 2013 the activity of different components of ITB natural focus was confirmed by the detection and official registration of patients. Moreover, in the Rostov Region for the first time ever the circulation of HME and HGA causative agents was recorded and territorially combined foci of HME and HGA with ITB were identified. The results obtained allow assuming the genesis of a focus of ixodic tick-borne borreliosis and monocytic and granulocytic ehrlichioses owing to annual expansion of the areal of ticks, infected by these pathogens, and animals on which the ticks are feeding. PCR-analysis is of significant value for assessment of spread of causative agents of the “tick-borne” infections in the Rostov Region, forecasting of epidemiological situation, as well as implementation of preventive measures in the region

Benchmark data and model independent event classification for the large hadron collider

We describe the outcome of a data challenge conducted as part of the Dark Machines (https://www.darkmachines.org) initiative and the Les Houches 2019 workshop on Physics at TeV colliders. The challenged aims to detect signals of new physics at the Large Hadron Collider (LHC) using unsupervised machine learning algorithms. First, we propose how an anomaly score could be implemented to define model-independent signal regions in LHC searches. We define and describe a large benchmark dataset, consisting of > 1 billion simulated LHC events corresponding to 10 fb−1 of proton-proton collisions at a center-of-mass energy of 13 TeV. We then review a wide range of anomaly detection and density estimation algorithms, developed in the context of the data challenge, and we measure their performance in a set of realistic analysis environments. We draw a number of useful conclusions that will aid the development of unsupervised new physics searches during the third run of the LHC, and provide our benchmark dataset for future studies at https://www.phenoMLdata.org. Code to reproduce the analysis is provided at https://github.com/bostdiek/DarkMachines-UnsupervisedChallenge

Cholera Forecast for the Year 2019 Based on Assessment of Epidemiological Situation Around the World, Across CIS and Russia in 2009–2018

Analysis of cholera incidence for the period of 2009–2018 was performed. The upward tendency in the morbidity rate dynamics around the world (compared to 2009) with an average annual growth rate of 5,352 % was revealed. For the first time during the 7th pandemic caused by V. cholerae O1 El Tor, WHO reported 1227391 cases of cholera world-wide in 2017, out of which 1032481 (84.1%) were registered in Yemen, where the war continues and one of the largest epidemics in the world. There have been cross-border epidemiological complications in several African countries. Endemic foci continue to exist and spread in Asia, Africa and the Caribbean. Under the epidemiological surveillance in Russia, 744 strains of V. cholerae El Tor – ctxA– tcpA–, ctxA– tcpA+ and V. cholerae О139 ctxA– and tcpA– were isolated from the surface water bodies, as well as single strains of El Tor ctxA+ tcpA+. As a result of INDEL- and  PCR-genotyping, the isolation of strains with identical genotypes and new ones was established. To make the prognosis for 2019, the risk of activation (continuation) of the cholera epidemic process in the world was assessed, taking into account emergencies of different origin and risk factors. The cholera forecast at the global level and in  Russia for 2019 is unfavorable

Molecular Genetic Analysis of the Complete Genome of Tick-Borne Encephalitis Virus (Siberia Subtype): Modern Kolarovo-2008 Isolate

Determined is the complete genome sequence of Kolarovo-2008 strain (Siberia subtype) of Tick-borne encephalitis virus (TBEV), isolated from a tick in the suburbs of the Tomsk city. Nucleotide sequence analysis testifies of the fact that the level of genetic differences within the Siberian subtype of TBEV amounts to 10 % of the nucleotide sequence and to 7 % of amino-acid sequence for certain virus genes. 3'-HTO of the genome of Siberian subtype has the highest rate of variability and the homology level ranging from 65 to 97 %. Kolarovo-2008 and Vasilchenko (isolated in Novosibirsk in 1969) strains have the highest level of genome homology. The level of dissimilarity between the two Tomsk strains is substantially higher: the total number of amino-acid substitutions in Tomsk Zausaev and Kolarovo-2008 strains equals to 124, and 3'HTO level of homology is 79 %. Identified genetic variability of the Siberian subtype of TBEV is of a great importance for further development and enhancement of tick-borne encephalitis virus diagnostics

Обнаружение и генотипирование Anaplasma phagocytophilum в клещах I. persulcatus и D. reticulatus , собранных в г. Томске в 2015–2016 гг.

Introduction. The detection of the first cases of tick-borne human granulocytic anaplasmosis in Russia, discovery of genetic markers for Anaplasma spp. in ixodid ticks and reporting of a significant number of cases of tick-borne infections in the southern part of Western Siberia give reason to suppose that causative agents of tick-borne anaplasmosis may be transmitted in Tomsk and its suburbs. Objective. To study the distribution and species biodiversity of A. phagocytophilum in ixodid ticks in Tomsk Region. Materials and methods. The analysis of 690 individual ixodid ticks (larvae and adults) was carried out for Ixodes persulcatus (n = 530) and Dermacentor reticulatus (n = 160) ticks collected in 2015–2016 on the territory of urban and suburban biotopes of Tomsk. Primary screening of ticks for the presence of genetic material of A. phagocytophilum was conducted using two-round PCR with species-specific primers for the 16S rRNA gene. The amplification (1,220 kB) of the groESL fragment of the heat shock protein operon was performed for positive isolates with subsequent determination of the nucleotide sequence in the gene fragment for phylogenetic analysis. Results. The number of A. phagocytophilum positive samples for I. persulcatus (larvae) was 1.2 ± 0.6%, I. persulcatus (adult) was 1.8 ± 0.7%; and D. reticulatus (adult) was 0.6 ± 0.3%. Analysis of the nucleotide sequence of the gene fragments in groESL operon for nine isolates confirmed that the genetic material of the granulocytic anaplasmosis was detected. Phylogenetic analysis showed that all the isolates belonged to the first group of the “new cluster” of A. phagocytophilum. Conclusion. The causative agent of human granulocytic anaplasmosis has been newly detected in I. persulcatus ticks collected in urban and suburban biotopes of Tomsk and in D. reticulatus from urban foci.Введение. Выявление первых случаев заболевания клещевым гранулоцитарным анаплазмозом человека в Российской Федерации, обнаружение генетических маркеров анаплазмозов в иксодовых клещах, регистрация значительного количества случаев различных клещевых инфекций на юге Западной Сибири ставят вопрос о возможной циркуляции возбудителя анаплазмоза в г. Томске и его пригородах. Цель исследования. Изучение распространения и видового разнообразия A. phagocytophilum в иксодовых клещах на территории Томской области. Материалы и методы. Проведен анализ 690 индивидуальных образцов личинок и имаго иксодовых клещей видов Ixodes persulcatus (n = 530) и Dermacentor reticulatus (n = 160), собранных в 2015–2016 гг. на территории городских и пригородных биотопов г. Томска. Первичный скрининг клещей на наличие генетического материала A. phagocytophilum проводили с помощью двухраундовой полимеразной цепной реакции в присутствии родоспецифичных праймеров из области гена 16S рРНК. Для положительных изолятов осуществлялось амплифицирование фрагмента (1 220 пар нуклеотидов) groESL-оперона белков теплового шока с последующим определением нуклеотидной последовательности фрагмента гена и проведением филогенетического анализа. Результаты. Уровень инфицированности A. phagocytophilum у личинок I. persulcatus составил (1,2 ± 0,6)%; у половозрелых особей I. persulcatus – (1,8 ± 0,7)%; у половозрелых особей D. reticulatus–(0,6 ± 0,3)%. Анализ нуклеотидной последовательности фрагмента groESL-оперона для девяти изолятов подтвердил обнаружение генетического материала возбудителя гранулоцитарного анаплазмоза. Филогенетический анализ показал, что все изоляты относятся к первой группе «нового» кластера A. phagocytophilum. Вывод. Возбудитель гранулоцитарного анаплазмоза человека впервые обнаружен в клещах I. рersulcatus, собранных в городских и пригородных биотопах г. Томска, и D. reticulatus из городского биотопа

Constraints on Higgs boson properties using WW∗(→ eνμν) jj production in 36.1fb-1 of √s=13 TeV pp collisions with the ATLAS detector

This article presents the results of two studies of Higgs boson properties using the WW∗(→ eνμν) jj final state, based on a dataset corresponding to 36.1 fb - 1 of s=13 TeV proton–proton collisions recorded by the ATLAS experiment at the Large Hadron Collider. The first study targets Higgs boson production via gluon–gluon fusion and constrains the CP properties of the effective Higgs–gluon interaction. Using angular distributions and the overall rate, a value of tan (α) = 0.0 ± 0.4 (stat.) ± 0.3 (syst.) is obtained for the tangent of the mixing angle for CP-even and CP-odd contributions. The second study exploits the vector-boson fusion production mechanism to probe the Higgs boson couplings to longitudinally and transversely polarised W and Z bosons in both the production and the decay of the Higgs boson; these couplings have not been directly constrained previously. The polarisation-dependent coupling-strength scale factors are defined as the ratios of the measured polarisation-dependent coupling strengths to those predicted by the Standard Model, and are determined using rate and kinematic information to be aL=0.91-0.18+0.10(stat.)-0.17+0.09(syst.) and aT= 1.2 ± 0.4 (stat.)-0.3+0.2(syst.). These coupling strengths are translated into pseudo-observables, resulting in κVV=0.91-0.18+0.10(stat.)-0.17+0.09(syst.) and ϵVV=0.13-0.20+0.28 (stat.)-0.10+0.08(syst.). All results are consistent with the Standard Model predictions

Measurement of the energy asymmetry in tt¯ j production at 13 TeV with the ATLAS experiment and interpretation in the SMEFT framework

A measurement of the energy asymmetry in jet-associated top-quark pair production is presented using 139fb-1 of data collected by the ATLAS detector at the Large Hadron Collider during pp collisions at s=13TeV. The observable measures the different probability of top and antitop quarks to have the higher energy as a function of the jet scattering angle with respect to the beam axis. The energy asymmetry is measured in the semileptonic tt¯ decay channel, and the hadronically decaying top quark must have transverse momentum above 350GeV. The results are corrected for detector effects to particle level in three bins of the scattering angle of the associated jet. The measurement agrees with the SM prediction at next-to-leading-order accuracy in quantum chromodynamics in all three bins. In the bin with the largest expected asymmetry, where the jet is emitted perpendicular to the beam, the energy asymmetry is measured to be - 0.043 ± 0.020 , in agreement with the SM prediction of - 0.037 ± 0.003. Interpreting this result in the framework of the Standard Model effective field theory (SMEFT), it is shown that the energy asymmetry is sensitive to the top-quark chirality in four-quark operators and is therefore a valuable new observable in global SMEFT fits