Hostname: page-component-78c5997874-m6dg7 Total loading time: 0 Render date: 2024-11-13T05:03:25.749Z Has data issue: false hasContentIssue false
  • English
  • Français

Genome informatics of influenza A: from data sharing to shared analytical capabilities

Published online by Cambridge University Press:  01 July 2010

Daniel A. Janies ,
Igor O. Voronkin ,
Manirupa Das ,
Jori Hardman ,
Travis W. Treseder  and
Jonathon Studer
Daniel A. Janies*
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
Igor O. Voronkin
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
Manirupa Das
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
Jori Hardman
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
Travis W. Treseder
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
Jonathon Studer
Affiliation:
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
*
*Corresponding author. E-mail: Daniel.Janies@osumc.edu
Get access Rights & Permissions [Opens in a new window]

Abstract

Emerging infectious diseases are critical issues of public health and the economic and social stability of nations. As demonstrated by the international response to the severe acute respiratory syndrome (SARS) and influenza A, rapid genomic sequencing is a crucial tool to understand diseases that occur at the interface of human and animal populations. However, our ability to make sense of sequence data lags behind our ability to acquire the data. The potential of sequence data on pathogens is not fully realized until raw data are translated into public health intelligence. Sequencing technologies have become highly mechanized. If the political will for data sharing remains strong, the frontier for progress in emerging infectious diseases will be in analysis of sequence data and translation of results into better public health science and policy. For example, applying analytical tools such as Supramap (http://supramap.osu.edu) to genomic data for pathogens, public health scientists can track specific mutations in pathogens that confer the ability to infect humans or resist drugs. The results produced by the Supramap application are compelling visualizations of pathogen lineages and features mapped into geographic information systems that can be used to test hypotheses and to follow the spread of diseases across geography and hosts and communicate the results to a wide audience.

Keywords

genomicsinformaticspathogensphylogeneticsdata sharingGISAIDGenBankSupramapinfluenza Aepidemiologyevolutionpublic health
Type
Review Article
Information
Animal Health Research Reviews , Volume 11 , Issue 1: Influenza in Animals , June 2010 , pp. 73 - 79
Copyright
Copyright © Cambridge University Press 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Asian Development Bank (ADB) (2003). http://www.adb.org/Documents/Books/ADO/2003/update/sars.pdfGoogle Scholar
Alliance for Taxpayer Access (2006). Worldwide momentum for public access to publicly funded research. Available online at http://www.taxpayeraccess.org/issues/access/access_resources/worldwide-momentum-for-public-access-to-publ.shtmlGoogle Scholar
Bao, Y, Bolotov, P, Dernovoy, D, Kiryutin, B, Zaslavsky, L, Tatusova, T, Ostell, J and Lipman, D (2008). The Influenza Virus Resource at the National Center for Biotechnology Information. Journal of Virology 82: 596–601.CrossRefGoogle ScholarPubMed
Barr, C (2009). Bank bailout could cost $4 trillion. Available online at http://money.cnn.com/2009/01/27/news/bigger.bailout.fortune/Google Scholar
Bogner, P, Capua, I, Lipman, J, Cox, NJ, Lipmans, DJ et al. (2006). A global initiative on sharing avian flu data. Nature 442: 981.CrossRefGoogle Scholar
Brown, D (2006). Bird flu fears ignite debate on scientists' sharing of data. Available online at http://www.washingtonpost.com/wp-dyn/content/article/2006/05/24/AR2006052402293.htmlGoogle Scholar
Brownstein, J, Freifeld, C, Reis, B and Mandl, K (2008). Surveillance sans frontières: internet-based emerging infectious disease intelligence and the HealthMap project. PLoS Medicine 5: e151. doi:10.1371/journal.pmed.0050151.CrossRefGoogle ScholarPubMed
Brunak, S, Danchin, A, Hattori, M, Nakamura, H, Shinozaki, K, Matise, T and Preuss, D (2002). Nucleotide sequence database policies. Science 298: 1333.CrossRefGoogle ScholarPubMed
Butler, D (2008). Politically correct names given to flu viruses. Available online at www.nature.com/uidfinder/10.1038/452923aCrossRefGoogle Scholar
Butler, D (2009a). Flu database rocked by legal row. Nature 460: 786–787.CrossRefGoogle ScholarPubMed
Butler, D (2009b). Flu database row escalates. Available online at http://blogs.nature.com/news/thegreatbeyond/2009/09/flu_database_row_escalates.htmlGoogle Scholar
Canadian Broadcasting Corporation (CRC). (2003). The Economic Impact of SARS. Available online at www.cbc.ca/news/background/sars/economicimpact.htmGoogle Scholar
Chen, H, Smith, G, Li, K, Wang, J and Fan, X (2006). Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. Proceedings of the National Academy of Sciences, USA 103: 2845–2850.CrossRefGoogle ScholarPubMed
Federal Ministry of Food, Agriculture and Consumer Protection, Germany (2009). http://www.bmelv.de/cln_102/SharedDocs/Pressemitteilungen/2009/249-Ai-Influenza-Datenbank%20Bonn.htmlGoogle Scholar
FlorCruz, J (2003). China censors CNN SARS report. Available online at h http://www.cnn.com/2003/WORLD/asiapcf/east/05/14/sars.censor/Google Scholar
Garrett, L and Fidler, D (2007). Sharing H5N1 viruses to stop a global influenza pandemic. Public Library of Science, Medicine 4: e330. doi:10.1371/journal.pmed.0040330.Google ScholarPubMed
Garten, R, Davis, T, Russell, C, Shu, B, Lindstrom, S, Balish, A, Sessions, WM, Xu, X, Skepner, E, Deyde, V, Okomo-Adhiambo, M, Gubareva, L, Barnes, J, Smith, CB, Emery, SL, Hillman, MJ, Rivailler, P, Smagala, J, de Graaf, M, Burke, DF, Fouchier, RAM, Pappas, C, Alpuche-Aranda, CM, López-Gatell, H, Olivera, H, López, I, Myers, CA, Faix, D, Blair, PJ, Yu, C, Keene, KM, JrDotson, PD, Boxrud, D, Sambol, AR, Abid, SH, St. George, K, Bannerman, T, Moore, AL, Stringer, DJ, Blevins, P, Demmler-Harrison, GJ, Ginsberg, M, Kriner, P, Waterman, S, Smole, S, Guevara, HF, Belongia, EA, Clark, PA, Beatrice, ST, Donis, R, Katz, J, Finelli, L, Bridges, CB, Shaw, M, Jernigan, DB, Uyeki, DM, Smith, DJ, Klimov, AI and Cox, NJ (2009). Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197–201.CrossRefGoogle ScholarPubMed
Gee, H (2000). Homegrown computer roots out phylogenetic networks. Nature. http://www.nature.com/nature/journal/v404/n6775/pdf/404214b0.pdfGoogle ScholarPubMed
Gerberding, J (2005). Pandemic planning and preparedness. Hearing of the108th United States Congress Committee on Energy and Commerce.Google Scholar
GISAID (2008). GISAID EpiFlu Database Access Agreement. http://tinyurl.com/gisaidGoogle Scholar
Hill, A, Guralnick, R, Wilson, M, Habib, F and Janies, D (2009). Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. Infection, Genetics, and Evolution 9: 169–178.CrossRefGoogle ScholarPubMed
Hovmöller, R, Alexandrov, B, Hardman, J and Janies, D (2010). Tracking the geographic spread of avian influenza (H5N1) with multiple phylogenetic trees. Cladistics 26: 1–13.CrossRefGoogle ScholarPubMed
Janies, D, Hill, A, Guralnick, R, Habib, F, Waltari, E and Wheeler, WC (2007). Genomic analysis and geographic visualization of the spread of avian influenza (H5N1). Systematic Biology 56: 321–329.CrossRefGoogle ScholarPubMed
Janies, D, Habib, F, Alexandrov, B, Hill, A, Pol, D (2008). Evolution of genomes, host shifts, and geographic spread of SARS-CoV and related coronaviruses. Cladistics 24: 111–130.CrossRefGoogle ScholarPubMed
Janies, D, Treseder, T, Alexandrov, B, Habib, F, Chen, J, Ferreira, R, Çatalyürek, U, Varón, A and Wheeler, WC (2010a). The Supramap project: linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics. In press.Google Scholar
Janies, D, Voronkin, I, Studer, J, Hardman, J, Alexandrov, B, Treseder, T and Valson, C (2010b). Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. International Journal of Health Geographics 9: 13.CrossRefGoogle ScholarPubMed
MacDonald, N, Parks, D, Beiko, R (2009). SeqMonitor: influenza analysis pipeline and visualization. PLoS Current Influenza 2009 September 22: RRN1040.Google ScholarPubMed
Macken, C, Lu, H, Goodman, J and Boykin, L (2001). The value of a database in surveillance and vaccine selection. In: Osterhaus, ADME, Cox, N and Hampson, AW (eds) Options for the Control of Influenza IV, Vol. 1219. Amsterdam: Elsevier Science, pp. 103–106.Google Scholar
Nature (2006). Dreams of flu data. Nature 440: 255–256.CrossRefGoogle Scholar
NIH (2003). Data Sharing Policy and Implementation Guidance. Available online at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.htmlGoogle Scholar
NIH (2008). National Institutes of Health Public Access. Available online at http://publicaccess.nih.gov/index.htmGoogle Scholar
Novel Swine-Origin Influenza A H1N1 Virus Investigation Team (2009). Emergence of a novel swine-origin influenza A (H1N1) virus in humans. New England Journal of Medicine 360: 2605–2615.CrossRefGoogle Scholar
Pan, P (2009). In Ukraine, H1N1 pandemic sets off panic and politicking. Available online at http://www.washingtonpost.com/wp-dyn/content/article/2009/11/20/AR2009112004023_pf.htmlGoogle Scholar
Presanis, A, De Angelis, D, The New York City Swine Flu Investigation Team, Hagy, A, Reed, C, Riley, S, Cooper, B, Finelli, L, Biedrzycki, P and Lipsitch, M (2009). The severity of pandemic H1N1 Influenza in the United States from April to July 2009: A Bayesian Analysis. PLoS Medicine 6: e1000207. doi:10.1371/journal.pmed.1000207CrossRefGoogle ScholarPubMed
Salzberg, S, Kingsford, C, Cattoli, G, Spiro, D, Janies, D, Aly, M, Brown, I, Couacy-Hymann, E, De Mia, G, Dung, D, Guercio, A, Joannis, T, Ali, A, Osmani, A, Padalino, I, Saad, M, Savić, V, Sengamalay, N, Yingst, S, Zaborsky, J, Zorman-Rojs, O, Ghedin, E, Capua, I (2007). Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases 13: 5.CrossRefGoogle ScholarPubMed
Stevenson, M (2009). Mexico swine flu deaths spur global epidemic fears. Available online at http://www.guardian.co.uk/world/feedarticle/8473318Google Scholar
Valente, M (2009). ARGENTINA: Experts Put H1N1 Flu Outbreak in Perspective. Available online at http://www.ipsnews.net/news.asp?idnews=47388Google Scholar
Varón, A, Vinh, L, Wheeler, WC (2009). POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26: 72–85.CrossRefGoogle ScholarPubMed
WHO (2009a). Cumulative number of confirmed human cases of avian influenza A (H5N1) reported to WHO. Available online at http://www.who.int/csr/disease/avian_influenza/country/cases_table_2010_03_16/en/index.htmlGoogle Scholar
WHO (2009b). Viral gene sequences to assist update diagnostics for swine influenza A (H1N1). 25 April 2009. Available online at http://www.who.int/csr/disease/swineflu/Gene_sequences_20090425.pdfGoogle Scholar
WHO (2010). Pandemic (H1N1) 2009 – update 92. Available online at http://www.who.int/csr/don/2010_03_19/en/index.htmlGoogle Scholar
Wilson, K, Tigerstrom, B, and McDougall, C (2008). Protecting global health security through the international health regulations: requirements and challenges. Canadian Medical Association Journal 179: 44–48.CrossRefGoogle ScholarPubMed
Zamiska, N (2006). How academic flap hurt world effort on Chinese bird flu. The Wall Street Journal, 24 February 2006: A1.Google Scholar
Zwickl, D and Hillis, D (2002). Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51: 588–598.CrossRefGoogle ScholarPubMed