Derek Smith

Professor of Infectious Disease Informatics, Department of Zoology, and Director of Centre for Pathogen Evolution

Derek Smith uses antigenic cartography, along with genetic and population biology techniques, to study basic questions in pathogen evolution, and coevolution with the acquired immunity in host populations. Learn more.

Research Areas

Evolution and population dynamics

Pathogen evolution

Acquired immunity

Techniques

Antigenic cartography

Research Theme

Publications

Journal articles

2023

Mykytyn, AZ., Rosu, ME., Kok, A., Rissmann, M., van Amerongen, G., Geurtsvankessel, C., de Vries, RD., Munnink, BBO., Smith, DJ., Koopmans, MPG., Lamers, MM., Fouchier, RAM. and Haagmans, BL., 2023. Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1. Lancet Microbe, v. 4
Doi: 10.1016/S2666-5247(22)00384-6

2022

Ying, B., Whitener, B., VanBlargan, LA., Hassan, AO., Shrihari, S., Liang, C-Y., Karl, CE., Mackin, S., Chen, RE., Kafai, NM., Wilks, SH., Smith, DJ., Carreño, JM., Singh, G., Krammer, F., Carfi, A., Elbashir, SM., Edwards, DK., Thackray, LB. and Diamond, MS., 2022. Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains. Sci Transl Med, v. 14
Doi: 10.1126/scitranslmed.abm3302

Huang, AT., Salje, H., Escoto, AC., Chowdhury, N., Chávez, C., Garcia-Carreras, B., Rutvisuttinunt, W., Maljkovic Berry, I., Gromowski, GD., Wang, L., Klungthong, C., Thaisomboonsuk, B., Nisalak, A., Trimmer-Smith, LM., Rodriguez-Barraquer, I., Ellison, DW., Jones, AR., Fernandez, S., Thomas, SJ., Smith, DJ., Jarman, R., Whitehead, SS., Cummings, DAT. and Katzelnick, LC., 2022. Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand. PLoS Pathog, v. 18
Doi: 10.1371/journal.ppat.1010500

Mykytyn, AZ., Rissmann, M., Kok, A., Rosu, ME., Schipper, D., Breugem, TI., van den Doel, PB., Chandler, F., Bestebroer, T., de Wit, M., van Royen, ME., Molenkamp, R., Oude Munnink, BB., de Vries, RD., GeurtsvanKessel, C., Smith, DJ., Koopmans, MPG., Rockx, B., Lamers, MM., Fouchier, RAM. and Haagmans, BL., 2022. Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct. Sci Immunol, v. 7
Doi: 10.1126/sciimmunol.abq4450

Rosu, ME., Lexmond, P., Bestebroer, TM., Hauser, BM., Smith, DJ., Herfst, S. and Fouchier, RAM., 2022. Substitutions near the HA receptor binding site explain the origin and major antigenic change of the B/Victoria and B/Yamagata lineages. Proc Natl Acad Sci U S A, v. 119
Doi: http://doi.org/10.1073/pnas.2211616119

Rössler, A., Netzl, A., Knabl, L., Schäfer, H., Wilks, SH., Bante, D., Falkensammer, B., Borena, W., von Laer, D., Smith, DJ. and Kimpel, J., 2022. BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants. Nat Commun, v. 13
Doi: 10.1038/s41467-022-35312-3

Wilks, SH., Mühlemann, B., Shen, X., Türeli, S., LeGresley, EB., Netzl, A., Caniza, MA., Chacaltana-Huarcaya, JN., Corman, VM., Daniell, X., Datto, MB., Dawood, FS., Denny, TN., Drosten, C., Fouchier, RAM., Garcia, PJ., Halfmann, PJ., Jassem, A., Jeworowski, LM., Jones, TC., Kawaoka, Y., Krammer, F., McDanal, C., Pajon, R., Simon, V., Stockwell, MS., Tang, H., van Bakel, H., Veguilla, V., Webby, R., Montefiori, DC. and Smith, DJ., 2022. Mapping SARS-CoV-2 antigenic relationships and serological responses. bioRxiv,
Doi: 10.1101/2022.01.28.477987

2021

Kong, H., Burke, DF., da Silva Lopes, TJ., Takada, K., Imai, M., Zhong, G., Hatta, M., Fan, S., Chiba, S., Smith, D., Neumann, G. and Kawaoka, Y., 2021. Plasticity of the Influenza Virus H5 HA Protein. mBio, v. 12
Doi: http://doi.org/10.1128/mBio.03324-20

Kemp, L., Aldridge, DC., Booy, O., Bower, H., Browne, D., Burgmann, M., Burt, A., Cunningham, AA., Dando, M., Dick, JTA., Dye, C., Weiss Evans, S., Gallardo, B., Godfray, HCJ., Goodfellow, I., Gubbins, S., Holt, LA., Jones, KE., Kandil, H., Martin, P., McCaughan, M., McLeish, C., Meany, T., Millett, K., ÓhÉigeartaigh, SS., Patron, NJ., Rhodes, C., Roy, HE., Shackelford, G., Smith, D., Spence, N., Steiner, H., Sundaram, LS., Voeneky, S., Walker, JR., Watkins, H., Whitby, S., Wood, J. and Sutherland, WJ., 2021. 80 questions for UK biological security. PLoS One, v. 16
Doi: 10.1371/journal.pone.0241190

Amanat, F., Strohmeier, S., Meade, P., Dambrauskas, N., Mühlemann, B., Smith, DJ., Vigdorovich, V., Sather, DN., Coughlan, L. and Krammer, F., 2021. Vaccination with SARS-CoV-2 variants of concern protects mice from challenge with wild-type virus. PLoS Biol, v. 19
Doi: http://doi.org/10.1371/journal.pbio.3001384

Katzelnick, LC., Coello Escoto, A., Huang, AT., Garcia-Carreras, B., Chowdhury, N., Maljkovic Berry, I., Chavez, C., Buchy, P., Duong, V., Dussart, P., Gromowski, G., Macareo, L., Thaisomboonsuk, B., Fernandez, S., Smith, DJ., Jarman, R., Whitehead, SS., Salje, H. and Cummings, DAT., 2021. Antigenic evolution of dengue viruses over 20 years. Science, v. 374
Doi: 10.1126/science.abk0058

2020

Martinez-Sobrido, L., Blanco-Lobo, P., Rodriguez, L., Fitzgerald, T., Zhang, H., Nguyen, P., Anderson, CS., Holden-Wiltse, J., Bandyopadhyay, S., Nogales, A., DeDiego, ML., Wasik, BR., Miller, BL., Henry, C., Wilson, PC., Sangster, MY., Treanor, JJ., Topham, DJ., Byrd-Leotis, L., Steinhauer, DA., Cummings, RD., Luczo, JM., Tompkins, SM., Sakamoto, K., Jones, CA., Steel, J., Lowen, AC., Danzy, S., Tao, H., Fink, AL., Klein, SL., Wohlgemuth, N., Fenstermacher, KJ., El Najjar, F., Pekosz, A., Sauer, L., Lewis, MK., Shaw-Saliba, K., Rothman, RE., Liu, Z-Y., Chen, K-F., Parrish, CR., Voorhees, IEH., Kawaoka, Y., Neumann, G., Chiba, S., Fan, S., Hatta, M., Kong, H., Zhong, G., Wang, G., Uccellini, MB., García-Sastre, A., Perez, DR., Ferreri, LM., Herfst, S., Richard, M., Fouchier, R., Burke, D., Pattinson, D., Smith, DJ., Meliopoulos, V., Freiden, P., Livingston, B., Sharp, B., Cherry, S., Dib, JC., Yang, G., Russell, CJ., Barman, S., Webby, RJ., Krauss, S., Danner, A., Woodard, K., Peiris, M., Perera, RAPM., Chan, MCW., Govorkova, EA., Marathe, BM., Pascua, PNQ., Smith, G., Li, Y-T., Thomas, PG. and Schultz-Cherry, S., 2020. Characterizing Emerging Canine H3 Influenza Viruses. PLoS Pathog, v. 16
Doi: http://doi.org/10.1371/journal.ppat.1008409

2019

Dias, M., Pattabiraman, C., Siddappa, S., Gowda, M., Shet, A., Smith, D., Muehlemann, B., Tamma, K., Solomon, T., Jones, T. and Krishna, S., 2019. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum Wellcome Open Research,
Doi: http://doi.org/10.12688/wellcomeopenres.14438.2

Kawakami, C., Yamayoshi, S., Akimoto, M., Nakamura, K., Miura, H., Fujisaki, S., Pattinson, DJ., Shimizu, K., Ozawa, H., Momoki, T., Saikusa, M., Yasuhara, A., Usuku, S., Okubo, I., Toyozawa, T., Sugita, S., Smith, DJ., Watanabe, S. and Kawaoka, Y., 2019. Genetic and antigenic characterisation of influenza A(H3N2) viruses isolated in Yokohama during the 2016/17 and 2017/18 influenza seasons Eurosurveillance, v. 24
Doi: http://doi.org/10.2807/1560-7917.es.2019.24.6.1800467

Gao, J., Couzens, L., Burke, DF., Wan, H., Wilson, P., Memoli, MJ., Xu, X., Harvey, R., Wrammert, J., Ahmed, R., Taubenberger, JK., Smith, DJ., Fouchier, RAM. and Eichelberger, MC., 2019. Antigenic Drift of the Influenza A(H1N1)pdm09 Virus Neuraminidase Results in Reduced Effectiveness of A/California/7/2009 (H1N1pdm09)-Specific Antibodies. MBio, v. 10
Doi: http://doi.org/10.1128/mBio.00307-19

Koel, BF., Burke, DF., van der Vliet, S., Bestebroer, TM., Rimmelzwaan, GF., Osterhaus, ADME., Smith, DJ. and Fouchier, RAM., 2019. Epistatic interactions can moderate the antigenic effect of substitutions in haemagglutinin of influenza H3N2 virus Journal of General Virology,
Doi: http://doi.org/10.1099/jgv.0.001263

2018

Muhlemann, B., Jones, TC., de Barros Damgaard, P., Allentoft, ME., Shevnina, I., Logvin, A., Usmanova, E., Panyushkina, IP., Boldgiv, B., Bazartseren, T., Tashbaeva, K., Merz, V., Lau, N., Smrčka, V., Voyakin, D., Kitov, E., Epimakhov, A., Pokutta, D., Vicze, M., Price, TD., Moiseyev, V., Hansen, AJ., Orlando, L., Rasmussen, S., Sikora, M., Vinner, L., Osterhaus, ADME., Smith, DJ., Glebe, D., Fouchier, RAM., Drosten, C., Sjogren, K-G., Kristiansen, K. and Willerslev, E., 2018. Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature, v. 562
Doi: 10.1038/s41586-018-0406-6

Dias, M., Pattabiraman, C., Siddappa, S., Gowda, M., Shet, A., Smith, D., Muehlemann, B., Tamma, K., Solomon, T., Jones, T. and Krishna, S., 2018. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res, v. 3
Doi: http://doi.org/10.12688/wellcomeopenres.14438.2

Koel, B., Burke, D., der Vliet, SV., Bestebroer, T., Rimmelzwaan, G., Osterhaus, ADME., Smith, D. and Fouchier, RAM., 2018. Epistatic interactions can moderate the antigenic effect of substitutions in hemagglutinin of influenza H3N2 virus
Doi: 10.1101/506030

Katzelnick, LC., Coello Escoto, A., McElvany, BD., Chávez, C., Salje, H., Luo, W., Rodriguez-Barraquer, I., Jarman, R., Durbin, AP., Diehl, SA., Smith, DJ., Whitehead, SS. and Cummings, DAT., 2018. Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus. PLoS Negl Trop Dis, v. 12
Doi: 10.1371/journal.pntd.0006862

2017

Skowronski, DM., Chambers, C., De Serres, G., Sabaiduc, S., Winter, A-L., Dickinson, JA., Gubbay, JB., Fonseca, K., Drews, SJ., Charest, H., Martineau, C., Krajden, M., Petric, M., Bastien, N., Li, Y. and Smith, DJ., 2017. Serial Vaccination and the Antigenic Distance Hypothesis: Effects on Influenza Vaccine Effectiveness During A(H3N2) Epidemics in Canada, 2010-2011 to 2014-2015. J Infect Dis, v. 215
Doi: 10.1093/infdis/jix074

Pattabiraman, C., Dias, M., Siddappa, S., Gowda, M., Shet, A., Smith, D., Muehlemann, B., Tamma, K., Solomon, T., Jones, T. and Krishna, S., 2017. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum
Doi: 10.1101/204503

Richard, M., Knauf, S., Lawrence, P., Mather, AE., Munster, VJ., Müller, MA., Smith, D. and Kuiken, T., 2017. Factors determining human-to-human transmissibility of zoonotic pathogens via contact. Curr Opin Virol, v. 22
Doi: http://doi.org/10.1016/j.coviro.2016.11.004

2016

Mosterín Höpping, A., McElhaney, J., Fonville, JM., Powers, DC., Beyer, WEP. and Smith, DJ., 2016. The confounded effects of age and exposure history in response to influenza vaccination. Vaccine, v. 34
Doi: 10.1016/j.vaccine.2015.11.058

Mosterín Höpping, A., Fonville, JM., Russell, CA., James, S. and Smith, DJ., 2016. Influenza B vaccine lineage selection--an optimized trivalent vaccine. Vaccine, v. 34
Doi: 10.1016/j.vaccine.2016.01.042

Li, C., Hatta, M., Burke, DF., Ping, J., Zhang, Y., Ozawa, M., Taft, AS., Das, SC., Hanson, AP., Song, J., Imai, M., Wilker, PR., Watanabe, T., Watanabe, S., Ito, M., Iwatsuki-Horimoto, K., Russell, CA., James, SL., Skepner, E., Maher, EA., Neumann, G., Klimov, AI., Kelso, A., McCauley, J., Wang, D., Shu, Y., Odagiri, T., Tashiro, M., Xu, X., Wentworth, DE., Katz, JM., Cox, NJ., Smith, DJ. and Kawaoka, Y., 2016. Selection of antigenically advanced variants of seasonal influenza viruses. Nat Microbiol, v. 1
Doi: http://doi.org/10.1038/nmicrobiol.2016.58

James, SL., Blacksell, SD., Nawtaisong, P., Tanganuchitcharnchai, A., Smith, DJ., Day, NPJ. and Paris, DH., 2016. Antigenic Relationships among Human Pathogenic Orientia tsutsugamushi Isolates from Thailand. PLoS Negl Trop Dis, v. 10
Doi: http://doi.org/10.1371/journal.pntd.0004723

2015

Swayne, DE., Suarez, DL., Spackman, E., Jadhao, S., Dauphin, G., Kim-Torchetti, M., McGrane, J., Weaver, J., Daniels, P., Wong, F., Selleck, P., Wiyono, A., Indriani, R., Yupiana, Y., Sawitri Siregar, E., Prajitno, T., Smith, D. and Fouchier, R., 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. J Virol, v. 89
Doi: http://doi.org/10.1128/JVI.00025-15

Smith, GJD., Donis, RO. and 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 Other Respir Viruses, v. 9
Doi: http://doi.org/10.1111/irv.12324

Koel, BF., Mögling, R., Chutinimitkul, S., Fraaij, PL., Burke, DF., van der Vliet, S., de Wit, E., Bestebroer, TM., Rimmelzwaan, GF., Osterhaus, ADME., Smith, DJ., Fouchier, RAM. and de Graaf, M., 2015. Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses. J Virol, v. 89
Doi: http://doi.org/10.1128/JVI.02962-14

Beyer, WEP., McElhaney, J., Smith, DJ., Monto, AS., Nguyen-Van-Tam, JS. and Osterhaus, ADME., 2015. Reply: Letter to the editor, Cochrane rearranged. Vaccine, v. 33
Doi: http://doi.org/10.1016/j.vaccine.2014.05.045

Bedford, T., Riley, S., Barr, IG., Broor, S., Chadha, M., Cox, NJ., Daniels, RS., Gunasekaran, CP., Hurt, AC., Kelso, A., Klimov, A., Lewis, NS., Li, X., McCauley, JW., Odagiri, T., Potdar, V., Rambaut, A., Shu, Y., Skepner, E., Smith, DJ., Suchard, MA., Tashiro, M., Wang, D., Xu, X., Lemey, P. and Russell, CA., 2015. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature, v. 523
Doi: 10.1038/nature14460

Katzelnick, LC., Fonville, JM., Gromowski, GD., Bustos Arriaga, J., Green, A., James, SL., Lau, L., Montoya, M., Wang, C., VanBlargan, LA., Russell, CA., Thu, HM., Pierson, TC., Buchy, P., Aaskov, JG., Muñoz-Jordán, JL., Vasilakis, N., Gibbons, RV., Tesh, RB., Osterhaus, ADME., Fouchier, RAM., Durbin, A., Simmons, CP., Holmes, EC., Harris, E., Whitehead, SS. and Smith, DJ., 2015. Dengue viruses cluster antigenically but not as discrete serotypes. Science, v. 349
Doi: 10.1126/science.aac5017

Huang, S-W., Tai, C-H., Fonville, JM., Lin, C-H., Wang, S-M., Liu, C-C., Su, I-J., Smith, DJ. and Wang, J-R., 2015. Mapping Enterovirus A71 Antigenic Determinants from Viral Evolution. J Virol, v. 89
Doi: http://doi.org/10.1128/JVI.02035-15

Althouse, BM., Scarpino, SV., Meyers, LA., Ayers, JW., Bargsten, M., Baumbach, J., Brownstein, JS., Castro, L., Clapham, H., Cummings, DA., Del Valle, S., Eubank, S., Fairchild, G., Finelli, L., Generous, N., George, D., Harper, DR., Hébert-Dufresne, L., Johansson, MA., Konty, K., Lipsitch, M., Milinovich, G., Miller, JD., Nsoesie, EO., Olson, DR., Paul, M., Polgreen, PM., Priedhorsky, R., Read, JM., Rodríguez-Barraquer, I., Smith, DJ., Stefansen, C., Swerdlow, DL., Thompson, D., Vespignani, A. and Wesolowski, A., 2015. Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Sci, v. 4
Doi: http://doi.org/10.1140/epjds/s13688-015-0054-0

2014

Barr, IG., Russell, C., Besselaar, TG., Cox, NJ., Daniels, RS., Donis, R., Engelhardt, OG., Grohmann, G., Itamura, S., Kelso, A., McCauley, J., Odagiri, T., Schultz-Cherry, S., Shu, Y., Smith, D., Tashiro, M., Wang, D., Webby, R., Xu, X., Ye, Z., Zhang, W. and Writing Committee of the World Health Organization Consultation on Northern Hemisphere Influenza Vaccine Composition for 2013–2014, , 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, v. 32
Doi: 10.1016/j.vaccine.2014.02.014

Ludi, AB., Horton, DL., Li, Y., Mahapatra, M., King, DP., Knowles, NJ., Russell, CA., Paton, DJ., Wood, JLN., Smith, DJ. and Hammond, JM., 2014. Antigenic variation of foot-and-mouth disease virus serotype A. J Gen Virol, v. 95
Doi: 10.1099/vir.0.057521-0

Bedford, T., Suchard, MA., Lemey, P., Dudas, G., Gregory, V., Hay, AJ., McCauley, JW., Russell, CA., Smith, DJ. and Rambaut, A., 2014. Integrating influenza antigenic dynamics with molecular evolution. Elife, v. 3
Doi: 10.7554/eLife.01914

Westgeest, KB., Russell, CA., Lin, X., Spronken, MIJ., Bestebroer, TM., Bahl, J., van Beek, R., Skepner, E., Halpin, RA., de Jong, JC., Rimmelzwaan, GF., Osterhaus, ADME., Smith, DJ., Wentworth, DE., Fouchier, RAM. and de Graaf, M., 2014. Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011. J Virol, v. 88
Doi: http://doi.org/10.1128/JVI.02163-13

Lemey, P., Rambaut, A., Bedford, T., Faria, N., Bielejec, F., Baele, G., Russell, CA., Smith, DJ., Pybus, OG., Brockmann, D. and Suchard, MA., 2014. Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLoS Pathog, v. 10
Doi: 10.1371/journal.ppat.1003932

Watanabe, T., Zhong, G., Russell, CA., Nakajima, N., Hatta, M., Hanson, A., McBride, R., Burke, DF., Takahashi, K., Fukuyama, S., Tomita, Y., Maher, EA., Watanabe, S., Imai, M., Neumann, G., Hasegawa, H., Paulson, JC., Smith, DJ. and Kawaoka, Y., 2014. Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential. Cell Host Microbe, v. 15
Doi: http://doi.org/10.1016/j.chom.2014.05.006

Koel, BF., van der Vliet, S., Burke, DF., Bestebroer, TM., Bharoto, EE., Yasa, IWW., Herliana, I., Laksono, BM., Xu, K., Skepner, E., Russell, CA., Rimmelzwaan, GF., Perez, DR., Osterhaus, ADME., Smith, DJ., Prajitno, TY. and Fouchier, RAM., 2014. Antigenic variation of clade 2.1 H5N1 virus is determined by a few amino acid substitutions immediately adjacent to the receptor binding site. mBio, v. 5
Doi: http://doi.org/10.1128/mBio.01070-14

Koel, BF., van der Vliet, S., Burke, DF., Bestebroer, TM., Bharoto, EE., Yasa, IW., Herliana, I., Laksono, BM., Xu, K., Skepner, E., Russell, CA., Rimmelzwaan, GF., Perez, DR., Osterhaus, AD., Smith, DJ., Prajitno, TY. and Fouchier, RA., 2014. Correction for Koel et al., Antigenic Variation of Clade 2.1 H5N1 Virus Is Determined by a Few Amino Acid Substitutions Immediately Adjacent to the Receptor Binding Site. MBio, v. 5
Doi: http://doi.org/10.1128/mBio.01645-14

Fonville, JM., Wilks, SH., James, SL., Fox, A., Ventresca, M., Aban, M., Xue, L., Jones, TC., Le, NMH., Pham, QT., Tran, ND., Wong, Y., Mosterin, A., Katzelnick, LC., Labonte, D., Le, TT., van der Net, G., Skepner, E., Russell, CA., Kaplan, TD., Rimmelzwaan, GF., Masurel, N., de Jong, JC., Palache, A., Beyer, WEP., Le, QM., Nguyen, TH., Wertheim, HFL., Hurt, AC., Osterhaus, ADME., Barr, IG., Fouchier, RAM., Horby, PW. and Smith, DJ., 2014. Antibody landscapes after influenza virus infection or vaccination. Science, v. 346
Doi: 10.1126/science.1256427

Burke, DF. and Smith, DJ., 2014. A recommended numbering scheme for influenza A HA subtypes. PLoS One, v. 9
Doi: 10.1371/journal.pone.0112302

Gilbert, M., Koel, BF., Bestebroer, TM., Lewis, NS., Smith, DJ. and Fouchier, RAM., 2014. Serological evidence for non-lethal exposures of Mongolian wild birds to highly pathogenic avian influenza H5N1 virus. PLoS One, v. 9
Doi: http://doi.org/10.1371/journal.pone.0113569

Ke, C., Lu, J., Wu, J., Guan, D., Zou, L., Song, T., Yi, L., Zeng, X., Liang, L., Ni, H., Kang, M., Zhang, X., Zhong, H., He, J., Lin, J., Smith, D., Burke, D., Fouchier, RAM., Koopmans, M. and Zhang, Y., 2014. Circulation of reassortant influenza A(H7N9) viruses in poultry and humans, Guangdong Province, China, 2013. Emerg Infect Dis, v. 20
Doi: http://doi.org/10.3201/eid2012.140765

van den Hoogen, BG., van Boheemen, S., de Rijck, J., van Nieuwkoop, S., Smith, DJ., Laksono, B., Gultyaev, A., Osterhaus, ADME. and Fouchier, RAM., 2014. Excessive production and extreme editing of human metapneumovirus defective interfering RNA is associated with type I IFN induction. J Gen Virol, v. 95
Doi: http://doi.org/10.1099/vir.0.066100-0

Burke, DF. and Smith, DJ., 2014. A recommended numbering scheme for influenza a ha subtypes PLoS ONE, v. 9
Doi: http://doi.org/10.1371/journal.pone

Schultz-Cherry, S., Webby, RJ., Webster, RG., Kelso, A., Barr, IG., McCauley, JW., Daniels, RS., Wang, D., Shu, Y., Nobusawa, E., Itamura, S., Tashiro, M., Harada, Y., Watanabe, S., Odagiri, T., Ye, Z., Grohmann, G., Harvey, R., Engelhardt, O., Smith, D., Hamilton, K., Claes, F. and Dauphin, G., 2014. Influenza gain-of-function experiments: their role in vaccine virus recommendation and pandemic preparedness. mBio, v. 5
Doi: http://doi.org/10.1128/mBio.02430-14

Barr, IG., Russell, C., Besselaar, TG., Cox, NJ., Daniels, RS., Donis, R., Engelhardt, OG., Grohmann, G., Itamura, S., Kelso, A., McCauley, J., Odagiri, T., Schultz-Cherry, S., Shu, Y., Smith, D., Tashiro, M., Wang, D., Webby, R., Xu, X., Ye, Z. and Zhang, W., 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, v. 32
Doi: http://doi.org/10.1016/j.vaccine.2014.02.014

2013

Lewis, NS., Javakhishvili, Z., Russell, CA., Machablishvili, A., Lexmond, P., Verhagen, JH., Vuong, O., Onashvili, T., Donduashvili, M., Smith, DJ. and Fouchier, RAM., 2013. Avian influenza virus surveillance in wild birds in Georgia: 2009-2011. PLoS One, v. 8
Doi: http://doi.org/10.1371/journal.pone.0058534

Fouchier, RAM. and Kawaoka, Y., 2013. Gain-of-function experiments on H7N9 Nature, v. 500
Doi: 10.1038/500150a

Beyer, WEP., McElhaney, J., Smith, DJ., Monto, AS., Nguyen-Van-Tam, JS. and Osterhaus, ADME., 2013. Cochrane re-arranged: Support for policies to vaccinate elderly people against influenza Vaccine,

Koel, BF., Burke, DF., Bestebroer, TM., van der Vliet, S., Zondag, GCM., Vervaet, G., Skepner, E., Lewis, NS., Spronken, MIJ., Russell, CA., Eropkin, MY., Hurt, AC., Barr, IG., de Jong, JC., Rimmelzwaan, GF., Osterhaus, ADME., Fouchier, RAM. and Smith, DJ., 2013. Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science, v. 342
Doi: 10.1126/science.1244730

Fouchier, RAM., Kawaoka, Y., Cardona, C., Compans, RW., García-Sastre, A., Govorkova, EA., Guan, Y., Herfst, S., Orenstein, WA., Peiris, JSM., Perez, DR., Richt, JA., Russell, C., Schultz-Cherry, SL., Smith, DJ., Steel, J., Tompkins, SM., Topham, DJ., Treanor, JJ., Tripp, RA., Webby, RJ. and Webster, RG., 2013. Gain-of-function experiments on H7N9 Science, v. 341
Doi: http://doi.org/10.1126/science.1243325

Ampofo, WK., Al Busaidy, S., Cox, NJ., Giovanni, M., Hay, A., Huang, S., Inglis, S., Katz, J., Mokhtari-Azad, T., Peiris, M., Savy, V., Sawanpanyalert, P., Venter, M., Waddell, AL., Wickramasinghe, G., Zhang, W., Ziegler, T. and WHO Writing Group, , 2013. 9 December 2011. ... Vaccine, v. 31
Doi: http://doi.org/10.1016/j.vaccine.2013.05.049

2012

Westgeest, KB., de Graaf, M., Fourment, M., Bestebroer, TM., van Beek, R., Spronken, MIJ., de Jong, JC., Rimmelzwaan, GF., Russell, CA., Osterhaus, ADME., Smith, GJD., Smith, DJ. and Fouchier, RAM., 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, v. 93
Doi: 10.1099/vir.0.043059-0

Klimov, AI., Garten, R., Russell, C., Barr, IG., Besselaar, TG., Daniels, R., Engelhardt, OG., Grohmann, G., Itamura, S., Kelso, A., McCauley, J., Odagiri, T., Smith, D., Tashiro, M., Xu, X., Webby, R., Wang, D., Ye, Z., Yuelong, S., Zhang, W., Cox, N. and Writing Committee of the World Health Organization Consultation on Southern Hemisphere Influenza Vaccine Composition for 2012, , 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, v. 30
Doi: http://doi.org/10.1016/j.vaccine.2012.07.089

Wilks, S., de Graaf, M., Smith, DJ. and Burke, DF., 2012. A review of influenza haemagglutinin receptor binding as it relates to pandemic properties. Vaccine, v. 30
Doi: http://doi.org/10.1016/j.vaccine.2012.02.076

Russell, CA., Fonville, JM., Brown, AEX., Burke, DF., Smith, DL., James, SL., Herfst, S., van Boheemen, S., Linster, M., Schrauwen, EJ., Katzelnick, L., Mosterín, A., Kuiken, T., Maher, E., Neumann, G., Osterhaus, ADME., Kawaoka, Y., Fouchier, RAM. and Smith, DJ., 2012. The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Science, v. 336
Doi: http://doi.org/10.1126/science.1222526

Herfst, S., Schrauwen, EJA., Linster, M., Chutinimitkul, S., De Wit, E., Munster, VJ., Sorrell, EM., Bestebroer, TM., Burke, DF., Smith, DJ., Rimmelzwaan, GF., Osterhaus, ADME. and Fouchier, RAM., 2012. Airborne transmission of influenza A/H5N1 virus between ferrets Science, v. 336
Doi: http://doi.org/10.1126/science.1213362

Lemey, P., Rambaut, A., Bedford, T., Faria, NR., Bielejec, F., Baele, G., Russell, CA., Smith, DJ., Pybus, OG., Brockmann, D. and Suchard, MA., 2012. The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing

2011

Bodewes, R., de Mutsert, G., van der Klis, FRM., Ventresca, M., Wilks, S., Smith, DJ., Koopmans, M., Fouchier, RAM., Osterhaus, ADME. and Rimmelzwaan, GF., 2011. Prevalence of antibodies against seasonal influenza A and B viruses in children in Netherlands. Clin Vaccine Immunol, v. 18
Doi: http://doi.org/10.1128/CVI.00396-10

Lorusso, A., Vincent, AL., Harland, ML., Alt, D., Bayles, DO., Swenson, SL., Gramer, MR., Russell, CA., Smith, DJ., Lager, KM. and Lewis, NS., 2011. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008 J GEN VIROL, v. 92
Doi: http://doi.org/10.1099/vir.0.027557-0

Huang, SW., Kiang, D., Smith, DJ. and Wang, JR., 2011. Evolution of re-emergent virus and its impact on enterovirus 71 epidemics Experimental Biology and Medicine, v. 236
Doi: http://doi.org/10.1258/ebm.2010.010233

Lewis, NS., Daly, JM., Russell, CA., Horton, DL., Skepner, E., Bryant, NA., Burke, DF., Rash, AS., Wood, JLN., Chambers, TM., Fouchier, RAM., Mumford, JA., Elton, DM. and Smith, DJ., 2011. Antigenic and genetic evolution of equine influenza A (H3N8) virus from 1968 to 2007. J Virol, v. 85
Doi: http://doi.org/10.1128/JVI.05319-11

Abbas, MA., Spackman, E., Fouchier, R., Smith, D., Ahmed, Z., Siddique, N., Sarmento, L., Naeem, K., McKinley, ET., Hameed, A., Rehmani, S. and Swayne, DE., 2011. H7 avian influenza virus vaccines protect chickens against challenge with antigenically diverse isolates VACCINE, v. 29
Doi: http://doi.org/10.1016/j.vaccine.2011.07.064

Mansfield, KL., Horton, DL., Johnson, N., Li, L., Barrett, ADT., Smith, DJ., Galbraith, SE., Solomon, T. and Fooks, AR., 2011. Flavivirus-induced antibody cross-reactivity J GEN VIROL, v. 92
Doi: http://doi.org/10.1099/vir.0.031641-0

Sandbulte, MR., Westgeest, KB., Gao, J., Xu, XY., Klimov, AI., Russell, CA., Burke, DF., Smith, DJ., Fouchier, RAM. and Eichelberger, MC., 2011. Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses P NATL ACAD SCI USA, v. 108
Doi: http://doi.org/10.1073/pnas.1113801108

2010

Barr, IG., McCauley, J., Cox, N., Daniels, R., Engelhardt, OG., Fukuda, K., Grohmann, G., Hay, A., Kelso, A., Klimov, A., Odagiri, T., Smith, D., Russell, C., Tashiro, M., Webby, R., Wood, J., Ye, ZP., Zhang, WQ. and World Hlth Org Consultation No Hem, , 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, v. 28
Doi: http://doi.org/10.1016/j.vaccine.2009.11.043

Van Kerkhove, MD., Asikainen, T., Becker, NG., Bjorge, S., Desenclos, JC., dos Santos, T., Fraser, C., Leung, GM., Lipsitch, M., Longini, IM., McBryde, ES., Roth, CE., Shay, DK., Smith, DJ., Wallinga, J., White, PJ., Ferguson, NM., Riley, S. and WHO Informal Network Math Modellin, , 2010. Studies Needed to Address Public Health Challenges of the 2009 H1N1 Influenza Pandemic: Insights from Modeling PLOS MED, v. 7
Doi: http://doi.org/10.1371/journal.pmed.1000275

Horton, DL., McElhinney, LM., Marston, DA., Wood, JLN., Russell, CA., Lewis, N., Kuzmin, IV., Fouchier, RAM., Osterhaus, ADME., Fooks, AR. and Smith, DJ., 2010. Quantifying antigenic relationships among the lyssaviruses. J Virol, v. 84
Doi: http://doi.org/10.1128/JVI.01153-10

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. and Fouchier, RAM., 2010. Virulence-associated substitution D222G in the hemagglutinin of 2009 pandemic influenza A(H1N1) virus affects receptor binding. J Virol, v. 84
Doi: http://doi.org/10.1128/JVI.01136-10

Paget, WJ., Balderston, C., Casas, I., Donker, G., Edelman, L., Fleming, D., Larrauri, A., Meijer, A., Puzelli, S., Rizzo, C., Simonsen, L. and EPIA collaborators, , 2010. Assessing the burden of paediatric influenza in Europe: the European Paediatric Influenza Analysis (EPIA) project. Eur J Pediatr, v. 169
Doi: http://doi.org/10.1007/s00431-010-1164-0

Barr, IG., McCauley, J., Cox, N., Daniels, R., Engelhardt, OG., Fukuda, K., Grohmann, G., Hay, A., Kelso, A., Klimov, A., Odagiri, T., Smith, D., Russell, C., Tashiro, M., Webby, R., Wood, J., Ye, Z. and Zhang, W., 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, v. 28
Doi: http://doi.org/10.1016/j.vaccine.2009.11.043

Smith, DJ. and Fouchier, RAM., 2010. Use of antigenic cartography seed strain seleciton Avian Diseases, v. 54

Smith, D., 2010. The role of antigenic cartography in monitoring INFLUENZA OTHER RESP, v. 4

2009

Garten, RJ., Davis, CT., Russell, CA., Shu, B., Lindstrom, S., Balish, A., Sessions, WM., Xu, XY., 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., Lopez-Gatell, H., Olivera, H., Lopez, I., Myers, CA., Faix, D., Blair, PJ., Yu, C., Keene, KM., Dotson, PD., Boxrud, D., Sambol, AR., Abid, SH., George, KS., 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. and Cox, NJ., 2009. Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans SCIENCE, v. 325
Doi: http://doi.org/10.1126/science.1176225

Huang, SW., Hsu, YW., Smith, DJ., Kiang, D., Tsai, HP., Lin, KH., Wang, SM., Liu, CC., Su, IJ. and Wang, JR., 2009. Reemergence of enterovirus 71 in 2008 in Taiwan: Dynamics of genetic and antigenic evolution from 1998 to 2008 Journal of Clinical Microbiology, v. 47
Doi: http://doi.org/10.1128/JCM.00630-09

WHO/OIE/FAO H5N1 Evolution Working Group, , 2009. Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses. Influenza Other Respir Viruses, v. 3
Doi: http://doi.org/10.1111/j.1750-2659.2009.00078.x

WHO Informal Network for Mathematical Modelling for Pandemic Influenza H1N1 2009 (Working Group on Data Needs), , 2009. Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS Curr, v. 1
Doi: http://doi.org/10.1371/currents.RRN1135

Park, AW., Daly, JM., Lewis, NS., Smith, DJ., Wood, JLN. and Grenfell, BT., 2009. Quantifying the Impact of Immune Escape on Transmission Dynamics of Influenza SCIENCE, v. 326
Doi: http://doi.org/10.1126/science.1175980

Voordouw, ACG., Beyer, WEP., Smith, DJ., Sturkenbom, MCJM. and Stricker, BHC., 2009. Evaluation of serological trials submitted for annual re-licensure of influenza vaccines to regulatory authorities between 1992 and 2002 VACCINE, v. 28
Doi: http://doi.org/10.1016/j.vaccine.2009.09.138

Huang, S-W., Hsu, Y-W., Smith, DJ., Kiang, D., Tsai, H-P., Lin, K-H., Wang, S-M., Liu, C-C., Su, I-J. and Wang, J-R., 2009. Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008. J Clin Microbiol, v. 47
Doi: http://doi.org/10.1128/JCM.00630-09

Brown, IH., Capua, I., Cattoli, G., Chen, HL., Cox, N., Davis, CT., Donis, RO., Fouchier, RAM., Garten, R., Guan, Y., Hay, A., Kawaoka, Y., Mackenzie, J., McCauley, J., Mumford, E., Olsen, C., Perdue, ML., Russell, CA., Smith, C., Smith, D., Smith, GJD., Shu, Y., Tashiro, M., Vijaykrishna, D., Webster, R. and WHO OIE FAO H5N1 Evolution Workin, , 2009. Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses INFLUENZA OTHER RESP, v. 3
Doi: http://doi.org/10.1111/j.1750-2659.2009.00078.x

2008

Russell, CA., Jones, TC., Barr, IG., Cox, NJ., Garten, RJ., Gregory, V., Gust, ID., Hampson, AW., Hay, AJ., Hurt, AC., De Jong, JC., Kelso, A., Klimov, AI., Kageyama, T., Komadina, N., Lapedes, AS., Lin, YP., Mosterin, A., Obuchi, M., Odagiri, T., Osterhaus, ADME., Rimmelzwaan, GF., Shaw, MW., Skepner, E., Stohr, K., Tashiro, M., Fouchier, RAM. and Smith, DJ., 2008. The global circulation of seasonal influenza A (H3N2) viruses Science, v. 320
Doi: http://doi.org/10.1126/science.1154137

Russell, CA., Jones, TC., Barr, IG., Cox, NJ., Garten, RJ., Gregory, V., Gust, ID., Hampson, AW., Hay, AJ., Hurt, AC., de Jong, JC., Kelso, A., Klimov, AI., Kageyama, T., Komadina, N., Lapedes, AS., Lin, YP., Mosterin, A., Obuchi, M., Odagiri, T., Osterhaus, ADME., Rimmelzwaan, GF., Shaw, MW., Skepner, E., Stohr, K., Tashiro, M., Fouchier, RAM. and Smith, DJ., 2008. Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses Vaccine, v. 26
Doi: http://doi.org/10.1016/j.vaccine.2008.07.078

WHO/OIE/FAO H5N1 Evolution Working Group, , 2008. Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Emerg Infect Dis, v. 14
Doi: http://doi.org/10.3201/eid1407.071681

Russell, CA., Jones, TC., Barr, IG., Cox, NJ., Garten, RJ., Gregory, V., Gust, ID., Hampson, AW., Hay, AJ., Hurt, AC., de Jong, JC., Kelso, A., Klimov, AI., Kageyama, T., Komadina, N., Lapedes, AS., Lin, YP., Mosterin, A., Obuchi, M., Odagiri, T., Osterhaus, ADME., Rimmelzwaan, GF., Shaw, MW., Skepner, E., Stohr, K., Tashiro, M., Fouchier, RAM. and Smith, DJ., 2008. The global circulation of seasonal influenza A (H3N2) viruses. Science, v. 320
Doi: http://doi.org/10.1126/science.1154137

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

Russell, CA., Jones, TC., Barr, IG., Cox, NJ., Garten, RJ., Gregory, V., Gust, ID., Hampson, AW., Hay, AJ., Hurt, AC., de Jong, JC., Kelso, A., Klimov, AI., Kageyama, T., Komadina, N., Lapedes, AS., Lin, YP., Mosterin, A., Obuchi, M., Odagiri, T., Osterhaus, ADME., Rimmelzwaan, GF., Shaw, MW., Skepner, E., Stohr, K., Tashiro, M., Fouchier, RAM. and Smith, DJ., 2008. Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses. Vaccine, v. 26 Suppl 4
Doi: http://doi.org/10.1016/j.vaccine.2008.07.078

2007

de Jong, JC., Smith, DJ., Lapedes, AS., Donatelli, I., Campitelli, L., Barigazzi, G., Van Reeth, K., Jones, TC., Rimmelzwaan, GF., Osterhaus, A. and Fouchier, RAM., 2007. Antigenic and genetic evolution of swine influenza A (H3N2) viruses in Europe JOURNAL OF VIROLOGY, v. 81
Doi: http://doi.org/10.1128/Jvi.02458-06

Berkhoff, EGM., Geelhoed-Mieras, MM., Jonges, M., Smith, DJ., Fouchier, RAM., Osterhaus, ADME. and Rimmelzwaan, GF., 2007. An amino acid substitution in the influenza A virus hemagglutinin associated with escape from recognition by human virus-specific CD4(+) T-cells VIRUS RES, v. 126
Doi: http://doi.org/10.1016/j.virusres.2007.02.018

Philippa, J., Baas, C., Beyer, W., Bestebroer, T., Fouchier, R., Smith, D., Schaftenaar, W. and Osterhaus, A., 2007. Vaccination against highly pathogenic avian influenza H5N1 virus in zoos using an adjuvanted inactivated H5N2 vaccine VACCINE, v. 25
Doi: http://doi.org/10.1016/j.vaccine.2007.01.121

2006

Smith, DJ., 2006. Erratum: Predictability and preparedness in influenza control [Science [392]] Science, v. 312

Smith, DJ., 2006. Predictability and preparedness in influenza control (vol 312, pg 392, 2006) SCIENCE, v. 312

Smith, DJ., 2006. Predictability and preparedness in influenza control SCIENCE, v. 312
Doi: http://doi.org/10.1126/science.1122665

2005

Rimmelzwaan, GF., Berkhoff, EGM., Nieuwkoop, NJ., Smith, DJ., Fouchier, RAM. and Osterhaus, A., 2005. 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, v. 86
Doi: http://doi.org/10.1099/vir.0.80867-0

Fouchier, RAM., Munster, V., Wallensten, A., Bestebroer, TM., Herfst, S., Smith, D., Rimmelzwaan, GF., Olsen, B. and Osterhaus, ADME., 2005. Characterization of a novel influenza a virus hemagglutinin subtype (H16) obtained from black-headed gulls J VIROL, v. 79
Doi: http://doi.org/10.1128/JVI.79.5.2814-2822.2005

2004

Smith, DJ., Lapedes, AS., de Jong, JC., Bestebroer, TM., Jones, TC., Rimmelzwaan, GF., Osterhaus, ADME. and Fouchier, RAM., 2004. Mutations, drift, and the influenza archipelago. Discov Med, v. 4

Smith, DJ., Lapedes, AS., de Jong, JC., Bestebroer, TM., Rimmelzwaan, GF., Osterhaus, A. and Fouchier, RAM., 2004. Mapping the antigenic and genetic evolution of influenza virus SCIENCE, v. 305
Doi: http://doi.org/10.1126/science.1097211

Voordouw, ACG., Sturkenboom, MCJM., Dieleman, JP., Stijnen, T., Smith, DJ., van der Lei, J. and Stricker, BHC., 2004. Annual revaccination against influenza and mortality risk in community-dwelling elderly parsons JAMA-J AM MED ASSOC, v. 292

Boon, ACM., de Mutsert, G., van Baarle, D., Smith, DJ., Lapedes, AS., Fouchier, RAM., Sintnicolaas, K., Osterhaus, ADME. and Rimmelzwaan, GF., 2004. Recognition of homo- and heterosubtypic variants of influenza A viruses by human CD8(+) T lymphocytes J IMMUNOL, v. 172

1999

Smith, DJ., Forrest, S., Ackley, DH. and Perelson, AS., 1999. Variable efficacy of repeated annual influenza vaccination. Proc Natl Acad Sci U S A, v. 96
Doi: http://doi.org/10.1073/pnas.96.24.14001

1998

Smith, DJ., Forrest, S., Ackley, DH. and Perelson, AS., 1998. Using lazy evaluation to simulate realistic-size repertoires in models of the immune system. Bull Math Biol, v. 60
Doi: http://doi.org/10.1006/bulm.1997.0035

1997

Smith, DJ., Forrest, S., Hightower, RR. and Perelson, AS., 1997. Deriving shape space parameters from immunological data. J Theor Biol, v. 189
Doi: http://doi.org/10.1006/jtbi.1997.0495

Burke, DF., Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015 Influenza and other Respiratory Viruses,
Doi: http://doi.org/10.1111/irv.12469

Katzelnick, L., Coello Escoto, A., Huang, A., Garcia-Carreras, B., Chowdhury, N., Maljkovic Berry, I., Chavez, C., Buchy, P., Duong, V., Dussart, P., Gromowski, G., Macareo, L., Thaisomboonsuk, B., Fernandez, S., Smith, D., Jarman, R., Whitehead, S., Salje, H. and Cummings, D., Antigenic evolution of dengue viruses over 20 years Science,
Doi: 10.1126/science.abk0058

Richard, M., Schrauwen, E., de Graaf, M., Bestebroer, T., Spronken, M., van Boheemen, S., de Meulder, D., Lexmond, P., Linster, M., Herfst, S., Smith, D., van den Brand, J., Burke, DF., Kuiken, T., Rimmelzwaan, G., Osterhaus, ADME. and Fouchier, RAM., Limited airborne transmission of influenza A/H7N9 virus between ferrets Nature,

Mühlemann, B., Jones, TC., Damgaard, PDB., Allentoft, ME., Shevnina, I., Logvin, A., Usmanova, E., Panyushkina, IP., Boldgiv, B., Bazartseren, T., Tashbaeva, K., Merz, V., Lau, N., Smrčka, V., Voyakin, D., Kitov, E., Epimakhov, A., Pokutta, D., Vicze, M., Price, TD., Moiseyev, V., Hansen, AJ., Orlando, L., Rasmussen, S., Sikora, M., Vinner, L., Osterhaus, ADME., Smith, DJ., Glebe, D., Fouchier, RAM., Drosten, C., Sjögren, K-G., Kristiansen, K. and Willerslev, E., Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature, v. 557
Doi: 10.1038/s41586-018-0097-z

Smith, D., Influenza virus infection history drives and shapes antibody responses to influenza vaccination Nature Medicine,

Mühlemann, B., Margaryan, A., de Barros Damgaard, P., Allentoft, ME., Vinner, L., Hansen, AJ., Weber, A., Bazaliiskii, VI., Molak, M., Arneborg, J., Bogdanowicz, W., Falys, C., Sablin, M., Smrčka, V., Sten, S., Tashbaeva, K., Lynnerup, N., Sikora, M., Smith, DJ., Fouchier, RAM., Drosten, C., Sjögren, K-G., Kristiansen, K., Willerslev, E. and Jones, TC., Ancient human parvovirus B19 in Eurasia reveals long-term association of the virus with humans Proceedings of the National Academy of Sciences of the United States of America,

Smith, D., Jones Kelly, T., James, S., Netzl, A., Tureli, S. and Wilks, S., Defining the risk of SARS-CoV-2 variants on immune protection Nature,

Linster, M., Schrauwen, EJA., van der Vliet, S., Burke, DF., Lexmond, P., Bestebroer, TM., Smith, DJ., Herfst, S., Koel, BF. and Fouchier, RAM., The molecular basis for antigenic drift of human A/H2N2 influenza viruses Journal of Virology,
Doi: http://doi.org/10.1128/jvi.01907-18

Smith, D., Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age Science, v. 369
Doi: 10.1126/science.aaw8977

Book chapters

2008

Smith, DJ., Jan, DJ., Bestebroer, TM., Rimmelzwaan, GF., Osterhaus, ADME., Fouchier, RAM., Lapedes, AS., Jones, TC. and Russell, CA., 2008. Antigenic cartography of human and swine influenza A(H3N2) viruses
Doi: http://doi.org/10.1002/9780470770672.ch4

1999

Smith, DJ., Forrest, S., Ackley, DH. and Perelson, AS., 1999. Modeling the Effects of Prior Infection on Vaccine Efficacy
Doi: 10.1007/978-3-642-59901-9_8

Lipsitch, M. and Smith, D., Applications of quantitative modeling to influenza virus transmission dynamics, antigenic and genetic evolution, and molecular structure
Doi: 10.1002/9781118636817.ch27

Conference proceedings

2021

Garcia-Carreras, B., Huang, AT., Mavian, C., Salje, H., Katzelnick, L., Escoto, AC., Chowdhury, N., Chavez, C., Rutvisuttinunt, W., Berry, IM., Klungthong, C., Thaisomboonsuk, B., Nisalak, A., Iamsirithaworn, S., Doung-Ngern, P., Rodriguez-Barraquer, I., Ellison, DW., Jones, AR., Fernandez, S., Endy, T., Smith, DJ., Jarman, RG., Whitehead, SS. and Cummings, DA., 2021. PHYLODYNAMICS VERSUS EPIDEMIOLOGICAL DYNAMICS OF DENGUE IN BANGKOK, 1994-2014 AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, v. 105

Katzelnick, L., Escoto, AC., Huang, A., Garcia-Carreras, B., Chowdhury, N., Berry, IM., Chavez, C., Buchy, P., Duong, V., Dussart, P., Gromowski, G., Macareo, L., Thaisomboonsuk, B., Fernandez, S., Smith, D., Jarman, R., Whitehead, S., Salje, H. and Cummings, D., 2021. ANTIGENIC EVOLUTION OF DENGUE VIRUSES OVER MULTIPLE DECADES AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, v. 105

2017

Katzelnick, L., Wang, C., Pierson, TC., Smith, DJ., Whitehead, SS. and Harris, E., 2017. NATURAL AND LABORATORY-DERIVED GENETIC VARIATION IN DENGUE VIRUS TYPE 2 AT ENVELOPE PROTEIN POSITIONS 202 AND 203 MODULATES ANTIGENIC AND IMMUNOGENIC PROPERTIES AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, v. 95

2008

Smith, DJ., De Jong, JC., Lapedes, AS., Jones, TC., Russell, CA., Bestebroer, TM., Rimmelzwaan, GF., Osterhaus, ADME. and Fouchier, RAM., 2008. Antigenic cartography of human and swine influenza A(H3N2) viruses Novartis Foundation Symposium, v. 290

Webster, RG., Smith, DJ., Osterhaus, A., Skehel, JJ., Kawaoka, Y., Holmes, EC., Anderson, LJ., Wood, JM., Kahn, JS., Peiris, JSM., Su, IJ. and Tambyah, PA., 2008. Discussion Novartis Foundation Symposium, v. 290

Webster, RG., Wood, JM., Peiris, JSM., Osterhaus, A., Anderson, LJ., Skehel, JJ., Tambyah, PA., Smith, DJ. and Hoffmann, E., 2008. Discussion Novartis Foundation Symposium, v. 290

Webster, RG., Xin, L., Osterhaus, A., Smith, DJ., Skehel, JJ., Peiris, JSM., Anderson, LJ., Leo, YS., Kahn, JS., Wood, JM., Hoffmann, E. and Su, IJ., 2008. Discussion Novartis Foundation Symposium, v. 290

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

Webster, RG., Holmes, EC., Vasudevan, S., Osterhaus, A., Peiris, JSM., Su, IJ., Smith, DJ., Lane, D., Lai, MM., Kahn, JS. and Anderson, LJ., 2008. Discussion Novartis Foundation Symposium, v. 290

Webster, RG., Skehel, JJ., Peiris, JSM., Lai, MM., Kawaoka, Y., Smith, DJ., Holmes, EC., Osterhaus, A. and Wood, JM., 2008. Discussion Novartis Foundation Symposium, v. 290

Osterhaus, A., Peiris, JSM., Skehel, JJ., Webster, RG., Wood, JM., Smith, DJ., Holmes, EC., Hoffmann, E., Anderson, LJ. and Lai, MM., 2008. Discussion Novartis Foundation Symposium, v. 290

2004

Rimmelzwaan, GF., Boon, ACM., de Mutsert, G., Fouchier, RAM., van Baarle, D., Smith, DJ., Lapedes, AS., Sintnicolaas, K. and Osterhaus, ADME., 2004. Recognition of influenza virus epitope variants by human CTL OPTIONS FOR THE CONTROL OF INFLUENZA V, v. 1263
Doi: http://doi.org/10.1016/j.ics.2004.02.061

2003

Smith, DJ., 2003. Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection VACCINE, v. 21
Doi: http://doi.org/10.1016/S0264-410X(03)00068-9

2001

Smith, DJ., Lapedes, AS., Forrest, S., de Jong, JC., Osterhaus, ADME., Fouchier, RAM., Cox, NJ. and Perelson, AS., 2001. Modeling the effects of updating the influenza vaccine on the efficacy of repeated vaccination International Congress Series, v. 1219
Doi: 10.1016/S0531-5131(01)00401-0

1997

Smith, DJ., Forrest, S., Ackley, DH. and Perelson, AS., 1997. Modeling the effects of prior infection on vaccine efficacy Proceedings of the IEEE International Conference on Systems, Man and Cybernetics, v. 1

Other publications

2022

Liu, Y., Liu, J., Zou, J., Kalveram, B., Machado, RRG., Ren, P., Türeli, S., Smith, DJ., Weaver, SC., Xie, X. and Shi, P-Y., 2022. Cross-neutralization and cross-protection among SARS-CoV-2 viruses bearing different variant spikes. Signal Transduct Target Ther, v. 7
Doi: 10.1038/s41392-022-01137-1

Derek Smith

Professor of Infectious Disease Informatics, Department of Zoology, and Director of Centre for Pathogen Evolution

Research Areas

Techniques

Research Theme

Publications

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

1999

1998

1997

2008

1999

2021

2017

2008

2004

2003

2001

1997

2022

Contact us

About this site

Athena Swan

athena_swan_bronze_award_logo_for_website_footer.jpg

Connect with us

x_for_website_50_x_50.png

Study at Cambridge

About the University

Research at Cambridge