A rapid visualization pipeline for the 2009 A/H1N1 influenza pandemic

Donovan Parks Norm MacDonald Rob Beiko

• A little biology

• Motivation

• Data acquisition pipeline

• GenGIS: a genomic GIS framework

• Examples

Outline

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Photo obtained from commons.wikimedia.org

H1N1 Biology

2/10

MNPN … IDK

Modified photo from commons.wikimedia.org

Motivation

3/10

• Move from reactive to preventive health strategy

• Increased sampling requires automated tools

Pandemic Year Deaths worldwide (est.)

Fatality rate

Spanish flu 1918-19 20 to 100 million > 2.5%

Asian flu 1956-58 2 million < 0.1%Hong Kong flu 1968-69 1 million < 0.1%

Seasonal flu Every year 0.25-0.5 million < 0.1%

Pipeline Overview

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GeoNamesData Acquisition

Pipeline

Phylogenetic Trees

Sequence Metadata

InteractiveExploration

GenGIS

NCBIInfluenza

SeqMonitor

Data Acquisition Pipeline

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http://ws.geonames.org/search?q=nova scotia

NCBI Records

GeoNames

...<name>Nova Scotia</name><lat>45.000150425</lat><lng>-62.998652994</lng>...

XML File

NCBIInfluenza

Data AcquisitionPipeline

Local Database

MUSCLE RAxML

SeqMonitor

SeqMonitor

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http://ratite.cs.dal.ca/SeqMonitor/

GenGIS: A Genomic GIS Framework

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Global Genetic Diversity of NA

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NA Polymorphism

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October 19, 2009

Conclusions

• Global, continuous sequencing of infectious diseases would allows us to implement preventive health strategies.

• Automated tools will be necessary to provide analyses to inform such policies.

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Further Information

• SeqMonitor: http://ratite.cs.dal.ca/SeqMonitor– MacDonald, N. J., Parks, D. H., and Beiko, R. G. SeqMonitor: Influenza

Analysis Pipeline and Visualization. PLoS Currents: Influenza. 23 September 2009: RRN1040.

• GenGIS: http://kiwi.cs.dal.ca/GenGIS– Parks, D. H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J.,

Brooks, S., and Beiko, R. G. GenGIS: A geospatial information system for genomic data. Genome Res. July 27, 2009.

– Parks, D. H., MacDonald, N. J., and Beiko, R. G. Tracking the evolution and geographic spread of influenza A. PLoS Currents: Influenza. 21 August 2009: RRN1014.