Coronaviruses: There and Back Again
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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of Equine rotavirus Circulating in Sport Horses of Argentina During a 17-year Period (1992-2008) JOURNAL Unpublished REFERENCE 2 (bases 1 to 972) AUTHORS Garaicoechea,L., Mino,S.O., Barrandeguy,M. and Parreno,V. TITLE Direct Submission JOURNAL Submitted (29-DEC-2009) Virology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. -
Broad Receptor Engagement of an Emerging Global Coronavirus May Potentiate Its Diverse Cross-Species Transmissibility
Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility Wentao Lia,1, Ruben J. G. Hulswita,1, Scott P. Kenneyb,1, Ivy Widjajaa, Kwonil Jungb, Moyasar A. Alhamob, Brenda van Dierena, Frank J. M. van Kuppevelda, Linda J. Saifb,2, and Berend-Jan Boscha,2 aVirology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; and bDepartment of Veterinary Preventive Medicine, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691 Contributed by Linda J. Saif, April 12, 2018 (sent for review February 15, 2018; reviewed by Tom Gallagher and Stefan Pöhlmann) Porcine deltacoronavirus (PDCoV), identified in 2012, is a common greatly increase the potential for successful adaptation to a new enteropathogen of swine with worldwide distribution. The source host (6, 12). A pivotal criterion of cross-species transmission and evolutionary history of this virus is, however, unknown. concerns the ability of a virus to engage a receptor within the PDCoV belongs to the Deltacoronavirus genus that comprises pre- novel host, which for CoVs, is determined by the receptor dominantly avian CoV. Phylogenetic analysis suggests that PDCoV specificity of the viral spike (S) entry protein. originated relatively recently from a host-switching event be- The porcine deltacoronavirus (PDCoV) is a recently discov- tween birds and mammals. Insight into receptor engagement by ered CoV of unknown origin. PDCoV (species name coronavirus PDCoV may shed light into such an exceptional phenomenon. Here HKU15) was identified in Hong Kong in pigs in the late 2000s we report that PDCoV employs host aminopeptidase N (APN) as an (13) and has since been detected in swine populations in various entry receptor and interacts with APN via domain B of its spike (S) countries worldwide (14–24). -
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wjpls, 2020, Vol. 6, Issue 6, 152-161 Review Article ISSN 2454-2229 Pratik et al. World Journal of Pharmaceutical World Journaland Life of Pharmaceutica Sciencesl and Life Science WJPLS www.wjpls.org SJIF Impact Factor: 6.129 THE NOVEL CORONAVIRUS (COVID-19) CAUSATIVE AGENT FOR HUMAN RESPIRATORY DISEASES Pratik V. Malvade1*, Rutik V. Malvade2, Shubham P. Varpe3 and Prathamesh B. Kadu3 1Pravara Rural College of Pharmacy, Pravaranagar, 413736, Dist. - Ahmednagar (M.S.) India. 2Pravara Rural Engineering College, Loni, 413736, Dist. - Ahmednagar (M.S.) India. 3Ashvin College Of Pharmacy, Manchi Hill, Ashvi Bk., 413714, Dist.- Ahmednagar (M.S.) India. *Corresponding Author: Pratik V. Malvade Pravara Rural College of Pharmacy, Pravaranagar, 413736, Dist. - Ahmednagar (M.S.) India. Article Received on 08/04/2020 Article Revised on 29/04/2020 Article Accepted on 19/05/2020 ABSTRACT The newly founded human coronavirus has named as Covid-19. The full form of Covid-19 is “Co-Corona, vi- virus and d- disease”. The Covid-19 is also named as 2019-nCoV because of it was firstly identified at the end of 2019. The coronavirus are the group of various types of viruses i.e. some have positive-sense, single stranded RNA and they are covered within the envelope made up of protein. Still now days seven human coronaviruses are identified are Nl 63, 229E, OC43, HKU1, SARS-CoV, MERS-CoV and latest Covid-19 also known as SARS-CoV-2. From above all, the SARS-CoV and MERS-CoV causes the highest outbreak but the outbreak of Covid-19 is much more than the other any virus. -
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. -
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" -
Complete Sections As Applicable
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2010.023a-dV officers) Short title: A new genus and three new species in the subfamily Coronavirinae (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Raoul J. de Groot and Alexander E. Gorbalenya List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If Submission on behalf of the Coronavirus Study in doubt, contact the appropriate subcommittee Group. Authors are CSG members (R.J de chair (fungal, invertebrate, plant, prokaryote or Groot, Chair) vertebrate viruses) ICTV-EC or Study Group comments and response of the proposer: Date first submitted to ICTV: Date of this revision (if different to above): Page 1 of 5 MODULE 2: NEW SPECIES Code 2010.023aV (assigned by ICTV officers) To create new species within: Genus: Deltacoronavirus (new) Subfamily: Coronavirinae Family: Coronaviridae Order: Nidovirales And name the new species: GenBank sequence accession number(s) of reference isolate: Bulbul coronavirus HKU11 [FJ376619] Thrush coronavirus HKU12 [FJ376621=NC_011549] Munia coronavirus HKU13 [FJ376622=NC_011550] Reasons to justify the creation and assignment of the new species: According to the demarcation criteria as outlined in Module 3 and agreed upon by the Coronavirus Study Group, the new coronaviruses isolated from Bulbul, Thrush and Munia are representatives of separates species. -
Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses
Article DOI: https://doi.org/10.3201/eid2704.203945 Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses Appendix Appendix Table. Citations for in-text tables, by coronavirus and host category Pathogen (abbreviation) Category Table Reference Alphacoronavirus 1 (ACoV1); strain canine enteric coronavirus Receptor 1 (1) (CCoV) Reservoir host(s) 2 (2) Spillover host(s) 2 (3–6) Clinical manifestation 3 (3–9) Alphacoronavirus 1 (ACoV1); strain feline infectious peritonitis Receptor 1 (10) virus (FIPV) Reservoir host(s) 2 (11,12) Spillover host(s) 2 (13–15) Susceptible host 2 (16) Clinical manifestation 3 (7,9,17,18) Bat coronavirus HKU10 Receptor 1 (19) Reservoir host(s) 2 (20) Spillover host(s) 2 (21) Clinical manifestation 3 (9,21) Ferret systemic coronavirus (FRSCV) Receptor 1 (22) Reservoir host(s) 2 (23) Spillover host(s) 2 (24,25) Clinical manifestation 3 (9,26) Human coronavirus NL63 Receptor 1 (27) Reservoir host(s) 2 (28) Spillover host(s) 2 (29,30) Nonsusceptible host(s) 2 (31) Clinical manifestation 3 (9,32–34) Human coronavirus 229E Receptor 1 (35) Reservoir host(s) 2 (28,36,37) Intermediate host(s) 2 (38) Spillover host(s) 2 (39,40) Susceptible host(s) 2 (41) Clinical manifestation 3 (9,32,34,38,41–43) Porcine epidemic diarrhea virus (PEDV) Receptor 1 (44,45) Reservoir host(s) 2 (32,46) Spillover host(s) 2 (47) Clinical manifestation 3 (7,9,32,48) Rhinolophus bat coronavirus HKU2; strain swine acute Receptor 1 (49) diarrhea syndrome coronavirus (SADS-CoV) Reservoir host(s) 2 (49) Spillover host(s) 2 -
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). -
Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds
J Vet Res 62, 249-255, 2018 DOI:10.2478/jvetres-2018-0035 REVIEW ARTICLE Coronaviruses in avian species – review with focus on epidemiology and diagnosis in wild birds Justyna Miłek, Katarzyna Blicharz-Domańska Department of Poultry Diseases, National Veterinary Research Institute, 24-100 Puławy, Poland [email protected] Received: May 2, 2018 Accepted: September 19, 2018 Abstract Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. -
Animal Reservoirs and Hosts for Emerging Alpha- and Betacoronaviruses
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 3 September 2020 doi:10.20944/preprints202009.0058.v1 Review Animal Reservoirs and Hosts for Emerging Alpha- and Betacoronaviruses Ria R. Ghai, Ann Carpenter, Meghan K. Herring, Amanda Y. Liew, Krystalyn B. Martin, Susan I. Gerber, Aron J. Hall, Jonathan M. Sleeman, Sophie VonDobschuetz and Casey Barton Behravesh 1 U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States (R. Ghai, A. Carpenter, M. Herring, A. Liew, K. Martin, S. Gerber, A Hall, C Barton Behravesh) 2 Emory University, Atlanta, GA, United States (M. Herring, A. Liew, K. Martin) 3 U.S. Geological Survey National Wildlife Health Center, Madison, WI, United States (J. Sleeman) 4 Food and Agriculture Organization of the United Nations, Rome, Italy (S. VonDobschuetz) Running Title: Animal hosts for emerging alpha and betacoronaviruses Article Summary: A review of coronaviruses in wildlife, livestock, and companion animals, and comprehensive data on receptor usage, hosts, and clinical presentation of 15 previously or currently emerging alpha-or beta-coronaviruses in people and animals. Abstract: The ongoing global pandemic caused by coronavirus disease 2019 (COVID-19) has once again demonstrated the significance of the Coronaviridae family in causing human disease outbreaks. As SARS-CoV-2 was first detected in December 2019, information on its tropism, host range, and clinical presentation in animals is limited. Given the limited information, data from other coronaviruses may be useful to inform scientific inquiry, risk assessment and decision-making. We review the endemic and emerging alpha- and betacoronavirus infections of wildlife, livestock, and companion animals, and provide information on the receptor usage, known hosts, and clinical signs associated with each host for 15 coronaviruses discovered in people and animals.