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Resource (ViPR) February 2020 New Features in ViPR

New 2019-nCoV portal!!! Loading Virus Pathogen Database and Analysis Resource (ViPR)... Viral Bioinformatics Workshop Modules 2019-nCoV 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 Taxonomy: Group IV ((+)ssRNA); ; Coronavirinae; ; (2019-nCoV) portal in ViPR to Wuhan seafood market virus Virion: enveloped, spherical, 60-140 nm in diameter with spikes of about 9-12 nm technologies to infectious diseases: EV-D68 : ~30 kb positive-sense, single-stranded RNA support research efforts on this emerging RNA Transcript: 5' cap, 3' poly-A tail Proteome: 10 proteins and related in neurological Transmission: Some early cases had some link to a seafood and animal market, suggesting animal-to-human transmission. Later cases indicate sustained human-to- public health threat. This open-access human transmission. Phylogeny: More closely related to bat-SL-CoVZC45 and bat-SL-CoVZXC21 than SARS disease 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, 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. • Module 1: Next generation sequencing necessary genomic data and analytical tools References: GenBank: MN908947; PMID: 31978945; CDC – 2019-nCoV

2019-nCov Data Highlights Virus News (NGS) technologies for pathogen for 2019-nCoV and related . 2019-nCoV Updated 31 January 2020 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) sequencing Jan 30, 2020: A genomic report of the 2019 Novel Coronavirus Doherty Institute scientists first to grow and Here you can: share Wuhan coronavirus Wuhan coronavirus 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, Epidemiology Reports with 56 deaths, according to the most recent WHO Situation Report • Module 2: Phylogenetics 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 • access integrated data: genome, and Coronavirus (2019-nCoV) from Wuhan, China is now available in ViPR. View Genome. Scientific Publications More 2019-nCoV news. • Module 3: Comparative genomics analysis Latest Publications protein sequences, immune epitopes, 3D Host factor data for SARS-CoV and MERS-CoV Host factor response data from 21 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 View the full agenda here. data for SARS-CoV, MERS-CoV, etc. Host Factor Data component. Quick Search A section of the new 2019-nCoV portalViPR will search in data fields associated with genome, gene and protein data. (Details including wildcard usage) Workshop Format landing page Keyword: • use a suite of analysis and visualization Go

Connect with Us tools: multiple sequence alignment, Approximately 50% lecture and 50% hands-

phylogenetic tree construction and The ViPR team has also analyzed theInformation 2019- about 2019-nCoV on practical exercises in the analysis of NGS ViPR Mailing List visualization, metadata-driven comparative nCoV genomic data and immune epitopes data and the use of analytical tools and data sequence analysis, sequence variation in other Betacoronaviruses. These results resources in ViPR and IRD for use analysis, BLAST, short peptide search, PCR are described in analysis reports that are case exploration. primer design, genome annotation, etc. accessible from the Latest Analysis Reports Who Should Apply • store and share data through your personal section on the 2019-nCoV landing page. Workbench. This workshop is intended for graduate students, postdoctoral students, and faculty- Bacterial and Viral Bioinformatics level researchers working on viral infectious Loading Virus Pathogen Database and AnalysisAbout Resource Us Community (ViPR)... Announcements Links Resources Support Workshop, Chicago, March 23-27, 2020 diseases.

Search Analyze Save to Workbench The new Bacterial-Viral BRC (BV-BRC), a Search our comprehensive database for: Analyze data online: Use your workbench to: Registration Sequences & strains Sequence Alignment Store and share data Immune epitopes Phylogenetic Tree Combine working sets collaboration between the PATRIC /RAST 3D protein structures Sequence Variation (SNP) Integrate your data with ViPR data Host Factor Data Metadata-driven Comparative Analysis Store and share analyses Antiviral Drugs BLAST Custom search alert and IRD /ViPR teams, will be offering a joint Registration is free. Participants must pay for Plasmid Data VIGOR4 Genome Annotator Browse All Search Types Browse All Tools bacterial and viral bioinformatics workshop their own travel, lodging and meals. Supported Programs Click on a supported program of interest to go to program description page. at the Argonne National Laboratory in the NIAID Functional Genomics NIAID Systems Biology suburbs of Chicago, Illinois. Please register early to ensure a seat. Virus Families

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

Flaviviridae Togaviridae Paramyxoviridae

Featured Virus News • March 25-27, 2020: Viral Bioinformatics Click on a featured virus of interest to go to virus-specific home page. Updated 31 January 2020 CDC's 2019 Novel Coronavirus (2019-nCoV) Situation Summary report New! Jan 30,2019 : A genomic report of the 2019 Ebolavirus Novel Coronavirus (2019-nCoV) using IRD/ViPR 2019-nCoV Doherty Institute scientists first to grow and share Wuhan coronavirus Wuhan coronavirus 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) Participants may attend one or both sections. of the 2019 Novel Coronavirus (2019-nCoV) 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 ViPR is now available, visit The new 2019-nCoV portal can be accessed www.viprbrc.org from the ViPR homepage - Featured Viruses Viral bioinformatics workshop, Qatar, 2019

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