DOCSLIB.ORG

Latest Ncbi-Taxonomist Docker Image Can Be Pulled from Registry.Gitlab.Com/Janpb/ Ncbi-Taxonomist:Latest

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. pip3 on Ubuntu. 1.1 Local pip install (no root required) $: pip install ncbi-taxonomist --user 3 ncbi-taxonomist Documentation, Release 1.2.1+8580b9b On Linux, ncbi-taxonomist will be installed to $HOME/.local/bin. If you cannot invoke ncbi-taxonomist from the command line, its’ likely $HOME/.local/bin is not in your $PATH (check echo $PATH). In such a case, choose one of the following possibilities: • add $HOME/.local/bin to your $PATH: – echo "export PATH=${PATH}:$HOME/.local/bin" >> ~/.bashrc • add an alias: – see man bash or https://www.tldp.org/LDP/abs/html/aliases.html • use $HOME/.local/bin/ncbi-taxonomist implicitly 1.2 Global pip install (root required) $: pip install ncbi-taxonomist ncbi-taxonomist should be now in /usr/local/bin and in you $PATH. 4 Chapter 1. Installation CHAPTER 2 Basic functions All ncbi-taxonomist commands have the following underlying structure: ncbi-taxonomist <command> <options> This section shows the basic usage of ncbi-taxonomist. More complex examples, inlcuding data extraction with jq can be found here. The output is a single JSON object or XML tree per line for each queried taxid, name, or accessions. The examples show pretty printed single results for clarity only. Contents • Collect – Output format * JSON output * XML output • Map – Taxids and names – Mapping accession – Supported access Entrez databases – Output format * JSON output · Single mapping result · Multiple mapping results * XML output · Single mapping result 5 ncbi-taxonomist Documentation, Release 1.2.1+8580b9b · Multiple mapping results • Resolve – Taxids and names – Accessions – Output format * JSON output · Single mapping result · Multiple mapping results * XML output · Single mapping result · Multiple mapping results • Import – Local database schema – Import taxa via collect – Import taxa via resolve – Import accessions • Subtree – Collecting subtrees * Between two given ranks * Collect one specific rank * Collect from a given rank to root and print XML * Collect from a given rank to lowest rank – Output format * JSON output * XML output • Group – Creating a group – Retrieve a group 2.1 Collect The collect command fetches taxa from the Entrez database. If Taxids or names sharing parts of the same lineage, these taxa are printed only once. 6 Chapter 2. Basic functions ncbi-taxonomist Documentation, Release 1.2.1+8580b9b 2.1.1 Output format The output describes the collected taxa, one per line. A single taxon has the following structure, for example chim- panzee (tx9598): { "taxid" : 9598, "rank" : "species", "parentid" : 9596, "name" : "Pan troglodytes", "names" : { "Pan troglodytes" : "scientific_name", "chimpanzee" : "GenbankCommonName" } } Collecting taxa for chimpanzee and human: ncbi-taxonomist collect -n chimpanzee human JSON output {"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"}, ,!"parentid":null,"name":"cellular organisms"} {"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid ,!":131567,"name":"Eukaryota"} {"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid ,!":2759,"name":"Opisthokonta"} {"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid ,!":33154,"name":"Metazoa"} {"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208, ,!"name":"Eumetazoa"} {"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072, ,!"name":"Bilateria"} {"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid ,!":33213,"name":"Deuterostomia"} {"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511, ,!"name":"Chordata"} {"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid ,!":7711,"name":"Craniata"} {"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid ,!":89593,"name":"Vertebrata"} {"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid ,!":7742,"name":"Gnathostomata"} {"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid ,!":7776,"name":"Teleostomi"} {"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid ,!":117570,"name":"Euteleostomi"} {"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"}, ,!"parentid":117571,"name":"Sarcopterygii"} {"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"}, ,!"parentid":8287,"name":"Dipnotetrapodomorpha"} {"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid ,!":1338369,"name":"Tetrapoda"} {"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523, ,!"name":"Amniota"} (continues on next page) 2.1. Collect 7 ncbi-taxonomist Documentation, Release 1.2.1+8580b9b (continued from previous page) {"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524, ,!"name":"Mammalia"} {"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674, ,!"name":"Theria"} {"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525, ,!"name":"Eutheria"} {"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid ,!":9347,"name":"Boreoeutheria"} {"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"}, ,!"parentid":1437010,"name":"Euarchontoglires"} {"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146, ,!"name":"Primates"} {"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid ,!":9443,"name":"Haplorrhini"} {"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"}, ,!"parentid":376913,"name":"Simiiformes"} {"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid ,!":314293,"name":"Catarrhini"} {"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"}, ,!"parentid":9526,"name":"Hominoidea"} {"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid ,!":314295,"name":"Hominidae"} {"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid ,!":9604,"name":"Homininae"} {"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598, ,!"name":"Homo"} {"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human": ,!"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"} {"taxid":9596,"rank":"genus","names":{"Pan":"scientific_name"},"parentid":207598,"name ,!":"Pan"} {"taxid":9598,"rank":"species","names":{"Pan troglodytes":"scientific_name", ,!"chimpanzee":"GenbankCommonName"},"parentid":9596,"name":"Pan troglodytes"} XML output <taxon><taxid>131567</taxid><rank>no rank</rank><name>cellular organisms</name> ,!<parentid>None</parentid><names><name type="scientific_name">cellular organisms</ ,!name></names></taxon> <taxon><taxid>2759</taxid><rank>superkingdom</rank><name>Eukaryota</name><parentid> ,!131567</parentid><names><name type="scientific_name">Eukaryota</name></names></ ,!taxon> <taxon><taxid>33154</taxid><rank>clade</rank><name>Opisthokonta</name><parentid>2759</ ,!parentid><names><name type="scientific_name">Opisthokonta</name></names></taxon> <taxon><taxid>33208</taxid><rank>kingdom</rank><name>Metazoa</name><parentid>33154</ ,!parentid><names><name type="scientific_name">Metazoa</name></names></taxon> <taxon><taxid>6072</taxid><rank>clade</rank><name>Eumetazoa</name><parentid>33208</ ,!parentid><names><name type="scientific_name">Eumetazoa</name></names></taxon> <taxon><taxid>33213</taxid><rank>clade</rank><name>Bilateria</name><parentid>6072</ ,!parentid><names><name type="scientific_name">Bilateria</name></names></taxon> <taxon><taxid>33511</taxid><rank>clade</rank><name>Deuterostomia</name><parentid>33213 ,!</parentid><names><name type="scientific_name">Deuterostomia</name></names></taxon> <taxon><taxid>7711</taxid><rank>phylum</rank><name>Chordata</name><parentid>33511</ ,!parentid><names><name type="scientific_name">Chordata</name></names></taxon>
Load more

Recommended publications
  • Noroviruses: Q&A
    University of California, Berkeley 2222 Bancroft Way Berkeley, CA 94720 Appointments 510/642-2000 Online Appointment www.uhs.berkeley.edu Noroviruses: Q&A What are noroviruses? Noroviruses are a group of viruses that cause the “stomach flu” or gastroenteritis (GAS-tro-enter-I-tis) in people. The term “norovirus” was recently approved as the official name for this group of viruses. Several other names have been used for noroviruses, including: • Norwalk-like viruses (NLVs) • caliciviruses (because they belong to the virus family Caliciviridae) • small round structured viruses. Viruses are very different from bacteria and parasites, some of which can cause illnesses similar to norovirus infection. Viruses are much smaller, are not affected by treatment with antibiotics, and cannot grow outside of a person’s body. What are the symptoms of illness caused by noroviruses? The symptoms of norovirus illness usually include nausea, vomiting, diarrhea, and some stomach cramping. Sometimes people additionally have a low-grade fever, chills, headache, muscle aches and a general sense of tiredness. The illness often begins suddenly, and the infected person may feel very sick. The illness is usually brief, with symptoms lasting only about one or two days. In general, children experience more vomiting than adults. Most people with norovirus illness have both of these symptoms. What is the name of the illness caused by noroviruses? Illness caused by norovirus infection has several names, including: • stomach flu – this “stomach flu” is not related to the flu (or influenza), which is a respiratory illness caused by influenza virus • viral gastroenteritis – the most common name for illness caused by norovirus.
    [Show full text]
  • 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
    [Show full text]
  • Human Astrovirus 1–8 Seroprevalence Evaluation in a United States Adult Population
    UC Santa Cruz UC Santa Cruz Previously Published Works Title Human Astrovirus 1-8 Seroprevalence Evaluation in a United States Adult Population. Permalink https://escholarship.org/uc/item/9nz336gs Journal Viruses, 13(6) ISSN 1999-4915 Authors Meyer, Lena Delgado-Cunningham, Kevin Lorig-Roach, Nicholas et al. Publication Date 2021-05-25 DOI 10.3390/v13060979 Peer reviewed eScholarship.org Powered by the California Digital Library University of California viruses Article Human Astrovirus 1–8 Seroprevalence Evaluation in a United States Adult Population Lena Meyer , Kevin Delgado-Cunningham, Nicholas Lorig-Roach, Jordan Ford and Rebecca M. DuBois * Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; [email protected] (L.M.); [email protected] (K.D.-C.); [email protected] (N.L.-R.); [email protected] (J.F.) * Correspondence: [email protected] Abstract: Human astroviruses are an important cause of viral gastroenteritis globally, yet few studies have investigated the serostatus of adults to establish rates of previous infection. Here, we applied biolayer interferometry immunosorbent assay (BLI-ISA), a recently developed serosurveillance technique, to measure the presence of blood plasma IgG antibodies directed towards the human astrovirus capsid spikes from serotypes 1–8 in a cross-sectional sample of a United States adult population. The seroprevalence rates of IgG antibodies were 73% for human astrovirus serotype 1, 62% for serotype 3, 52% for serotype 4, 29% for serotype 5, 27% for serotype 8, 22% for serotype 2, 8% for serotype 6, and 8% for serotype 7. Notably, seroprevalence rates for capsid spike antigens correlate with neutralizing antibody rates determined previously.
    [Show full text]
  • Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection Samuel Cordey,1 Diem-Lan Vu,1 Manuel Schibler, Arnaud G
    RESEARCH Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection Samuel Cordey,1 Diem-Lan Vu,1 Manuel Schibler, Arnaud G. L’Huillier, Francisco Brito, Mylène Docquier, Klara M. Posfay-Barbe, Thomas J. Petty, Lara Turin, Evgeny M. Zdobnov, Laurent Kaiser Next-generation sequencing has identified novel astrovi- observed in community healthcare centers (2,3). Symp- ruses for which a pathogenic role is not clearly defined. toms are generally mild, with patient hospitalization We identified astrovirus MLB2 infection in an immunocom- usually not required; asymptomatic carriage has been petent case-patient and an immunocompromised patient described in 2% of children (4). who experienced diverse clinical manifestations, notably, Screening of fecal samples from persons with diarrhea meningitis and disseminated infection. The initial case-pa- and control samples in different parts of the world by un- tient was identified by next-generation sequencing, which revealed astrovirus MLB2 RNA in cerebrospinal fluid, biased next-generation sequencing (NGS) or reverse tran- plasma, urine, and anal swab specimens. We then used scription PCR (RT-PCR) has revealed the sporadic pres- specific real-time reverse transcription PCR to screen 943 ence of members of the Astroviridae family, previously fecal and 424 cerebrospinal fluid samples from hospital- unrecognized in humans, that are phylogenetically substan- ized patients and identified a second case of meningitis, tially distant from classic HAstVs (3,5–9). These viruses with positive results for the agent in the patient’s feces have been named HAstV-VA/HMO and HAstV-MLB, for and plasma. This screening revealed 5 additional positive Virginia, human-mink-ovine, and Melbourne, respectively, fecal samples: 1 from an infant with acute diarrhea and according to the place where they were first identified and 4 from children who had received transplants.
    [Show full text]
  • Fact Sheet Norovirus
    New Hampshire Department of Health and Human Services Fact Sheet Division of Public Health Services Norovirus What is norovirus? How is norovirus infection diagnosed? Noroviruses are a group of viruses that cause Laboratory diagnosis is difficult but there are the “stomach flu,” or gastrointestinal tests that can be performed in the New (stomach and digestive) illness. Norovirus Hampshire Public Health Lab in situations infection occurs occasionally in only one or a where there are multiple cases. Diagnosis is few people or it can be responsible for large often based on the combination of symptoms outbreaks, such as in long-term care facilities. and the short time of the illness. Who gets norovirus? What is the treatment for norovirus Norovirus infects people of all ages infection? worldwide. It may, however, be more No specific treatment is available. People who common in adults and older children. become dehydrated might need to be rehydrated by taking liquids by mouth. How does someone get norovirus? Occasionally patients may need to be Norovirus is spread from person to person via hospitalized to receive intravenous fluids. feces, but some evidence suggests that the virus is spread through the air during How can norovirus be prevented? vomiting. Good hand washing is the most While there is no vaccine for norovirus, there important way to prevent the transmission of are precautions people should take: norovirus. Outbreaks have been linked to sick • Wash hands with soap and warm water food handlers, ill health care workers, cases in after using the bathroom and after facilities such as nursing homes spreading to changing diapers other residents, contaminated shellfish, and • Wash hands with soap and warm water water contaminated with sewage.
    [Show full text]
  • 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.
    [Show full text]
  • Diarrheal Illness
    Diarrheal Illness [Announcer] This program is presented by the Centers for Disease Control and Prevention. [Karen Hunter] Hi, I’m Karen Hunter and today I’m talking with Dr. Steve Monroe, director of CDC’s Division of High-Consequence Pathogens and Pathology. Our conversation is based on his paper about viral gastroenteritis, which appears in CDC's journal, Emerging Infectious Diseases. Welcome Dr. Monroe. [Steve Monroe] Thank you Karen, it’s a pleasure to be here. [Karen Hunter] Dr. Monroe, what is viral gastroenteritis? [Steve Monroe] Gastroenteritis is an irritation of the stomach or intestinal tract. Most people experience this as severe diarrhea, vomiting, and stomach pain. For this reason, it is often referred to as stomach flu, even though it is not caused by a flu virus. The more general term is “diarrheal illness.” When caused by a virus, it is known as viral gastroenteritis. There are several viruses that can cause this illness. [Karen Hunter] Your paper focuses on two of these viruses – norovirus and rotavirus. What are the main differences between the two of them? [Steve Monroe] The main differences between norovirus and rotavirus are in the age of people most affected and in the approaches we use for control and prevention. Norovirus can infect people of all ages, while rotavirus is most commonly found in young children. And, while there’s an effective vaccine to prevent rotavirus infection, current efforts to control norovirus illness rely primarily on emphasizing good personal hygiene and infection control practices. [Karen Hunter] We’d like to hear about both of these viruses.
    [Show full text]
  • Novel Hepatitis D-Like Agents in Vertebrates and Invertebrates
    bioRxiv preprint doi: https://doi.org/10.1101/539924; this version posted February 4, 2019. 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. 1 Novel hepatitis D-like agents in vertebrates and invertebrates 2 3 4 Wei-Shan Chang1, John H.-O. Pettersson1, Callum Le Lay1, Mang Shi1, Nathan Lo1, Michelle 5 Wille2, John-Sebastian Eden1,3, Edward C. Holmes1 6 7 8 1Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, 9 School of Life and Environmental Sciences and Sydney Medical School, The University of 10 Sydney, Sydney, NSW 2006, Australia; [email protected] (WSC); 11 [email protected] (MS); [email protected] (ECH); 12 [email protected] (JP); [email protected] (NL) 13 2WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty 14 Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; 15 [email protected] (MW) 16 3Westmead Institute for Medical Research, Centre for Virus Research, Westmead NSW, 17 2145; Australia; [email protected] (JSE); 18 19 20 * Correspondence: [email protected]; Tel.: +61 2 9351 5591 21 bioRxiv preprint doi: https://doi.org/10.1101/539924; this version posted February 4, 2019. 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.
    [Show full text]
  • Non-Norovirus Viral Gastroenteritis Outbreaks Reported to the National Outbreak Reporting System, USA, 2009–2018 Claire P
    Non-Norovirus Viral Gastroenteritis Outbreaks Reported to the National Outbreak Reporting System, USA, 2009–2018 Claire P. Mattison, Molly Dunn, Mary E. Wikswo, Anita Kambhampati, Laura Calderwood, Neha Balachandran, Eleanor Burnett, Aron J. Hall During 2009–2018, four adenovirus, 10 astrovirus, 123 The Study rotavirus, and 107 sapovirus gastroenteritis outbreaks NORS is a dynamic, voluntary outbreak reporting were reported to the US National Outbreak Reporting system. For each reported outbreak, health depart- System (annual median 30 outbreaks). Most were at- ments report the mode of transmission, number of tributable to person-to-person transmission in long-term confirmed and suspected cases, and aggregate epi- care facilities, daycares, and schools. Investigations of demiologic and demographic information as avail- norovirus-negative gastroenteritis outbreaks should in- able. NORS defines outbreaks as >2 cases of similar clude testing for these viruses. illness associated with a common exposure or epi- demiologic link (9). Health departments determine n the United States, ≈179 million cases of acute gas- reported outbreak etiologies on the basis of available troenteritis (AGE) occur annually (1). Norovirus is I laboratory, epidemiologic, and clinical data; specific the leading cause of AGE in the United States; other laboratory testing protocols vary by health depart- viral causes include adenovirus (specifically group F ment. Outbreak etiologies are considered confirmed or types 40 and 41), astrovirus, sapovirus, and rotavi- when >2 laboratory-confirmed cases are reported rus (2,3). These viruses are spread primarily through and considered suspected when <2 laboratory-con- the fecal–oral route through person-to-person contact firmed cases are reported. Outbreaks are considered or through contaminated food, water, or fomites (4–8).
    [Show full text]
  • Understanding Human Astrovirus from Pathogenesis to Treatment
    University of Tennessee Health Science Center UTHSC Digital Commons Theses and Dissertations (ETD) College of Graduate Health Sciences 6-2020 Understanding Human Astrovirus from Pathogenesis to Treatment Virginia Hargest University of Tennessee Health Science Center Follow this and additional works at: https://dc.uthsc.edu/dissertations Part of the Diseases Commons, Medical Sciences Commons, and the Viruses Commons Recommended Citation Hargest, Virginia (0000-0003-3883-1232), "Understanding Human Astrovirus from Pathogenesis to Treatment" (2020). Theses and Dissertations (ETD). Paper 523. http://dx.doi.org/10.21007/ etd.cghs.2020.0507. This Dissertation is brought to you for free and open access by the College of Graduate Health Sciences at UTHSC Digital Commons. It has been accepted for inclusion in Theses and Dissertations (ETD) by an authorized administrator of UTHSC Digital Commons. For more information, please contact [email protected]. Understanding Human Astrovirus from Pathogenesis to Treatment Abstract While human astroviruses (HAstV) were discovered nearly 45 years ago, these small positive-sense RNA viruses remain critically understudied. These studies provide fundamental new research on astrovirus pathogenesis and disruption of the gut epithelium by induction of epithelial-mesenchymal transition (EMT) following astrovirus infection. Here we characterize HAstV-induced EMT as an upregulation of SNAI1 and VIM with a down regulation of CDH1 and OCLN, loss of cell-cell junctions most notably at 18 hours post-infection (hpi), and loss of cellular polarity by 24 hpi. While active transforming growth factor- (TGF-) increases during HAstV infection, inhibition of TGF- signaling does not hinder EMT induction. However, HAstV-induced EMT does require active viral replication.
    [Show full text]
  • Article Download (79)
    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.
    [Show full text]
  • Norovirus-Gen508.Pdf
    Norovirus Gastroenteritis: Management of Outbreaks in Healthcare Settings U.S. Department of Health and Human Services Centers for Disease Control and Prevention Norovirus The most common cause of cases of acute gastroenteritis and gastroenteritis outbreaks Can affect nearly everyone in the population (from children to the elderly and everyone in between!) particularly because there is no long term immunity to the virus Causes acute but self-limited diarrhea, often with vomiting, abdominal cramping, fever, and fatigue . Most individuals recover from acute symptoms with 2-3 days , but can be more severe in vulnerable populations Burden of Norovirus Infection #1 cause of acute gastroenteritis in U.S. 21 million cases annually . 1 in 14 Americans become ill each year . 71,000 hospitalized annually in U.S. 80 deaths annually among elderly in U.K. 91,000 emergency room visits overall in the U.S. Occurs year round with peak activity during the winter months Cases occur in all settings, across the globe Scallan et al. 2011. EID. 17(1): 7-15.; Patel et al. 2008. EID. 14(8); 1224-31.; Harris et al. 2008. EID. 14(10); 1546-52. Norovirus in Healthcare Facilities Norovirus is a recognized cause of gastroenteritis outbreaks in institutions. Healthcare facilities are the most commonly reported settings of norovirus gastroenteritis outbreaks in the US and other industrialized countries. Outbreaks of gastroenteritis in healthcare settings pose a risk to patients, healthcare personnel, and to the efficient provision of healthcare services. Norovirus Activity in Healthcare Incidence of norovirus outbreaks in acute care facilities and community hospitals within the United States remains unclear.
    [Show full text]