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Janies DA, Treseder T, Alexandrov B, Habib F, Chen JJ, Ferreira R, Çatalyürek Ü, Varón A, Wheeler WC. The Supramap project: linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics 2011; 27:61-66. [PMID: 32313364 PMCID: PMC7162175 DOI: 10.1111/j.1096-0031.2010.00314.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2010] [Indexed: 11/27/2022] Open
Abstract
Novel pathogens have the potential to become critical issues of national security, public health and economic welfare. As demonstrated by the response to Severe Acute Respiratory Syndrome (SARS) and influenza, genomic sequencing has become an important method for diagnosing agents of infectious disease. Despite the value of genomic sequences in characterizing novel pathogens, raw data on their own do not provide the information needed by public health officials and researchers. One must integrate knowledge of the genomes of pathogens with host biology and geography to understand the etiology of epidemics. To these ends, we have created an application called Supramap (http://supramap.osu.edu) to put information on the spread of pathogens and key mutations across time, space and various hosts into a geographic information system (GIS). To build this application, we created a web service for integrated sequence alignment and phylogenetic analysis as well as methods to describe the tree, mutations, and host shifts in Keyhole Markup Language (KML). We apply the application to 239 sequences of the polymerase basic 2 (PB2) gene of recent isolates of avian influenza (H5N1). We map a mutation, glutamic acid to lysine at position 627 in the PB2 protein (E627K), in H5N1 influenza that allows for increased replication of the virus in mammals. We use a statistical test to support the hypothesis of a correlation of E627K mutations with avian-mammalian host shifts but reject the hypothesis that lineages with E627K are moving westward. Data, instructions for use, and visualizations are included as supplemental materials at: http://supramap.osu.edu/sm/supramap/publications. © The Willi Hennig Society 2010.
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Affiliation(s)
- Daniel A Janies
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Travis Treseder
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Boyan Alexandrov
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Farhat Habib
- Indian Institute of Science Education and Research (IISER) Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India
| | - Jennifer J Chen
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Renato Ferreira
- Universidade Federal de Minas Gerais, Departamento de Ciência da Computação, Belo Horizonte, MG, Brazil
| | - Ümit Çatalyürek
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Andrés Varón
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
- Computer Science Department, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
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