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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Reoviridae Genome Search Result RVA Annotations 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 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 3 4 5 6 7 8 9 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 AB081594 1062 G3-P[4] -N/A- Human Homo India genomic VP7 VP7 protein
Reoviridae Loading Virus Pathogen Database and Analysis Resource (ViPR)... About Us Community Announcements Links Resources Support SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HELP yun.zhang@jcvi.org 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 26963 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
Genotype-based Analysis & Visualization VP7 tree
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:eu984102 Organism:Rotavirus 11 NSP5/NSP6 H1 RVA/Human-wt/BGD/Dhaka25/2002/G12P8 89.46 98.99 0E0 gb:eu984100 Organism:Rotavirus 7 NSP3 T1 RVA/Human-tc/USA/P/1974/G3P8 86.87 97.75 0E0 gb:eu984109 Organism:Rotavirus 9 VP7 G1 RVA/Human-tc/JPN/KU/1974/G1P8 92.37 93.58 0E0 gb:eu984098 Organism:Rotavirus 5 NSP1 A1 RVA/Human-wt/BGD/Dhaka25/2002/G12P8 93.41 97.60 0E0 gb:eu984103 Organism:Rotavirus 1 VP1 R1 RVA/Human-tc/USA/Wa/1974/G1P8 98.94 98.19 0E0 gb:eu984104 Organism:Rotavirus 2 VP2 C1 RVA/Human-tc/USA/P/1974/G3P8 93.22 97.68 0E0 gb:eu984099 Organism:Rotavirus 8 NSP2 N1 RVA/Human-wt/BGD/Dhaka25/2002/G12P8 90.08 92.34 0E0 gb:eu984101 Organism:Rotavirus 10 NSP4 E1 RVA/Human-tc/USA/D/1974/G1P8 70.40 98.67 0E0 gb:eu984105 Organism:Rotavirus 3 VP3 M1 RVA/Human-wt/BEL/B4633/2003/G12P8 96.80 99.04 0E0 gb:eu984108 Organism:Rotavirus 6 VP6 I1 RVA/Human-tc/GBR/ST3/1975/G4P6 88.05 97.49 0E0 gb:eu984106 Organism:Rotavirus 4 VP4 P[8] RVA/Human-wt/BEL/B3458/2003/G9P8 94.11 96.76 0E0 Results of Non-Genotyped Sequences No Sequences in the input fasta cannot be genotyped
Exploration of RVA Genotype Data
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
Genotype Geographic Distribution 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Strains Africa Asia Europe North_America Oceania 783 1,314 727 698 217 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
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% 200 2005 2006 2007 2008 2009 2010 2011 2012 2013 Vaccine 2005 2006 2007 2008 2009 2010 2011 2012 2013 No vaccine 0 Number of VP7 sequences 50 0
Antigenic Drift in the Context of Vaccination Genetic changes in VP7/G1 Country Position Chi-square Value Vaccine introduced in 2006 P-value <=2005 2006-2008 >=2009 B-cell Epitope USA 72 172.631 3.26E-38 201 Q, 6 R 23 Q, 4 R 4 Q, 32 R Yes Brazil 72 86.739 1.46E-19 79 Q 7 Q 6 Q, 24 R Yes No vaccine program Thailand 72 14.914 5.77E-04 1 Q, 2 R 26 Q, 5 R 205 Q, 16 R Yes 250 200 150 100 50 0 <=2005 2006-2008 >=2009 <=2005 2006-2008 >=2009 <=2005 2006-2008 >=2009 USA Brazil Thailand R Q Vaccine Vaccine No vaccine program
Suggestions Strain name Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch. Virol., 2011, 156(8):1397-413. PMID: 21597953 Metadata missing, format, field Sequence data scarcity, sampling bias
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. HHSN272201400028C