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Influenza Research Database (IRD) February 2020 New Features in IRD

Loading Pathogen Database and Analysis Resource (ViPR)... New 2019-nCoV portal!!! 2019-nCoV Viral Bioinformatics Workshop Modules About Us Community Announcements Links Resources Support We are pleased to announce the 2019 Novel SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HELP [email protected] 2019-nCoV • Keynote: Applications of omics technolo- : Group IV ((+)ssRNA); ; Coronavirinae; Betacoronavirus; Coronavirus (2019-nCoV) portal in ViPR to Wuhan seafood market pneumonia virus Virion: enveloped, spherical, 60-140 nm in diameter with spikes of about 9-12 nm gies to infectious : EV-D68 and re- : ~30 kb positive-sense, single-stranded RNA RNA Transcript: 5' cap, 3' poly-A tail support research efforts on this emerg- Proteome: 10 Transmission: Some early cases had some link to a seafood and animal market, lated in neurological suggesting animal-to- transmission. Later cases indicate sustained human-to- human transmission. ing public health threat. This open-access Phylogeny: More closely related to -SL-CoVZC45 and bat-SL-CoVZXC21 than SARS Epidemiology: First reported in Wuhan, China, in December 2019. The virus has rapidly spread to other regions of China and other countries, including Australia, Canada, France, • Module 1: Next generation sequencing resource is updated daily and provides the Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam, and the US. Clinical: Reported 2019-nCoV cases have ranged from no symptoms to severe pneumonia and death. Symptoms can include fever, cough, shortness of breath. References: GenBank: MN908947; PMID: 31978945; CDC – 2019-nCoV (NGS) technologies for pathogen sequenc- necessary genomic data and analytical tools 2019-nCov Data Highlights Virus News ing 2019-nCoV Updated 31 January 2020 for 2019-nCoV and related Betacoronaviruses. CDC's 2019 Novel Coronavirus (2019-nCoV) Situation Summary report Latest Analysis Reports Jan 30, 2020 : A genomic report of the 2019 Novel Coronavirus (2019-nCoV) Jan 30, 2020: A genomic report of the 2019 Novel Coronavirus Doherty Institute scientists first to grow and share Wuhan coronavirus Wuhan coronavirus • Module 2: Phylogenetics Here you can: A preliminary comparative genomics (revised) of the 2019 Novel Coronavirus (2019-nCoV) As of January 26, 2020 there have been 2,014 confirmed cases of 2019-nCoV in 11 countries, with 56 deaths, according to the most recent Epidemiology Reports WHO Situation Report A preliminary comparative genomics (revised) WHO Situation Report of the 2019 Novel Coronavirus (2019-nCoV) CDC Situation Summary The first genome sequence for the 2019 Novel • Module 3: Comparative genomics analysis Coronavirus (2019-nCoV) from Wuhan, China • access integrated data: genome, gene and is now available in ViPR. View Genome. Scientific Publications More 2019-nCoV news.

Latest Publications factor data for sequences, immune epitopes, 3D SARS-CoV and MERS-CoV Host factor response data from 21 View the full agenda here. transcriptomic and 4 proteomic experiments for various strains of SARS-CoV and MERS-CoV is protein structures, host virus interaction available in ViPR. Browse, search and analyze the datasets in the Host Factor Data component.

data for SARS-CoV, MERS-CoV, etc. Quick Search Workshop Format ViPR will search in data fields associated with A section of the new 2019-nCoV portalgenome, gene and protein data. (Details including wildcard usage) landing page Keyword: • use a suite of analysis and visualization Go Approximately 50% lecture and 50% hands- Connect with Us tools: multiple sequence alignment, phylo- on practical exercises in the analysis of NGS

genetic tree construction and visualization, Information about 2019-nCoV data and the use of analytical tools and data metadata-driven comparative sequence The ViPR team has also analyzed VtheiPR Mailing 2019- List resources in ViPR and IRD for virology use analysis, sequence variation analysis, nCoV genomic data and immune epitopes in case exploration. BLAST, short peptide search, PCR primer other Betacoronaviruses. These results are de- design, genome annotation, etc. scribed in analysis reports that are accessible Who Should Apply from the Latest Analysis Reports section on • store and share data through your personal the 2019-nCoV landing page. This workshop is intended for graduate Workbench. students, postdoctoral students, and faculty- level researchers working on viral infectious Bacterial and Viral Bioinformatics diseases. Loading Virus Pathogen Database and AnalysisAbout Resource Us Community (ViPR)... Announcements Links Resources Support Workshop, Chicago, March 23-27, 2020 Registration Search Analyze Save to Workbench Search our comprehensive database for: Analyze data online: Use your workbench to: The new Bacterial-Viral BRC (BV-BRC), a col- Sequences & strains Sequence Alignment Store and share data Immune epitopes Phylogenetic Tree Combine working sets Registration is free. Participants must pay for 3D protein structures Sequence Variation (SNP) Integrate your data with ViPR data laboration between the PATRIC /RAST and IRD Host Factor Data Metadata-driven Comparative Analysis Store and share analyses Antiviral Drugs BLAST Custom search alert their own travel, lodging and meals. Plasmid Data VIGOR4 Genome Annotator /ViPR teams, will be offering a joint bacterial Browse All Search Types Browse All Tools and viral bioinformatics workshop at the Supported Programs Please register early to ensure a seat. Click on a supported program of interest to go to program description page. Argonne National Laboratory in the suburbs NIAID Functional Genomics NIAID Systems Biology

Virus Families of Chicago, Illinois. Click on icon of family or species of interest. Click here to to view all families and species in list format. Don't know family of species? Provide species name

Single-Stranded Positive-Sense RNA Single-Stranded Negative-Sense RNA Double-Stranded RNA Double-Stranded DNA

New! • March 23-25, 2020: Bacterial Bioinformatics Coronaviridae Picornaviridae using PATRIC/RAST Togaviridae

Featured Virus News Click on a featured virus of interest to go to virus-specific home page. Updated 31 January 2020 • March 25-27, 2020: Viral Bioinformatics us- CDC's 2019 Novel Coronavirus (2019-nCoV) Situation Summary report New! Jan 30,2019 : A genomic report of the 2019 Novel Coronavirus (2019-nCoV) 2019-nCoV Doherty Institute scientists first to grow and ing IRD/ViPR share Wuhan coronavirus Wuhan coronavirus Hepatitis C virus Lassa Virus As of January 26, 2020 there have been 2,014 confirmed cases of 2019-nCoV in 11 countries, with 56 deaths, according to the most recent WHO Situation Report Highlights A preliminary comparative genomics (revised) of the 2019 Novel Coronavirus (2019-nCoV) Participants may attend one or both sections. The first genome sequence for the 2019 Novel Coronavirus (2019-nCoV) from Wuhan, China 3D Protein Structure is now available in ViPR. View Genome. Visualize protein structures in 3D. Users can highlight Kose et al. Intravenous injection of experimentally determined epitopes on the structure. encapsulated mRNA encoding a neutralizing monoclonal from immortalized B cells of a Key Highlights: survivor protected mice against viral infection and virus-associated arthritis and Visualize protein structure in 3D induced protective concentrations of serum Highlight sequence features (epitopes, etc.) antibody in macaques. on the structure Lancet reviews the resurgence of vector-borne Download highlighted protein structure image disease in the midst of Venezuela’s political and humanitarian crisis. Following ICTV approval, the Arenaviridae site is now accessed via the Bunyavirales icon. The icon also offers access to the Nairo, Hanta, Start Search Peribunya, Phasma, and sites. The February 2020 release ViPR also offers API retrieval of sequence and Tutorial associated metadata from all families in the Bunyavirales order, including: Fimoviridae, etc. Click here for API instructions and examples. of IRD is now available, visit The new 2019-nCoV portal can be accessed www.fludb.org from the ViPR homepage - Featured Viruses Viral bioinformatics workshop, Qatar, 2019

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