Following virus recombination and evolution

Transcription

1 Following virus recombination and evolution Coping with the avalanche of sequencing data Dmitry Kusnetsov, Anne Gleizes, Robin Liechti, Ioannis Xenarios, Philippe Le Mercier Vital-IT/Swiss-Prot group SIB Swiss Institute of Bioinformatics Geneva/Lausanne Switzerland Workshop Rome 7-9 th November 2012Influenza risk assessment and risk modelling: Pandemic influenza threats and beyond

2 Sequencing influenza is becoming a commodity More and more sequences deposited in the INSDC (International Nucleotide Sequence Database Consortium) such as GenBank@NCBI Some are linked to epidemiological data, but all of these sequences serve as a basis of the underlying genetic diversity of influenza In the coming years more diagnostic and direct sequencing of isolates using next generation sequencing will be performed, leading to a major increase in number of isolates but also a major cost reduction in data generation

3 Soon in your laboratory

4 Avalanche of sequences?

5 Yes, but we know what to do

6 Paradigm shift in biology and medecine more and more data

7 Developed with and for the Influenza experts 5 years in production with a daily update

8 Openflu: an epi/genetic influenza database Sequences grouped per isolates Isolates accompanied by a comprehensive record of data for epidemiology: Minimal data required: year, host species, country Support for additional data: vaccination, patient status, resistance to antibiotics, animal domestication status, etc Influenza-specific genetic knowledge and algorithms In-frame protein analysis Computed mutations

9 Openflu: data import/export Import: Sequence repositories User submissions GenBank daily OpenFlu Curation of imported data Export: GenBank, data as a structured comment No Influenza specific knowledge is lost after export although GenBank has just generic data model

10 More influenza by the days A snapshot from Openflu web site, 02 Nov 2012 There are more than 2400 isolates that do not pass The biocuration criteria and are not presented to the users

11 Analytical tools

12 Sequence similarity map (SSM) computed every days South American cluster Eurasian cluster North American cluster A/Mexico/InDRE7218/2012 A/chicken/Jalisco/CPA1/2012 Each sequence is a point on the map Similar sequences are close to each other Vicinity of avian and human sequences on the map suggests zoonosis

13 Multi-segment SSM a method to observe and analyze reassortant on all isolates A potential ph1n1 precursor area H1N1 SWL Seasonal H1N1 The map coordinates are calculated using all 8 segments Visualizes genetic differences between isolates based on the whole Influenza genome The map color is by H/N subtype Highlighted are all H1 isolates, including: Seasonal H1N1 Pandemic H1N1 (swl) Minor H1Nx strains persistent for a long time nearby the area where pandemic H1N1 strain finally appears in 2009

14 SSM: a scalable method to overlay evolution and annotations of Influenza virus Readable beyond 10K sequences (unlike phylogenetic trees) More than 1500 single-segment maps for each of 8 segments, both generic and detailed: By Influenza subtype, like the H7N3 map By species, like the avian map Multi-segment maps (for HA+NA and for all 8 segments) Nucleotide and Protein maps Re-calculated daily always up-to-date

15 Openflu used by several projects Data provided to several partners at FAO ISZVe for evaluation and assessments As data is deposited every day the methodologies scale-up and is robust, minimal manual intervention Therefore we can tune isolate selection further find and curate necessary isolates from OpenFlu Organize data transfes in form of robust web-services feeding data ondemand to 3 rd party databases and users Help and support in data analysis and computational resources

16 Let s do it together

17 What and how to select for FLURISK and EPT+ Example of H1N1 SWL

18 Influenza genomic SSM A potential H1N1 SWL precursor area H1N1 SWL Seasonal H1N1 All 8 segments Color by H/N subtype Highlighted are: Seasonal H1N1 H1N1 SWL An area where a minor H1N1 influenza branch was for a few years before H1N1 SWL was finally composed

19 H1N1 SWL area: 2003,2007

20 H1N1 SWL area: 2008,2009

21 The potential H1N1 SWL precursor Predominantly swine Three human cases in June 2009 Presumably, they are continuation of the H1N1 SWL precursor branch These three human isolates contain 5 of 8 H1N1 SWL segments

22 HA map comparing one human isolate vs. one swine isolate Two isolates from the potential H1N1 SWL precursor area: OFL_ISL_47524 OFL_ISL_39793 OFL_ISL_39793 A/Saskatchewan/5131/2009 OFL_ISL_47524 A/swine/Iowa/H03LS4/2003

23 NA and MP maps for the 2 isolates OFL_ISL_47524 OFL_ISL_47524 OFL_ISL_39793 OFL_ISL_39793

24 NP and NS maps for the 2 isolates OFL_ISL_47524 OFL_ISL_47524 OFL_ISL_39793 OFL_ISL_39793

25 PA and PB1 maps for the 2 isolates OFL_ISL_47524 OFL_ISL_39793 OFL_ISL_47524 OFL_ISL_39793

26 PB2 map for the 2 isolates OFL_ISL_47524 OFL_ISL_39793

27 Difference in segment composition HA,NA,MP NA,MP Differences from H1N1 SWL for the 3 human isolates: HA, NA, MP Differences from H1N1 SWL for swine isolates: NA, MP Differences between the 3 human and swine isolates: HA, NA

28 Zoonosis there was known