Article Download (79)
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Equine Rotavirus Strain Arg/E706/2008 VP7 (VP7) Gene, Partial Cds Genbank: GU373939.1 FASTA Graphics Popset
Equine rotavirus strain Arg/E706/2008 VP7 (VP7) gene, partial cds GenBank: GU373939.1 FASTA Graphics PopSet Go to: LOCUS GU373939 972 bp RNA linear VRL 25-JUL-2016 DEFINITION Equine rotavirus strain Arg/E706/2008 VP7 (VP7) gene, partial cds. ACCESSION GU373939 VERSION GU373939.1 KEYWORDS . SOURCE Equine rotavirus ORGANISM Equine rotavirus Viruses; Riboviria; Orthornavirae; Duplornaviricota; Resentoviricetes; Reovirales; Reoviridae; Sedoreovirinae; Rotavirus; unclassified Rotavirus. REFERENCE 1 (bases 1 to 972) AUTHORS Garaicoechea,L., Mino,S.O., Barrandeguy,M. and Parreno,V. TITLE Molecular Characterization of Equine rotavirus Circulating in Sport Horses of Argentina During a 17-year Period (1992-2008) JOURNAL Unpublished REFERENCE 2 (bases 1 to 972) AUTHORS Garaicoechea,L., Mino,S.O., Barrandeguy,M. and Parreno,V. TITLE Direct Submission JOURNAL Submitted (29-DEC-2009) Virology Institute, INTA, Dr Nicolas Repetto y de Los Reseros s/n, Castelar, Buenos Aires 1712, ArgentinaFEATURES Location/Qualifiers source 1..972 /organism="Equine rotavirus" /mol_type="genomic RNA" /strain="Arg/E706/2008" /isolation_source="fecal sample" /host="equine" /db_xref="taxon:10937" /country="Argentina: Buenos Aires" /collection_date="2008" /note="genotype: G14" gene 7..>972 /gene="VP7" CDS 7..>972 /gene="VP7" /codon_start=1 /product="VP7" /protein_id="AEF33475.1" /translation="MYGIEYTTILTFLISLILLNYILQLLTRIMDFIIYRFLLIIVLL SPFLNAQNYGINLPITGSMDTAYVNSTQENIFLTSTLCLYYPTEAATQIDDSSWKDTI SQLFLTKGWPTGSVYLKEYTDIASFSIDPQLYCDYNVVLMKYDEALQLDMSELADLIL NEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTNVATFEEV -
2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A. -
COVID-19) Outbreak in Algeria: a New Challenge for Prevention
Open Access Journal of Community Medicine & Health Care Review Article Novel Coronavirus Disease 2019 (COVID-19) Outbreak in Algeria: A New Challenge for Prevention Boukhatem MN* Département de Biologie et Physiologie Cellulaire, Faculté Abstract des Sciences de la Nature et de la Vie, Université - Saad In December 2019, the novel Coronavirus Disease 2019 (COVID-19) Dahlab - Blida 1, Blida, Algeria outbreak started in Wuhan, the capital of Hubei province in China. Since then *Corresponding author: Mohamed Nadjib it has spread to many other continents and regions, including low-income BOUKHATEM, Département de Biologie et Physiologie countries. With the current trajectory of the 2019-nCoV outbreak unknown, Cellulaire, Faculté des Sciences de la Nature et de la Vie, medical measures and public health will both be needed to contain spreading of Université – Saad Dahlab – Blida 1, Blida, Algeria; Email: the 2019-nCoV and to improve patient outcomes. [email protected] It is imperative to increase attentiveness of tourists and travelers about the Received: March 24, 2020; Accepted: March 31, dangers and suitable protective recommendations and for health professionals 2020; Published: April 07, 2020 to be attentive and vigilant if a patient with pneumonia or severe respiratory symptoms reports a recent history of travel to the country affected with SARS- CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Preventive measures should be taken by National and local health authorities of the affected countries, including Algeria, in order to increase hospital hygiene and desinfection. Finally, it is fundamental to explore the explanations for people’s poor compliance with recommendations and rules and to take exact measures in order to improve them. -
Latest Ncbi-Taxonomist Docker Image Can Be Pulled from Registry.Gitlab.Com/Janpb/ Ncbi-Taxonomist:Latest
ncbi-taxonomist Documentation Release 1.2.1+8580b9b Jan P Buchmann 2020-11-15 Contents: 1 Installation 3 2 Basic functions 5 3 Cookbook 35 4 Container 39 5 Frequently Asked Questions 49 6 Module references 51 7 Synopsis 63 8 Requirements and Dependencies 65 9 Contact 67 10 Indices and tables 69 Python Module Index 71 Index 73 i ii ncbi-taxonomist Documentation, Release 1.2.1+8580b9b 1.2.1+8580b9b :: 2020-11-15 Contents: 1 ncbi-taxonomist Documentation, Release 1.2.1+8580b9b 2 Contents: CHAPTER 1 Installation Content • Local pip install (no root required) • Global pip install (root required) ncbi-taxonomist is available on PyPi via pip. If you use another Python package manager than pip, please consult its documentation. If you are installing ncbi-taxonomist on a non-Linux system, consider the propsed methods as guidelines and adjust as required. Important: Please note If some of the proposed commands are unfamiliar to you, don’t just invoke them but look them up, e.g. in man pages or search online. Should you be unfamiliar with pip, check pip -h Note: Python 3 vs. Python 2 Due to co-existing Python 2 and Python 3, some installation commands may be invoked slighty different. In addition, development and support for Python 2 did stop January 2020 and should not be used anymore. ncbi-taxonomist requires Python >= 3.8. Depending on your OS and/or distribution, the default pip command can install either Python 2 or Python 3 packages. Make sure you use pip for Python 3, e.g. -
And the New Coronavirus (SARS-Cov-2)
General characteristics of the Human Coronavirus (HCoVs) and the new coronavirus (SARS-CoV-2) that produces COVID-19 illness. Dora Rosete1, Gabriel Cortez1, and Carlos Guti´errez2 1National Institute of Respiratory Diseases 2Affiliation not available September 11, 2020 Abstract The new coronavirus has been named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible of the COVID- 19 illness, it is a virus that belongs to the Coronavirus family, it is the third virus in this family that causes an epidemic. It originated in China and has spread throughout the world. It is highly pathogenic and transmissible that mainly affects the respiratory tract and can cause death. There is not antiviral drug or vaccines against COVID-19 illness, infected person only have supportive treatments. Recently, some antiviral drugs and vaccines are being valued. In this review, we described the general characteristics of HCoVs and latest research of the transmission, prevention and clinical characteristics of SARS-CoV-2 and some treatments and vaccines more development for to combat COVID-19 illness. General characteristics of the Human Coronavirus (HCoVs) and the new coronavirus (SARS- CoV-2) that produces COVID-19 illness. Dora Patricia Rosete-Olvera, Gabriel Palma-Cort´es,Carlos Cabello-Guti´errez. Department of Research in Virology and Mycology, National Institute of Respiratory Diseases. Ismael Cos´ıo Villegas (INER), Calzada de Tlalpan No. 4502, Colonia Secci´onXVI. Tlalpan 14080, M´exicoCDMX. Correspondence M en C Dora Patricia Rosete Olvera Department of Research in Virology and Mycology National Institute of Respiratory Diseases, Ismael Cos´ıoVillegas, CDMX. Email: [email protected] Phone: 55 54 87 17 00. -
Alignment-Free Machine Learning Approaches for the Lethality Prediction of Potential Novel Human-Adapted Coronavirus Using Genomic Nucleotide
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.15.176933; this version posted July 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide Rui Yin1,*, Zihan Luo2, Chee Keong Kwoh1 1 Biomedical Informatics Lab, Nanyang Technological University, Singapore, Singapore 2 School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei Province, China * [email protected] Abstract A newly emerging novel coronavirus appeared and rapidly spread worldwide and World 1 Health Organization declared a pandemic on March 11, 2020. The roles and 2 characteristics of coronavirus have captured much attention due to its power of causing 3 a wide variety of infectious diseases, from mild to severe on humans. The detection of 4 the lethality of human coronavirus is key to estimate the viral toxicity and provide 5 perspective for treatment. We developed alignment-free machine learning approaches for 6 an ultra-fast and highly accurate prediction of the lethality of potential human-adapted 7 coronavirus using genomic nucleotide. We performed extensive experiments through six 8 different feature transformation and machine learning algorithms in combination with 9 digital signal processing to infer the lethality of possible future novel coronaviruses 10 using previous existing strains. The results tested on SARS-CoV, MERS-Cov and 11 SARS-CoV-2 datasets show an average 96.7% prediction accuracy. -
Avian Orthoreovirus Segment S4, Complete Genome NCBI Reference Sequence: NC 015135.1
Avian orthoreovirus segment S4, complete genome NCBI Reference Sequence: NC_015135.1 FASTA Graphics Go to: LOCUS NC_015135 1192 bp RNA linear VRL 13-AUG-2018 DEFINITION Avian orthoreovirus segment S4, complete genome. ACCESSION NC_015135 VERSION NC_015135.1 DBLINK BioProject: PRJNA485481 KEYWORDS RefSeq. SOURCE Avian orthoreovirus ORGANISM Avian orthoreovirus Viruses; Riboviria; Orthornavirae; Duplornaviricota; Resentoviricetes; Reovirales; Reoviridae; Spinareovirinae; Orthoreovirus. REFERENCE 1 AUTHORS Banyai,K., Dandar,E., Dorsey,K.M., Mato,T. and Palya,V. TITLE The genomic constellation of a novel avian orthoreovirus strain associated with runting-stunting syndrome in broilers JOURNAL Virus Genes 42 (1), 82-89 (2011) PUBMED 21116842 REFERENCE 2 (bases 1 to 1192) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (11-FEB-2011) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 1192) AUTHORS Banyai,K. TITLE Direct Submission JOURNAL Submitted (29-SEP-2010) Banyai K., Hungarian Academy of Sciences, Veterinary Medical Research Institute, Hungaria krt. 21., Budapest, H-1143, HUNGARY COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to FR694200. COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..1192 /organism="Avian orthoreovirus" /mol_type="genomic RNA" /strain="AVS-B" /db_xref="taxon:38170" /segment="S4" /country="USA" gene 24..1127 /gene="sigma-NS" /locus_tag="AOrVsS4_gpp1" /db_xref="GeneID:10220435" -
Forty Years with Coronaviruses
VIEWPOINT Forty years with coronaviruses Susan R. Weiss I have been researching coronaviruses for more than forty years. This viewpoint summarizes some of the major findings in coronavirus research made before the SARS epidemic and how they inform current research on the newly emerged SARS-CoV-2. A virulent new coronavirus is currently didn’t want to continue working in that including infectious bronchitis virus and bo- holding hostage much of the human popu- field. In reading the literature, I came upon vine coronavirus. There were a handful of Downloaded from https://rupress.org/jem/article-pdf/217/5/e20200537/1041300/jem_20200537.pdf by guest on 30 March 2020 lation worldwide. This virus, SARS-CoV-2, coronaviruses as an attractive topic, with presentations on human coronavirus 229E, a which causes the COVID-19 disease, so much possible. The model coronavirus, poorly understood agent of the common cold. emerged in China from bats into a presumed mouse hepatitis virus (MHV), was easy to Leaving that meeting, and with the en- intermediate species and then into humans. grow in tissue culture in the laboratory and couragement and mentorship of Neal It then spread around the globe with ongo- also provided compelling mouse models for Nathanson, my chair, and Don Gilden, a ing devastating effects. This round of human human disease, especially those of the liver professor in the neurology department, I coronavirus disease follows the appearance and the central nervous system. Julian Lei- was excited to expand my research to of the related lethal coronaviruses, SARS- bowitz, then at the University of California, studies utilizing the MHV animal models of CoV and MERS-CoV, in 2002 and 2012 re- San Diego, working on MHV, very gener- both encephalitis/chronic demyelinating spectively. -
Pharmatab 014.Pdf
NEWS LETTER . JUNE 2020 .VOLUME 1 . ISSUE 14 Bharathi Priya K, Shailaja K, Leena Muppa, Magimai Upagara Valan UPDATES ON DRUG TARGETS FOR SEVERE ACUTE RESPIRATORY SYNDROME CORONA VIRUS 2 (SARS-COV-2) Dr. S.Parasuraman, Associate Professor & Unit Head Pharmacology, AIMST University, Bedong, Malaysia Viruses are obligate intracellular parasites negative regulator of the RAAS system other antivirals, chloroquine is in phase I and and they do not carry out metabolic (downregulation of ACE2 directly affects phase II trials[5]. processes. Viruses utilize most of the cardiovascular function)[2] ACE2 inhibition The clinical eficacy of the enhanced platelet physiological machinery of the host and few induces ADAM17 gene expression, leading to inhibition, trypsin inhibitor, monoclonal drugs inhibiting viral replication without the release of tumor necrosis factor α (TNFα) antibodies, immunomodulator, Natural killer affecting the host cells. and cytokines such as interleukin 4 (IL-4) and cells, an immunosuppressive drug, and In 2019, Severe acute respiratory syndrome interferon γ (IFNγ); [3] increased cytokine vaccine also under the investigation. Globally, coronavirus 2 (SARS-CoV-2) is identiied concentrations activate further pro- about 3.4% of COVID-19 cases have died, and which is positive-sense single-stranded inlammatory pathways, leading to a cytokine the disease spreading can be prevented by ribonucleic acid (RNA) virus. SARS-CoV-2 is storm and [4] personal hygiene and by social distancing to the strain of beta-coronavirus which causes ADAM-17 also promotes the cleavage of ACE2 break the COVID chain. coronavirus disease 2019 (COVID-19), receptors. Anti-coronavirus therapies divided References: responsible for the COVID-19 pandemic. -
The COVID-19 Pandemic: a Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control
Journal of Clinical Medicine Review The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control Yosra A. Helmy 1,2,* , Mohamed Fawzy 3,*, Ahmed Elaswad 4, Ahmed Sobieh 5, Scott P. Kenney 1 and Awad A. Shehata 6,7 1 Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA; [email protected] 2 Department of Animal Hygiene, Zoonoses and Animal Ethology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt 3 Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt 4 Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt; [email protected] 5 Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA; [email protected] 6 Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat 32897, Egypt; [email protected] 7 Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany * Correspondence: [email protected] (Y.A.H.); [email protected] (M.F.) Received: 18 March 2020; Accepted: 21 April 2020; Published: 24 April 2020 Abstract: A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. -
Downloaded on 27Th
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.28.448043; this version posted June 30, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels Luke S. Hillary1,*, Evelien M. Adriaenssens2, David L. Jones1,3 and James E. McDonald1 1 – School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK 2 – Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK 3 – SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105, Australia * - Corresponding author Abstract Grassland ecosystems form 30-40%1 of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage2. Their productivity is closely related to soil microbial communities3, yet the role of viruses within these critical ecosystems is currently undercharacterised4 and in particular, our knowledge of soil RNA viruses is significantly limited5. Here, we applied viromics6 to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages7. -
Virology Is That the Study of Viruses ? Submicroscopic, Parasitic Particles
Current research in Virology & Retrovirology 2021, Vol.4, Issue 3 Editorial Bahman Khalilidehkordi Shahrekord University of Medical Sciences, Iran mobile genetic elements of cells (such as transposons, Editorial retrotransposons or plasmids) that became encapsulated in protein capsids, acquired the power to “break free” from Virology is that the study of viruses – submicroscopic, the host cell and infect other cells. Of particular interest parasitic particles of genetic material contained during a here is mimivirus, a huge virus that infects amoebae and protein coat – and virus-like agents. It focuses on the sub- encodes much of the molecular machinery traditionally sequent aspects of viruses: their structure, classification associated with bacteria. Two possibilities are that it’s a and evolution, their ways to infect and exploit host cells for simplified version of a parasitic prokaryote or it originated copy , their interaction with host organism physiology and as an easier virus that acquired genes from its host. The immunity, the diseases they cause, the techniques to iso- evolution of viruses, which frequently occurs together with late and culture them, and their use in research and ther- the evolution of their hosts, is studied within the field of apy. Virology is a subfield of microbiology.Structure and viral evolution. While viruses reproduce and evolve, they’re classification of Virus: A major branch of virology is virus doing not engage in metabolism, don’t move, and depend classification. Viruses are often classified consistent with on variety cell for copy . The often-debated question of the host cell they infect: animal viruses, plant viruses, fun- whether or not they’re alive or not could also be a matter gal viruses, and bacteriophages (viruses infecting bacte- of definition that does not affect the biological reality of vi- ria, which include the foremost complex viruses).