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Publications

2017 Publications

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  • Danuta M. Skowronski, Catharine Chambers, Gaston De Serres, Suzana Sabaiduc, Anne-Luise Winter, James A. Dickinson, Jonathan B. Gubbay, Kevin Fonseca, Steven J. Drews, Hugues Charest, Christine Martineau, Mel Krajden, Martin Petric, Nathalie Bastien, Yan Li, Derek J. Smith (2017). Serial Vaccination and the Antigenic Distance Hypothesis: Effects on Influenza Vaccine Effectiveness During A(H3N2) Epidemics in Canada, 2010–2011 to 2014–2015. Journal of Infectious Diseases215(7):1059-1099. doi:10.1093/infdis/jix074

  • Kazuya Nakamura, Masayuki Shirakura, Seiichiro Fujisaki, Noriko Kishida, David F. Burke, Derek J. Smith, Tomoko Kuwahara, Emi Takashita, Ikuyo Takayama, Mina Nakauchi, Mandeep Chadha, Varsha Potdar,  Arvind Bhushan, Bishnu Prasad Upadhyay, Geeta Shakya, Takato Odagiri, Tsutomu Kageyama, Shinji Watanabe (2017). Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015. Influenza and Other Respiratory Viruses, 11(5):399-403. doi:10.1111/irv.12469
  • Mathilde Richard, Sascha Knauf, Philip Lawrence, Alison E. Mather, Vincent J. Munster, Marcel A. Müller, Derek Smith, Thijs Kuiken (2017). Factors determining human-to-human transmissibility of zoonotic pathogens via contact. Current Opinion in Virology, 22:7-12. doi:10.1016/j.coviro.2016.11.004
  • Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters,  Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian Zmasek, Edward B. Klem, Richard H. Scheuermann (2017). Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Research, 45(D1):D466-D474. doi:10.1093/nar/gkw857

2016 Publications

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  • Ana Mosterín Höpping, Judith M.Fonville, Colin A.Russell, Sarah James, Derek J.Smith (2016). Influenza B vaccine lineage selection—An optimized trivalent vaccine. Vaccine, 34(13):1617-1622. doi:10.1016/j.vaccine.2016.01.042
  • Ana Mosterín Höpping, Janet McElhaney, Judith M. Fonville, Douglas C.Powers, Walter E.P. Beyer, Derek J. Smith (2016). The confounded effects of age and exposure history in response to influenza vaccination. Vaccine, 34(4):540-546. doi:10.1016/j.vaccine.2015.11.058
  • Sarah L. James, Stuart D. Blacksell, Pruksa Nawtaisong, Ampai Tanganuchitcharnchai, Derek J. Smith, Nicholas P. J. Day, Daniel H. Paris (2016). Antigenic Relationships among Human Pathogenic Orientia tsutsugamushi Isolates from Thailand. Crump J.A., ed. PLoS Neglected Tropical Diseases, 10(6):e0004723. doi:10.1371/journal.pntd.0004723
  • Chengjun Li, Masato Hatta, David F. Burke, Jihui Ping, Ying Zhang, Makoto Ozawa, Andrew S. Taft, Subash C. Das, Anthony P. Hanson, Jiasheng Song, Masaki Imai, Peter R. Wilker, Tokiko Watanabe, Shinji Watanabe, Mutsumi Ito, Kiyoko Iwatsuki-Horimoto, Colin A. Russell, Sarah L. James, Eugene Skepner, Eileen A. Maher, Gabriele Neumann, Alexander I. Klimov, Anne Kelso, John McCauley, Dayan Wang, Yuelong Shu, Takato Odagiri, Masato Tashiro, Xiyan Xu, David E. Wentworth, Jacqueline M. Katz, Nancy J. Cox, Derek J. Smith & Yoshihiro Kawaoka (2016). Selection of antigenically advanced variants of seasonal influenza viruses. Nature Microbiology, 1(6):16058. doi:10.1038/nmicrobiol.2016.58
  • Nicola S. Lewis, Colin A Russell, Pinky Langat, Tavis K. Anderson, Kathryn Berger, Filip Bielejec, David F. Burke, Gytis Dudas, Judith M. Fonville, Ron A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Philippe Lemey, Tung Nguyen, Bundit Nuansrichy, J.S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 consortium, Richard J Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Simon J. Watson, Ian H. Brown, Amy L. Vincent (2016). The global antigenic diversity of swine influenza A viruseseLife, 5. doi:10.7554/eLife.12217
  • Eefje J. A. Schrauwena, Mathilde Richard, David F. Burke, Guus F. Rimmelzwaana, Sander Herfsta and Ron A. M. Fouchier (2016). Amino Acid Substitutions That Affect Receptor Binding and Stability of the Hemagglutinin of Influenza A/H7N9 Virus. García-Sastre A., ed. Journal of Virology, 90(7):3794-3799. doi:10.1128/JVI.03052-15

2015 Publications

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  • Trevor Bedford, Steven Riley, Ian G. Barr, Shobha Broor, Mandeep Chadha, Nancy J. Cox, Rodney S. Daniels, C. Palani Gunasekaran, Aeron C. Hurt, Anne Kelso, Alexander Klimov, Nicola S. Lewis, Xiyan Li, John W. McCauley, Takato Odagiri, Varsha Potdar, Andrew Rambaut, Yuelong Shu, Eugene Skepner, Derek J. Smith, Marc A. Suchard, Masato Tashiro, Dayan Wang, Xiyan Xu, Philippe Lemey & Colin A. Russell (2015). Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature, 523(7559):217-220. doi:10.1038/nature14460
  • Leah C. Katzelnick, Judith M. Fonville, Gregory D. Gromowski, Jose Bustos Arriaga, Angela Green, Sarah L. James, Louis Lau, Magelda Montoya, Chunling Wang, Laura A. VanBlargan, Colin A. Russell, Hlaing Myat Thu, Theodore C. Pierson, Philippe Buchy, John G. Aaskov, Jorge L. Muñoz-Jordán, Nikos Vasilakis, Robert V. Gibbons, Robert B. Tesh, Albert D.M.E. Osterhaus, Ron A.M. Fouchier, Anna Durbin, Cameron P. Simmons, Edward C. Holmes, Eva Harris, Stephen S. Whitehead, Derek J. Smith (2015). Dengue viruses cluster antigenically but not as discrete serotypes. Science, 349(6254):1338-1343. doi:10.1126/science.aac5017
  • Sheng-Wen Huanga, Ching-Hui Taie, Judith M. Fonville, Chin-Hui Linb, Shih-Min Wanga, Ching-Chung Liua, Ih-Jen Sue, Derek J. Smith and Jen-Ren Wang (2015). Mapping Enterovirus A71 Antigenic Determinants from Viral Evolution. Sandri-Goldin R.M., ed. Journal of Virology, 89(22):11500-11506. doi:10.1128/JVI.02035-15
  • W. E. P. Beyer, J.McElhaney, D. J. Smith, A. S. Monto, J. S. Nguyen-Van-Tam, A. D. M. E. Osterhaus (2015) Reply: Letter to the Editor, Cochrane Rearranged. Vaccine, 33(1):13-14. doi:10.1016/j.vaccine.2014.05.045
  • Björn F. Koel, Ramona Mögling, Salin Chutinimitkula, Pieter L. Fraaij, David F. Burke, Stefan van der Vliet, Emmie de Wit, Theo M. Bestebroer, Guus F. Rimmelzwaan, Albert D. M. E. Osterhaus, Derek J. Smith, Ron A. M. Fouchier and Miranda de Graaf (2015). Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses. García-Sastre A., ed. Journal of Virology, 89(7):3763-3775. doi:10.1128/JVI.02962-14
  • David E. Swayne, David L. Suarez, Erica Spackman, Samadhan Jadhao, Gwenaelle Dauphin, Mia Kim-Torchetti, James McGrane, John Weaver, Peter Daniels, Frank Wong, Paul Selleck, Agus Wiyono, Risa Indriani, Yuni Yupiana, Elly Sawitri Siregar, Teguh Prajitno, Derek Smith and Ron Fouchier (2015). Antibody Titer Has Positive Predictive Value for Vaccine Protection against Challenge with Natural Antigenic-Drift Variants of H5N1 High-Pathogenicity Avian Influenza Viruses from Indonesia. García-Sastre A., ed. Journal of Virology, 89(7):3746-3762. doi:10.1128/JVI.00025-15
  • Benjamin M. Althouse, Samuel V. Scarpino, Lauren Ancel Meyers, John W. Ayers, Marisa Bargsten, Joan Baumbach, John S. Brownstein, Lauren Castro, Hannah Clapham, Derek A. T. Cummings, Sara Del Valle, Stephen Eubank, Geoffrey Fairchild, Lyn Finelli, Nicholas Generous, Dylan George, David R Harper, Laurent Hébert-Dufresne, Michael A. Johansson, Kevin Konty, Marc Lipsitch, Gabriel Milinovich, Joseph D. Miller, Elaine O. Nsoesie, Donald R. Olson, Michael Paul, Philip M Polgreen, Reid Priedhorsky, Jonathan M. Read, Isabel Rodríguez-Barraquer, Derek J. Smith, Christian Stefansen, David L. Swerdlow, Deborah Thompson, Alessandro Vespignani and Amy Wesolowski (2015). Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Science, 4(1):17. doi:10.1140/epjds/s13688-015-0054-0
  •  Gavin J. D. Smith, Ruben O. Donis, World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5 Evolution Working Group (2015). Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014. Influenza and Other Respiratory Viruses, 9(5):271-276. doi:10.1111/irv.12324

2014 Publications

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  • Lewis NS, Anderson TK, Kitikoon P, Skepner E, Burke DF, Vincent AL. (2014). Substitutions near the Hemagglutinin Receptor-Binding Site Determine the Antigenic Evolution of Influenza A H3N2 Viruses in U.S. Swine. Journal of Virology, 88(9):4752-4763. doi:10.1128/JVI.03805-13
  • Ke C, Lu J, Wu J, et al. (2014) Circulation of Reassortant Influenza A(H7N9) Viruses in Poultry and Humans, Guangdong Province, China, 2013. Emerging Infectious Diseases, 20(12):2034-2040. doi:10.3201/eid2012.140765
  • Lemey P, Rambaut A, Bedford T, et al. (2014). Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2. Ferguson NM, ed. PLOS Pathogens10(2):e1003932. doi:10.1371/journal.ppat.1003932
  • van den Hoogen BG, van Boheemen S, de Rijck J, et al. (2014). Excessive production and extreme editing of human metapneumovirus defective interfering RNA is associated with type I IFN induction. Journal of General Virology95(8):1625-1633. doi:10.1099/vir.0.066100-0
  • Ludi AB, Horton DL, Li Y, et al. (2014). Antigenic variation of foot-and-mouth disease virus serotype A. Journal of General Virology95(2):384-392. doi:10.1099/vir.0.057521-0
  • Westgeest KB, Russell CA, Lin X, et al. (2014). Genomewide Analysis of Reassortment and Evolution of Human Influenza A(H3N2) Viruses Circulating between 1968 and 2011. Journal of Virology88(5):2844-2857. doi:10.1128/JVI.02163-13
  • Bedford T, Suchard MA, Lemey P, et al. (2014). Integrating influenza antigenic dynamics with molecular evolution. eLife3. doi:10.7554/eLife.01914
  • Koel BF, van der Vliet S, Burke DF, et al. (2014). Antigenic Variation of Clade 2.1 H5N1 Virus Is Determined by a Few Amino Acid Substitutions Immediately Adjacent to the Receptor Binding Site. mBio5(3):e01070-14-e01070-14. doi:10.1128/mBio.01070-14
  • Watanabe T, Zhong G, Russell CA, et al. (2014). Circulating Avian Influenza Viruses Closely Related to the 1918 Virus Have Pandemic Potential. Cell Host & Microbe15(6):692-705. doi:10.1016/j.chom.2014.05.006
  • Barr IG, Russell C, Besselaar TG, et al. (2014). WHO recommendations for the viruses used in the 2013–2014 Northern Hemisphere influenza vaccine: Epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from October 2012 to January 2013. Vaccine, 32(37):4713-4725. doi:10.1016/j.vaccine.2014.02.014
  • Burke DF, Smith DJ. (2014). A Recommended Numbering Scheme for Influenza A HA Subtypes. Digard P, ed. PLoS One9(11):e112302. doi:10.1371/journal.pone.0112302
  • Fonville JM, Wilks SH, James SL, et al. (2014). Antibody landscapes after influenza virus infection or vaccination. Science346(6212):996-1000. doi:10.1126/science.1256427
  • Schultz-Cherry S, Webby RJ, Webster RG, et al. (2014). Influenza Gain-of-Function Experiments: Their Role in Vaccine Virus Recommendation and Pandemic Preparedness. mBio5(6):e02430-14. doi:10.1128/mBio.02430-14
  • Gilbert M, Koel BF, Bestebroer TM, Lewis NS, Smith DJ, Fouchier RAM. (2014). Serological Evidence for Non-Lethal Exposures of Mongolian Wild Birds to Highly Pathogenic Avian Influenza H5N1 Virus. Eugenin EA, ed. PLoS One, 9(12):e113569. doi:10.1371/journal.pone.0113569

2013 Publications

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  • Fonville J.M., Burke D.F., Lewis N.S., Katzelnick L.C., Russell C.A. (2013) Quantifying the Fitness Advantage of Polymerase Substitutions in Influenza A/H7N9 Viruses during Adaptation to Humans. Digard P, ed. PLoS One. 2013;8(9):e76047. doi:10.1371/journal.pone.0076047
  • Lewis N.S., Javakhishvili Z., Russell C.A., et al. (2013) Avian Influenza Virus Surveillance in Wild Birds in Georgia: 2009–2011. Tripp R, ed. PLoS One. 2013;8(3):e58534. doi:10.1371/journal.pone.0058534
  • Koel B.F., Burke D.F., Bestebroer T.M., et al. (2013) Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. Science. 342(6161):976-979. doi:10.1126/science.1244730
  • Fouchier R.A.M., Kawaoka Y., Cardona C., et al. (2013) Gain-of-Function Experiments on H7N9. Science341(6146):612-613. doi:10.1126/science.1243325
  • Richard M., Schrauwen E.J.A., de Graaf M., et al. (2013) Limited airborne transmission of H7N9 influenza A virus between ferrets. Nature. 501(7468):560-563. doi:10.1038/nature12476
  • Beyer W.E.P., McElhaney J., Smith D.J., Monto A.S., Nguyen-Van-Tam J.S., Osterhaus A.D.M.E. (2013) Cochrane re-arranged: Support for policies to vaccinate elderly people against influenza. Vaccine. 31(50):6030-6033. doi:10.1016/j.vaccine.2013.09.063
  • Fonville J.M., Carter C.L., Pizarro L., et al. (2013) Hyperspectral Visualization of Mass Spectrometry Imaging Data. Analytical Chemistry. 85(3):1415-1423. doi:10.1021/ac302330a
  • WHO Writing Group. (2013) Strengthening the influenza vaccine virus selection and development process: Outcome of the 2nd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at the Centre International de Conférences (CICG) Geneva, Switzerland, 7 to 9 December 2011. Vaccine. 31(32):3209-3221. doi:10.1016/j.vaccine.2013.05.049

2012 Publications

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  • Herfst S., Schrauwen E.J.A., Linster M., et al. (2012) Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets. Science. 336(6088):1534-1541. doi:10.1126/science.1213362
  • Westgeest K.B., de Graaf M., Fourment M., et al. (2012) Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution. Journal of General Virology. 93(9):1996-2007. doi:10.1099/vir.0.043059-0
  • Klimov A.I., Garten R., Russell C., et al. (2012) WHO recommendations for the viruses to be used in the 2012 Southern Hemisphere Influenza Vaccine: Epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from February to September 2011. Vaccine. 30(45):6461-6471. doi:10.1016/j.vaccine.2012.07.089
  • Russell C.A., Fonville J.M., Brown A.E.X., et al. (2012) The Potential for Respiratory Droplet-Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host. Science. 336(6088):1541-1547. doi:10.1126/science.1222526
  • Wilks S., de Graaf M., Smith D.J., Burke D.F. (2012) A review of influenza haemagglutinin receptor binding as it relates to pandemic properties. Vaccine. 30(29):4369-4376. doi:10.1016/j.vaccine.2012.02.076
  • Fonville J.M., Carter C., Cloarec O., et al. (2012) Robust Data Processing and Normalization Strategy for MALDI Mass Spectrometric Imaging. Analytical Chemistry. 84(3):1310-1319. doi:10.1021/ac201767g
  • Fonville J.M., Swart M., Vokáčová Z., et al. (2012) Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. Chemistry - A European Journal. 18(39):12372-12387. doi:10.1002/chem.201103593
  • Maher A.D., Fonville J.M., Coen M., Lindon J.C., Rae C.D., Nicholson J.K. (2012) Statistical Total Correlation Spectroscopy Scaling for Enhancement of Metabolic Information Recovery in Biological NMR Spectra. Analytical Chemistry. 84(2):1083-1091. doi:10.1021/ac202720f
  • Ferguson L.S., Wulfert F., Wolstenholme R., et al. (2012) Direct detection of peptides and small proteins in fingermarks and determination of sex by MALDI mass spectrometry profiling. The Analyst. 137(20):4686-4692. doi:10.1039/c2an36074h

2011 and Earlier Publications

  • Sandbulte MR, Westgeest KB, Gao J, Xu XY, Klimov AI, Russell CA, Burke DF, Smith DJ, Fouchier RAM, Eichelberger MC, Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses, P Natl Acad Sci USA 108(51):20748-20753 20 Dec 2011
  • Lewis NS, Daly JM, Russell CA, Horton DL, Skepner E, Bryant NA, Burke DF, Rash AS, Wood JL, Chambers TM, Fouchier RA, Mumford JA, Elton DM, Smith DJ. The antigenic and genetic evolution of equine influenza A(H3N8) virus from 1968-2007.       J Virol. 2011 Sep 21.
  • Mansfield KL, Horton DL, Johnson N, Li L, Barrett ADT, Smith DJ, Galbraith SE, Solomon T, Fooks AR; Flavivirus-induced antibody cross-reactivity, J Gen Virol. 2011 Dec; 92:2821-2829.
  • Abbas MA, Spackman E, Fouchier R, Smith D, Ahmed Z, Siddique N, Sarmento L, Naeem K, McKinley ET, Hameed A, Rehmani S, Swayne DE. H7 avian influenza virus vaccines protect chickens against challenge with antigenically diverse isolates. Vaccine. 2011 Jul 29.
  • Bodewes R, de Mutsert G, van der Klis FR, Ventresca M, Wilks S, Smith DJ, Koopmans M, Fouchier RA, Osterhaus AD, Rimmelzwaan GF. Prevalence of antibodies against seasonal influenza A and B viruses in children in Netherlands. Clinical Vaccine Immunology. 2011 Mar; 18(3):469-76. Epub 2011 Jan 5.
  • Lorusso A, Vincent AL, Harland ML, Alt D, Bayles DO, Swenson SL, Gramer MR, Russell CA, Smith DJ, Lager KM, Lewis NS. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008. J Gen Virol. 2011 Apr; 92(Pt 4):919-30. Epub 2010 Dec 22.

  • WHO/OIE/FAO H5N1 Evolution Working Group. Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses. Influenza Other Respi Viruses. 2009 Mar; 3(2):59-62.

  • Huang, SW; Kiang, D; Smith DJ; Wang, JR. Evolution of re-emergent virus and its impact on enterovirus 71 epidemics. Exp Biol Med 2011 Aug 1; 236(8):899-908.

  • Lorusso A, Vincent AL, Harland ML, Alt D, Bayles DO, Swenson SL, Gramer MR, Russell CA, Smith DJ,  Lager KM, Lewis NS. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008 J Gen Virol. 2011 April; 92(Pt 4): 919–930. doi: 10.1099/vir.0.027557-0.

  • Chutinimitkul S, Herfst S, Steel J, Lowen AC, Ye J, van Riel D, Schrauwen EJA, Bestebroer TM,  Koel B, Burke DF, Sutherland- Cash KH, Whittleston CS, Russell CA, Wales DJ, Smith DJ, Jonges M, Meijer A, Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus ADME, García-Sastre A, Perez DR, Fouchier RAM. Virulence-Associated Substitution D222G in the Hemagglutinin of 2009 Pandemic Influenza A(H1N1) Virus Affects Receptor Binding. J Virol. 2010 November; 84(22): 11802–11813.
     
  • Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr, McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S. Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS Medecine, 2010, Jun 1; 7(6):e1000275.

  • Fouchier RAM and DJ Smith. Use of antigenic cartography in vaccine seed strain selection. Avian diseases, 2010 Mar; 54(1 supp): 222-3.

  • Barr IG, J McCauley, N Cox, R Daniels, OG Engelhardt, K Fukuda, G Grohmann, A Hay, A Kelso, A Klimov, T Odagiri, D Smith, C Russell, M Tashiro, R Webby, J Wood, Z Ye, W Zhang. 2010 Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season.  Vaccine, 2010 Feb 3; 28(5):1156-67. Epub 2009 Dec 9.

  • Park AW, JM Daly, NS Lewis, DJ Smith, DLN Wood, BT Grenfell. Quantifying the impact of immune escape on transmission dynamics of influenza, Science.2009; 326(5953):726-8.

  • Voordouw, ACG , WEP Beyer, DJ Smith, MCJM Sturkenboom , BHCh Stricker, Evaluation of serological trials submitted for annual relicensure of influenza vaccines to regulatory authorities between 1992-2002, Vaccine. 28(2):392-7. Epub 2009 Oct 28.

  • Huang, S-W, Y-W Hsu, D Kiang, H-P Tsai, P-H Kuo, K-H Lin, S-M Wang, C-C Liu, DJ Smith, I-J Su, J-R Wang, Reemerging of Enterovirus 71 in 2008 in Taiwan: Dynamics of Genetic and Antigenic Evolution from 1998 to 2008, J Clin Microbiol. 47(11):3653-62. Epub 2009 Sep 23.

  • Garten RJ, Davis CT, Russell CA, 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 RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, 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 TM, Smith DJ, Klimov AI, Cox NJ (2009). Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans, Science, 2009 Jul 10; 325(5937):197-201. Epub 2009 May 22doi 10.1126/science.1176225.

  • Donis RO, GJD Smith, ML Perdue, IH Brown, H Chen, RAM Fouchier, Y Kawaoka, J Mackenzie, Y Shu, I Capua, NJ Cox, T Davis, R Garten, Y Guan, E Mumford, CA Russell, C Smith, D Smith, D Vijaykrishna. 2008. Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses. WHO/OIE/FAO H5N1 Evolution Working Group. Influenza Other Respi Viruses. 2009 Mar;3(2):59-62.

  • Russell CA, Jones TC, Barrd IG, Cox NJ, Gartene RJ, Gregoryf V, Gust ID, Hampsond AW, Hay AJ, Hurtd AC, de Jong JC Kelso A , Klimove AI, Kageyama T, Komadinad T, Lapedes AS,. Lin YP, Mosterin A,  Obuchig M, Odagirig T, Osterhaus A. D.M.E., Rimmelzwaan GF,  Shawe MW, Skepner E, Stohr K, Tashiro M,. Fouchier RAM, Smith DJ, Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses Vaccine vol. 26, no 4 (75 p.) 8375, 2008.

  • Russell CA, TC Jones, IG Barr, NJ Cox, R Garten, V Gregory, I Gust, AW Hampson, AJ Hay, AC Hurt, JC de Jong, AI Klimov, T Kageyama, N Komadina, AS Lapedes, YP Lin, A Mosterin, M Obuchi, T Odagiri, ADME Osterhaus, GF Rimmelzwaan, MW Shaw, E Skepner, K Stohr, M Tashiro, RAM Fouchier, DJ Smith. 2008. The global circulation of seasonal influenza A(H3N2) viruses. Science, Vol. 320, No. 5874pp. 340–346, 2008.

  • Donis RO, GJD Smith, ML Perdue, IH Brown, H Chen, RAM Fouchier, Y Kawaoka, J Mackenzie, Y Shu, I Capua, NJ Cox, T Davis, R Garten, Y Guan, E Mumford, CA Russell, C Smith, D Smith, D Vijaykrishna. 2008. Towards a unified nomenclature system for highly pathogenic avian influenza H5N1 viruses.  Emerging Infectious Diseases, Volume 14, 2008.

  • Smith DJ, JC de Jong, AS Lapedes, TC Jones, CA Russell, TM Bestebroer, GF Rimmelzwaan, ADME Osterhaus, RAM Fouchier.  Antigenic relationships among influenza A(H3N2) viruses. Novartis Foundation Symposium Proceedings, 2008.

  • Berkhoff EG, Geelhoed–Mieras MM, Jonges M, Smith DJ, Fouchier RA, Osterhaus AD, Rimmelzwaan GF. An amino acid substitution in the influenza A virus hemagglutinin associated with escape from recognition by human virus–specific CD4(+) T–cells. Virus Res, 126(1–2):282–7, 2007.

  • J.C. de Jong, D.J. Smith, A.S. Lapedes, I. Donatelli, L. Campitelli, G. Barigazzi, K. Van Reeth, T.C. Jones, G.F. Rimmelzwaan, A.D.M.E. Osterhaus, and R.A.M. Fouchier. Antigenic and genetic evolution of swine influenza A H3N2 viruses in Europe. Journal of Virology, Vol. 81, p. 4315–4322, 2007.

  • J. Philippa, C. Baas, W. Beyer, T. Bestebroer, R.A.M. Fouchier, D.J. Smith, W. Schaftenaar, A.D.M.E. Osterhaus. Vaccination against highly pathogenic avian influenza h5n1 virus in zoos using an adjuvanted inactivated H5n2 vaccine. Vaccine, 25(19):3800–8, 2007.

  • D. J. Smith. Predictability and preparedness in influenza control. Science Vol 312, 392–394, 2006.

  • D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, T. C. Jones, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Influenza virus surveillance: antigenic cartography and the influenza archipelago. Infectieziekten Bulletin, Vol 9, 330–335, 2005.

  • G.F. Rimmelzwaan, E.G.M. Berkhoff, N. Nieuwkoop, D.J. Smith, R.A.M. Fouchier and A.D.M.E. Osterhaus. Full restoration of viral fitness by multiple compensatory co–mutations in the nucleoprotein of influenza A virus cytotoxic T–lymphocyte escape mutants. Journal of General Virology, Vol 86, 1801–1805, 2005.

  • R.A.M. Fouchier, V. Munster, A. Wallensten, T.M. Bestebroer, S. Herfst, D.J. Smith, G.F. Rimmelzwwaan, B.Olsen, A.D.M.E. Osterhaus. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black–headed gulls. Journal of Virology, Vol 79, 2814–2822, 2005.

  • D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, T. C. Jones, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Mutations, drift, and the influenza archipelago. Discovery Medicine, Vol 4, 371–377, 2004.

  • A.C.G. Voordouw, M.C.J.M. Sturkenboom, J.P. Dieleman, T. Stijnen, D.J. Smith, J. van der Lei, B.H.C. Stricker. Annual revaccination against influenza effectively reduces mortality risk in community dwelling elderly. (pdf at JAMA). Journal of the American Medical Association, Vol 292, 2089–2095, 2004.

  • D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Mapping the Antigenic and Genetic Evolution of Influenza Virus. Science Vol 305, 371–376, 2004.

  • A.C.M.Boon, G. de Mutsert, D. van Baarle, D.J. Smith, A.S. Lapedes, R.A.M. Fouchier, K. Sintnicolaas, A.D.M.E. Osterhaus, and G.F. Rimmelzwaan. Recognition of homo– and heterosubtypic variants of influenza A viruses by human CD8+ T lymphocytes Journal of Immunology, Vol 172, 2453–2460, 2004.

  • G.F. Rimmelzwaan, A.C.M.Boon, G. de Mutsert, R.A.M. Fouchier, D. van Baarle, D.J. Smith, A.S. Lapedes, K. Sintnicolaas, A.D.M.E. Osterhaus. Recognition of influenza virus epitope variants by human CTL. In: Options for the control of influenza virus V, eds., Excerpta Medica, International Congress Series 1263, Amsterdam, 145, 2004.

  • D. J. Smith Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection  Vaccine, Vol 21, 1758–1761, 2003.

  • D. J. Smith, A. S. Lapedes, S. Forrest, J. C. deJong, A. D. M. E. Osterhaus, R. A. M. Fouchier, N. J. Cox, and A. S. Perelson, Modeling the effects of updating the influenza vaccine on the efficacy of repeated vaccination (pdf, postscript), In: Options for the control of influenza virus IV, eds. A.D.M.E. Osterhaus, N. Cox, and A. Hampson, Excerpta Medica, International Congress Series 1219, Amsterdam, 655–660, 2001.

  • D. J. Smith, S. Forrest, D. H. Ackley, and A. S. Perelson, Variable Efficacy of Repeated Annual Influenza Vaccination, Proceedings of the National Academy of Sciences, Vol 96, 14001–14006, 1999.

  • D. J. Smith, S. Forrest, and A. S. Perelson, Using lazy evaluation to simulate realistic–size repertoires in models of the immune system, Bulletin of Mathematical Biology, Vol 60, 647–658, 1998.

  • D. J. Smith, S. Forrest, and A. S. Perelson, Immunological memory is associative, in Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin, 105–112, 1998 (and Intnl. Conf. on Multiagent Systems, Workshop notes, 62–70, Kyoto, Japan, 1996).

  • D. J. Smith, The Cross–Reactive Immune Response: Analysis, Modeling, and Application to Vaccine Design, PhD Thesis, University of New Mexico, NM, 1997

  • D. J. Smith, S. Forrest, R. R. Hightower, and A. S. Perelson, Deriving Shape Space Parameters from Immunological Data, Journal of Theoretical Biology, Vol. 189, No. 2, 141–150, Nov. 1997.

  • D. J. Smith, S. Forrest, D. H. Ackley, and A. S. Perelson, Modeling the effects of prior infection on vaccine efficacy, in Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin, 144–152, 1998 (and Proc. IEEE Intnl. Conf. on Systems, Man, and Cybernetics, Orlando, Florida, 1997).

  • P. H. Stanford and D. J. Smith, The Multidimensional Scatter Code: A Data Fusion Technique with Exponential Capacity, in Proc. Intl. Conf. on Artificial Neural Networks, Vol. II, pp. 1432–1435, Sorrento Italy, 1994.

  • D. J. Smith et al, A VLSI Implementation of the Nestor RCE Neural Network, Texas Instruments Technical Journal, Vol. 7, No. 6, 1990.

  • D. J. Smith and P. H. Stanford, A Random Walk in Hamming Space, in Proc. IEEE Intl. Conf. on Neural Networks, Vol. II, pp. 465–470, San Diego CA, 1990.

  • B. I. Pawate et al, Memory Based Digital Signal Processing, in Proc. IEEE Intl. Conf. on Application Specific Signal Processing, Albuquerque NM, 1990.

  • S. Lusky et al, A Unified Design Representation Can Work, in Proc. ACM/IEEE Design Automation Conf., Las Vegas Nevada, 1989.

  • B. Kapoor et al, Logic Optimization Using Pattern Matching, in Proc. IEEE Intl. Workshop on Logic Synthesis, North Carolina, 1989.

  • T. Shiple et al, Area Evaluation Metrics for Transistor Placement, in Proc. IEEE Intl. Conf. on Computer Design, New York NY, 1988.

  • T. Yoshino and D. J. Smith and D. J. Matzke, An RTL Simulator Based on Functional Programming, Texas Instruments Technical Journal, Vol. 4, No. 3, 139–145, 1987.

  • I. Oliver, D. J. Smith, and J. R. H. Holland, A Study of Permutation Crossover Operators on the Traveling Salesman Problem, in Proc. Intl. Conf. on Genetic Algorithms, Boston MA, 1987.

  • D. J. Smith, Bin Packing with Adaptive Search, in Proc. Intl. Conf. on Genetic Algorithms, Pittsburgh PA, 1985.

  • D. J. Smith and L. Davis, Adaptive Search for Layout Synthesis, in Proc. Texas Instruments Semiconductor Group Technical Meeting, Dallas TX, 1985.

Public and Animal Health Documents

  • CA Russell, E Skepner, Smith DJ. 2014. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2015. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2014. “Report for the 2014 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2014. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2014-2015. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2013. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2014. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2013. “Report for the 2013 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2013. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2013-2014. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2012. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2013. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2012. “Report for the 2012 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2012. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2012-2013. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2011. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2012. Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.

  • Lewis NS, DJ Smith. 2011. “Report for the 2011 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2011. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2011-2012. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith, CA Russell. 2010. “Report for the 2010 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. National Institute for Medical Research, Mill Hill, UK.

  • Smith DJ, E Skepner, CA Russell. 2010. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2011. Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza vaccines for use in the 2010 influenza season (southern hemisphere winter). Weekly Epidemiological Record vol. 84, 41 (pp 421–436), 2009.

  • Smith DJ, E Skepner, CA Russell. 2009. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2009-2010. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza vaccines for use in the 2009-2010 influenza season (northern hemisphere winter). Weekly Epidemiological Record vol. 84, 9 (pp 65–76), 2009.

  • Lewis NS, CA Russell, DJ Smith. 2009. “Report for the 2008 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. National Institute for Medical Research, Mill Hill, UK.

  • Smith DJ, E Skepner, CA Russell. 2008. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2009. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 83, 41 (pp 365–372), 2008.

  • Smith DJ, E Skepner, CA Russell. 2008. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2008-2009. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2008–2009 influenza season. Weekly Epidemiological Record vol. 83, 9 (pp 77–88). 2008.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 82, 40 (pp 345–356) 2009.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2007-2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007–2008 influenza season. Weekly Epidemiological Record vol. 82, 9 (pp 69–76) 2009.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2007. World Health Organization, Geneva, Switzerland.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 82, 40 (pp 345–356) 2009.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2007-2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007–2008 influenza season. Weekly Epidemiological Record vol. 82, 9 (pp 69–76) 2009.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2007. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007 influenza season. Weekly Epidemiological Record vol. 81, 41 (pp 385–396), 2006.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2006-2007. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006-2007 influenza season. Weekly Epidemiological Record vol. 81, 41 (pp 82–86). 2006.

  • Smith DJ, TC Jones. 2005, “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2006. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006 influenza season. Weekly Epidemiological Record vol. 80, 40 (pp 341-352), 2005.

  • Smith DJ, TC Jones. 2005. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2005-2006. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006 influenza season. Weekly Epidemiological Record vol. 80, 40 (pp 341-352), 2005.

  • Smith DJ, TC Jones. 2004, “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2005. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2005 influenza season. Weekly Epidemiological Record vol. 79, 41 (pp 369–376), 2004.


Other Scientific Writing

  • ESWI’s General strategy towards young scientists, European Scientific Working Group on Influenza, Bulletin #24, 2008.

  • Access Science Q&A by Science Online, 2006.

  • Mapping the flu virus, Science and Public Affairs, a publication of the British Association for the Advancement of Science, 2006.

  • Mapping the antigenic and genetic evolution of influenza virus, European Scientific Working Group on Influenza, Influenza bulletin #19, 2004.

  • Influenza database tutorials, European Scientific Working Group on Influenza, Bulletin #17, 2002