Models for predicting the evolution of influenza to inform vaccine strain selection

References

• Carrat F, Flahault A. Influenza vaccine: The challenge of antigenic drift. Vaccine. 2007;25:6852–62. doi:10.1016/j.vaccine.2007.07.027
   PubMed Web of Science ®Google Scholar
• World Health Organization. Seasonal Influenza. Available at http://www.who.int/mediacentre/factsheets/fs211/en, 2016.
   Google Scholar
• Beire B, Bauer B, Schweiger B. Differentiation of influenza B virus lineages Yamagata and Victoria by real-time PCR. J Clin Microbiol. 2010;48(4):1425–27. doi:10.1128/JCM.02116-09
   PubMed Web of Science ®Google Scholar
• Grohskopf LA, Olsen SJ, Sokolow LZ, Bresee JS, Cox NJ, Broder KR, Karron RA, Walter EB. Prevention and control of seasonal influenza with vaccines: Recommendations of the advisory committee on immunization practices (ACIP) – United States, 2014–15 influenza season. MMWR Morb Mortal Wkly Rep. 2014;63(32):691–7.
   PubMed Web of Science ®Google Scholar
• Koelle K, Rasmussen DA. Influenza: Prediction is worth a shot. Nature. 2014;506(7490):47–49. doi:10.1038/nature13054
   PubMedGoogle Scholar
• Dos Santos G, Neumeier E, Bekkat-Berkani R. Influenza: Can we cope better with the unpredictable?. Hum Vaccin Immunother. 2016;12(3):699–708. doi:10.1080/21645515.2015.1086047
   PubMed Web of Science ®Google Scholar
• World Health Organization. Manual for the laboratory diagnosis and virological surveillance of influenza. Available at http://www.who.int/influenza/gisrs_laboratory/manual_diagnosis_surveillance_influenza/en, 2011.
   Google Scholar
• Xie H, Wan X-F, Ye Z, Plant EP, Zhao Y, Xu Y, Li X, Finch C, Zhao N, Kawano T, et al. H3N2 mismatch of 2014–15 Northern Hemisphere influenza vaccines and head-to-head comparison between human and ferret antisera derived antigenic maps. Sci Rep. 2015;5:15279. doi:10.1038/srep15279
   Google Scholar
• Centers for Disease Control and Prevention. Seasonal Influenza Vaccine Effectiveness, 2005–2015. Available at http://www.cdc.gov/flu/professionals/vaccination/effectiveness-studies.htm, 2015.
   Google Scholar
• Sun H, Yang J, Zhang T, Long P, Jia K, Yang G, Webby R, Wan X. Using sequence data to infer the antigenicity of influenza virus. mBio. 2013;4(4):e00230–13. doi:10.1128/mBio.00230-13
   PubMed Web of Science ®Google Scholar
• Özaltın OY, Prokopyev OA, Schaefer AJ. Optimal design of the seasonal influenza vaccine with manufacturing autonomy. Forthcoming at INFORMS Journal on Computing. 2017.
   Google Scholar
• Neher R, Bedford T. nextflu: Real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics. 2015;31(21):3546–48. doi:10.1093/bioinformatics/btv381
   PubMed Web of Science ®Google Scholar
• Choi JH, Jung HY, Kim HS, Cho HG. PhyloDraw: A phylogenetic tree drawing system. Bioinformatics. 2000;16(11):1056–58.
   PubMed Web of Science ®Google Scholar
• Gouy M, Guidon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27(2):221–4.
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. Interactive tree of life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics. 2006;23(1):127–8.
   PubMed Web of Science ®Google Scholar
• Price MN, Dehal PS, Arkin AP. FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–50. doi:10.1093/molbev/msp077
   PubMed Web of Science ®Google Scholar
• Shimodaira H, Hasegawa M. CONSEL: For assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001;17(12):1246–7.
   PubMed Web of Science ®Google Scholar
• Thorley JL, Page RD. RadCon: Phylogenetic tree comparison and consensus. Bioinformatics. 2000;16(5):486–7.
   PubMed Web of Science ®Google Scholar
• Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood. Bioinformatics. 1997;13(5):555–6.
   Google Scholar
• Bedford T, Neher R. Seasonal Influenza Circulation Patterns and Projections for 2017–2018. Available at http://www.biorxiv.org/content/early/2017/03/02/113035, 2017.
   Google Scholar
• Steinbrück L, McHardy AC. Allele dynamics plots for the study of evolutionary dynamics in viral populations. Nucleic Acids Res. 2011;39(1):e4. doi:10.1093/nar/gkq909
   PubMed Web of Science ®Google Scholar
• Smith DJ, Lapedes AS, Jong J, Bestebroer TM, Rimmelzwaan GF, Osterhaus A, Fouchier R. Mapping the antigenic and genetic evolution of influenza virus. Science. 2004;305(5682):371–6.
   PubMed Web of Science ®Google Scholar
• Cai Z, Zhang T, Wan X-F. A computational framework for influenza antigenic cartography. PLoS Comput Biol. 2010;6(10):e1000949. doi:10.1371/journal.pcbi.1000949
   PubMed Web of Science ®Google Scholar
• Food and Drug Administration. Vaccines and Related Biological Products Advisory Committee. Available at http://www.fda.gov/cber/advisory/vrbp/vrbpmain.htm, 2017.
   Google Scholar
• He J, Deem MW. Low-dimensional clustering detects incipient dominant influenza strain clusters. Protein Eng Des Sel. 2010;23(12):935–46. doi:10.1093/protein/gzq078
   PubMed Web of Science ®Google Scholar
• Everitt BS, Landau S, Leese M. Cluster Analysis, 5th ed. London: John Wiley & Sons, Ltd; 2011.
   Google Scholar
• Lapedes A, Farber R. The geometry of shape space: Application to influenza. J Theor Biol. 2001;212(1):57–69. doi:10.1006/jtbi.2001.2347
   PubMed Web of Science ®Google Scholar
• Steinbrück L, McHardy AC. Inference of genotype-phenotype relationships in the antigenic evolution of human influenza A (H3N2) viruses. PLoS Comput Biol. 2012;8(4):e1002492. doi:10.1371/journal.pcbi.1002492
   PubMed Web of Science ®Google Scholar
• Steinbrück L, Klingen TR, McHardy AC. Computational prediction of vaccine strains for human influenza A (H3N2) viruses. J Virol. 2014;88(20):12123–32. doi:10.1128/JVI.01861-14
   PubMed Web of Science ®Google Scholar
• Neher R, Russell C, Shraiman B. Predicting evolution from the shape of genealogical trees. eLife. 2014;3:e03568. doi:10.7554/eLife.03568
   PubMed Web of Science ®Google Scholar
• Neher R, Bedford T, Daniels R, Russell C, Shraiman B. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proc Natl Acad Sci. 2016;113(12):E1701–E1709. doi:10.1073/pnas.1525578113
   PubMed Web of Science ®Google Scholar
• Łuksza M, Lässig M. A predictive fitness model for influenza. Nature. 2014;507(7490):57–61. doi:10.1038/nature13087
   PubMed Web of Science ®Google Scholar
• Wilson IA, Cox NJ. Structural basis of immune recognition of influenza virus hemagglutinin. Annu Rev Immunol. 1990;8(1):737–87. doi:10.1146/annurev.iy.08.040190.003513
   PubMedGoogle Scholar
• Lee M-S, Chen J. Predicting antigenic variants of influenza A/H3N2 viruses. Emerg Infect Dis. 2004;10(8):1385. doi:10.3201/eid1008.040107
   PubMed Web of Science ®Google Scholar
• Lee M-S, Chen M-C, Liao Y-C, Hsiung CA. Identifying potential immunodominant positions and predicting antigenic variants of influenza A/H3N2 viruses. Vaccine. 2007;25(48):8133–39. doi:10.1016/j.vaccine.2007.09.039
   PubMed Web of Science ®Google Scholar
• Liao Y-C, Lee M-S, Ko C-Y, Hsiung CA. Bioinformatics models for predicting antigenic variants of influenza A/ H3N2 virus. Bioinformatics. 2008;24(4):505–12.
   PubMed Web of Science ®Google Scholar
• Lee EK, Nakaya HI, Yuan F, Querec TD, Burel G, Pietz FH, Benecke BA, Pulendran B. Machine learning for predicting vaccine immunogenicity. Interfaces. 2016;46(5):368–90.
   Web of Science ®Google Scholar
• Guyon I, Elisseeff A. An introduction to variable and feature selection. J Mach Learn Res. 2003;3(Mar):1157–82.
   Google Scholar
• Huang C-L, Wang C-J. A GA-based feature selection and parameters optimization for support vector machines. Expert Syst Appl. 2006;31(2):231–40.
   Web of Science ®Google Scholar
• Siedlecki W, Sklansky J. A note on genetic algorithms for large-scale feature selection. Pattern Recognit Lett. 1989;10(5):335–47.
   Web of Science ®Google Scholar
• Belser JA, Katz JM, Tumpey TM. The ferret as a model organism to study influenza A virus infection. Dis Model Mech. 2011;4(5):575–9. doi:10.1242/dmm.007823
   PubMed Web of Science ®Google Scholar
• Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, et al. Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses. Vaccine. 2008;26:D31–D34.
   PubMed Web of Science ®Google Scholar
• Lee M-S, Yang C-F. Cross-reactive H1N1 antibody responses to a live attenuated influenza vaccine in children: implication for selection of vaccine strains. J Infect Dis. 2003;188(9):1362–6. doi:10.1086/379045
   PubMed Web of Science ®Google Scholar
• Li Y, Myers JL, Bostick DL, Sullivan CB, Madara J, Linderman SL, Liu Q, Carter DM, Wrammert J, Esposito S, et al. Immune history shapes specificity of pandemic H1N1 influenza antibody responses. J Exp Med. 2013;210(8):1493–1500. doi:10.1084/jem.20130212
   PubMed Web of Science ®Google Scholar
• Xie H, Li L, Ye Z, Li X, Plant EP, Zoueva O, Zhao Y, Jing X, Lin Z, Kawano T, et al. Differential effects of prior influenza exposures on H3N2 cross-reactivity of human postvaccination sera. Clin Infect Dis. 2017;65(2):259–67. doi:10.1093/cid/cix269
   PubMed Web of Science ®Google Scholar
• McLean HQ, Thompson MG, Sundaram ME, Meece JK, McClure DL, Friedrich TC, Belongia EA. Impact of repeated vaccination on vaccine effectiveness against influenza A (H3N2) and B during 8 seasons. Clin Infect Dis. 2014;59(10):1375–85. doi:10.1093/cid/ciu680
   PubMed Web of Science ®Google Scholar
• Ohmit SE, Petrie JG, Malosh RE, Fry AM, Thompson MG, Monto AS. Influenza vaccine effectiveness in households with children during the 2012–2013 season: assessments of prior vaccination and serologic susceptibility. J Infect Dis. 2014;211(10):1519–28. doi:10.1093/infdis/jiu650
   PubMed Web of Science ®Google Scholar
• Saito N, Komori K, Suzuki M, Morimoto K, Kishikawa T, Yasaka T, Ariyoshi K. Negative impact of prior influenza vaccination on current influenza vaccination among people infected and not infected in prior season: A test-negative case-control study in Japan. Vaccine. 2017;35(4):687–93.
   PubMed Web of Science ®Google Scholar