Fast graph approaches to measure influenza transmission across geographically distributed host types

Adrienne Breland, Karen Schlauch, Mehmet Gunes, Frederick C. Harris

    Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

    Abstract

    Recent advances in next generation sequencing are provid- ing a number of large whole-genome sequence datasets stemming from globally distributed disease occurrences. This offers an unprecedented opportunity for epidemiological studies and the development of computationally efficient, robust tools for such studies. Here we present an analytic approach combining several existing tools that enables a quick, effective, and robust epidemiological analysis of large wholegenome datasets. In this report, our dataset contains over 4; 200 globally sampled Inuenza A virus isolates from multiple host type, subtypes, and years. These sequences are compared using an alignment-free method that runs in linear time. This enables us to generate a disease transmission network where sequences serve as nodes, and high-degree sequence similarity as edges. Mixing patterns are then used to examine statistical probabilities of edge formation among different host types from different global regions and from different localities within Southeast Asia. Our results reect notable amounts of inter-host and inter-regional transmission of Inuenza A viru

    Original languageEnglish
    Title of host publication2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010
    Pages594-601
    Number of pages8
    DOIs
    StatePublished - 2010
    Event2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010 - Niagara Falls, NY, United States
    Duration: 2 Aug 20104 Aug 2010

    Publication series

    Name2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010

    Conference

    Conference2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010
    Country/TerritoryUnited States
    CityNiagara Falls, NY
    Period2/08/104/08/10

    Keywords

    • Measurement

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