Rotavirus Genotyping and Enhanced Annotation in the Virus Pathogen Resource (ViPR) Yun Zhang J. Craig Venter Institute ASV 2016 June 19, 2016
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1 Rotavirus Genotyping and Enhanced Annotation in the Virus Pathogen Resource (ViPR) Yun Zhang J. Craig Venter Institute ASV 2016 June 19, 2016
2 Loading Virus Pathogen Database and Analysis About Resource Us Community (ViPR)... Announcements Links Resources Support Search Search our comprehensive database for: Genomes Analyze Analyze data online: Sequence Alignment Save to Workbench Use your workbench to: Store and share data Free virus database and analysis web resource funded by the US National Institute of Allergy and Infectious Diseases Genes & proteins Immune epitopes 3D protein structures Host Factor Data Phylogenetic Tree Sequence Variation (SNP) Metadata driven Comparative Analysis BLAST Combine working sets Integrate your data with ViPR data Store and share analyses Custom search alert Broad coverage of human pathogenic and related viruses Antiviral Drugs Browse All Search Types Browse All Tools Customized portals for high priority featured viruses 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 Tight integration of a wide variety of different data types with a broad array of analysis and visualization tools Caliciviridae Hepeviridae Arenaviridae Paramyxoviridae Reoviridae Herpesviridae Novel derived data only available in ViPR Coronaviridae Flaviviridae Featured Viruses Picornaviridae Togaviridae Click on a featured virus of interest to go to virus specific home page. Bunyaviridae Filoviridae Click on a featured virus link to go to virus specific sequence or protein search result page Highlights Rhabdoviridae Dengue Ebolavirus Hepatitis C virus Zika Virus Enterovirus D68 Genomes Start Search Enterovirus D68 Proteins Mature Peptides Mature viral protein products resulting from protease and self cleavage of the polyprotein are displayed according to their location in the genome and the polyprotein. Key Highlights: Visualize viral mature peptides Display location of mature peptide Access additional information relating to the mature peptide Virus News Zika virus (updated 7 Apr 2016) Sirohi et al. reported a 3.8 A resolution cryo EM structure of mature virion from ZIKV H/PF/2013. Zhu et al. compared pre epidemic and epidemic ZIKV sequences, showing amino acid changes in epidemic strains. Faria et al. used phylogenetic analysis of new, complete genomes to estimate a single entry into Brazil in 2013, prior to the 2014 World Cup, and coincident with reported outbreaks in the Pacific islands. ViPR supports research on ZIKV with weekly data updates (293 genomes as of 4 Apr), consistent mature peptide annotations, and a suite of bioinformatics analysis tools. Ebola virus (updated 7 Apr 2016) Corti, et al. reported that human mabs from blood samples of a 1995 EVD survivor neutralize outbreak variants of EBV and protect macaques as late as 5 d after lethal challenge. ViPR supports research on EBV with weekly data updates (1,794 genomes as of 4 Apr) and a suite of bioinformatics analysis tools. MERS CoV (updated 7 Apr 2016) van Doremalen et al extended earlier findings to show that when 4 amino acids in hamster DPP4 are changed to human DPP4 residues, the hamster protein acts as a MERS CoV receptor. Previous Scientific Reports Poxviridae Individual personal online Workbenches Large user community 1,375 sessions/week (2015 average) 36% from U.S. 64% international (Top 10 - India, UK, China, Canada, France, Brazil, Australia, Italy, South Korea) 152 citations in scientific publications (13JUN2016)
3 Reoviridae Genome Search Result RVA Annotations About Us Community Announcements Links Resources Support SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA VIRUS FAMILIES HELP ViPR Home Reoviridae Home Genome Search Results Your Selected Items: 0 items selected Add to Working Set Save Search Run Analysis Download Your search returned 4,033 genomes. Search Criteria Displaying 500 records per page, sorted by GenBank Protein Name in ascending order. Display Settings Select all 4,033 genomes < Previous Page: 9 of 9 More columns were returned than can be displayed without scrolling. Use scroll bars at top and bottom of display to move right and left or reduce the number of ViPR curation >600 records RotaC genotyping & ViPR concatenation ViPR curation VIGOR annotation 107E1B Rotavirus AB G3-P[4] -N/A- Human Homo India genomic VP7 VP7 protein
4 Reoviridae Loading Virus Pathogen Database and Analysis Resource (ViPR)... About Us Community Announcements Links Resources Support SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HELP ViPR Home Reoviridae Home Genome Search Genome Search Search for virus genomic sequences and related information. You can search for the whole virus family or search for specified genus, species etc. You can also find your strain or genome record if you have its information, such as strain name, accession. Rotavirus A (RVA) the major rotavirus group that infects humans, remains a major cause of morbidity in infants and children worldwide. Given the public health significance, ViPR has introduced dedicated options for searching RVA genomes. Make a selection in the taxonomy browser that includes RVA or check the Rotavirus A checkbox found below the browser. Results matching your criteria: 238 SELECT VIRUS(ES) TO INCLUDE IN SEARCH Jump to strain in taxonomy: Start to type strain to get suggestions Deselect All COLLECTION YEAR Start: YYYY ViPR curated controlled vocabulary GEOGRAPHIC GROUPING HOST SELECTION Species: Rotavirus A Deselect All (15507/15507 strains selected) (15507 Strains complete segments) Species: Rotavirus B Select All (0/403 strains selected) (403 Strains 477 complete segments) Species: Rotavirus C Select All (0/888 strains selected) (888 Strains 1114 complete segments) Species: Rotavirus D Select All (0/45 strains selected) (45 Strains 34 complete segments) Species: Rotavirus F Select All End: YYYY To add month to search, see Advance Search Options: Month Range COUNTRY Browse to and Select Rotavirus A COMPLETE SEQUENCES Complete Sequences Only ROTAVIRUS A SPECIFIC OPTIONS ViPR annotations GENOTYPE SEGMENTS MINIMUM SEGMENT LENGTH COMPLETE GENOME G G1 Ex: G1, G3, G% P P[8] Ex: P[2], P[7], P% Mixed Genotype only Specify Segment Lengths: RefSeq (nt) VP1 (R) 3302 VP2 (C) 2693 VP3 (M) 2591 VP4 (P) 2362 NSP1 (A) 1614 VP6 (I) 1356 NSP3 (T) 1105 NSP2 (N) 1059 VP7 (G) 1062 NSP4 (E) 751 NSP5/NSP6 (H) 667 Genomes with All Segments
5 Genotype-based Analysis & Visualization VP7 tree
6 RVA Genotyping Tool Reoviridae Rotavirus A Genotyping Report (SOP) Download Raw Result Loading Virus Pathogen Database and Analysis Resource (ViPR)... About Us Community Announcements Links Resources Support SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA VIRUS FAMILIES HELP yun.zhang@jcvi.org ViPR Home Reoviridae Home Rotavirus A Genotype Determination Results Results of Genotyped Sequences Sequence Identifier Segment Number Gene Name Genotype Closest Strain Query Coverage % Ident % E Value gb:eu Organism:Rotavirus 11 NSP5/NSP6 H1 RVA/Human-wt/BGD/Dhaka25/2002/G12P E0 gb:eu Organism:Rotavirus 7 NSP3 T1 RVA/Human-tc/USA/P/1974/G3P E0 gb:eu Organism:Rotavirus 9 VP7 G1 RVA/Human-tc/JPN/KU/1974/G1P E0 gb:eu Organism:Rotavirus 5 NSP1 A1 RVA/Human-wt/BGD/Dhaka25/2002/G12P E0 gb:eu Organism:Rotavirus 1 VP1 R1 RVA/Human-tc/USA/Wa/1974/G1P E0 gb:eu Organism:Rotavirus 2 VP2 C1 RVA/Human-tc/USA/P/1974/G3P E0 gb:eu Organism:Rotavirus 8 NSP2 N1 RVA/Human-wt/BGD/Dhaka25/2002/G12P E0 gb:eu Organism:Rotavirus 10 NSP4 E1 RVA/Human-tc/USA/D/1974/G1P E0 gb:eu Organism:Rotavirus 3 VP3 M1 RVA/Human-wt/BEL/B4633/2003/G12P E0 gb:eu Organism:Rotavirus 6 VP6 I1 RVA/Human-tc/GBR/ST3/1975/G4P E0 gb:eu Organism:Rotavirus 4 VP4 P[8] RVA/Human-wt/BEL/B3458/2003/G9P E0 Results of Non-Genotyped Sequences No Sequences in the input fasta cannot be genotyped
7 Exploration of RVA Genotype Data
![Others 10% G4-P[8]](/docs-images/72/67509223/images/8-5.jpg "4% G12-P[8] 7%")
![G3-P[8] 10%](/docs-images/72/67509223/images/8-6.jpg "G9-P[8] 11%")
![G2-P[4] 14%](/docs-images/72/67509223/images/8-7.jpg "G1-P[8] 34%")
8 Genotype Constellation Preference Human RVA G-P Genotypes Human RVA Internal Gene Genotypes Others 20% Others 10% G4-P[8] 4% G12-P[8] 7% G3-P[8] 10% G9-P[8] 11% G2-P[4] 14% G1-P[8] 34% I2-R2-C2- M2-A2-N2- T2-E2-H2 20% I1-R1-C1- M1-A1-N1- T1-E1-H1 70% G1 4, 9, 12 X P[4], [8] account for 80% of all RVA human strains. Others: the majority considered as reassortments
9 Genotype Geographic Distribution 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Strains Africa Asia Europe North_America Oceania 783 1, South_America 614 Global 4,353 G1-P[8] G2-P[4] G9-P[8] G3-P[8] G12-P[8] G12-P[6] G4-P[8] G8-P[6] Others
10 Genotype Variation in the Context of Vaccination 100% 90% USA Canada G12 G9 G8 G4 G3 G2 G1 80% 70% 60% 50% 40% 30% 20% 10% 0% Vaccine No vaccine 0 Number of VP7 sequences 50 0
11 Antigenic Drift in the Context of Vaccination Genetic changes in VP7/G1 Country Position Chi-square Value Vaccine introduced in 2006 P-value <= >=2009 B-cell Epitope USA E Q, 6 R 23 Q, 4 R 4 Q, 32 R Yes Brazil E Q 7 Q 6 Q, 24 R Yes No vaccine program Thailand E-04 1 Q, 2 R 26 Q, 5 R 205 Q, 16 R Yes <= >=2009 <= >=2009 <= >=2009 USA Brazil Thailand R Q Vaccine Vaccine No vaccine program
12 Suggestions Strain name Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch. Virol., 2011, 156(8): PMID: Metadata missing, format, field Sequence data scarcity, sampling bias
13 Acknowledgements Richard Scheuermann, PI Tim Stockwell, Viral Group Lead Dan Katzel Karla Stucker Seth Schobel Ed Klem, Technical Lead Sanjeev Kumar Hongtao Zhao Sherry He Lei Tong Rotavirus Classification Working Group No. HHSN C
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