Genetic diversity of hemagglutinin gene of A(H1N1)pdm09 influenza strains isolated in Taiwan and its potential impact on HA-neutralizing epitope interaction

References

• Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, Garten RJ, Gubareva LV, Xu X, Bridges CB, Uyeki TM, Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 2009; 360:2605 - 15; http://dx.doi.org/10.1056/NEJMoa0903810; PMID: 19423869
   PubMed Web of Science ®Google Scholar
• Naffakh N, van der Werf S. April 2009: an outbreak of swine-origin influenza A(H1N1) virus with evidence for human-to-human transmission. Microbes Infect 2009; 11:725 - 8; http://dx.doi.org/10.1016/j.micinf.2009.05.002; PMID: 19442755
   PubMed Web of Science ®Google Scholar
• Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009; 459:1122 - 5; http://dx.doi.org/10.1038/nature08182; PMID: 19516283
   PubMed Web of Science ®Google Scholar
• Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009; 325:197 - 201; http://dx.doi.org/10.1126/science.1176225; PMID: 19465683
   PubMed Web of Science ®Google Scholar
• Neumann G, Noda T, Kawaoka Y. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009; 459:931 - 9; http://dx.doi.org/10.1038/nature08157; PMID: 19525932
   PubMed Web of Science ®Google Scholar
• Shinde V, Bridges CB, Uyeki TM, Shu B, Balish A, Xu X, Lindstrom S, Gubareva LV, Deyde V, Garten RJ, et al. Triple-reassortant swine influenza A (H1) in humans in the United States, 2005-2009. N Engl J Med 2009; 360:2616 - 25; http://dx.doi.org/10.1056/NEJMoa0903812; PMID: 19423871
   PubMed Web of Science ®Google Scholar
• Skehel JJ, Wiley DC. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem 2000; 69:531 - 69; http://dx.doi.org/10.1146/annurev.biochem.69.1.531; PMID: 10966468
   PubMed Web of Science ®Google Scholar
• Barr IG, Cui L, Komadina N, Lee RT, Lin RT, Deng Y, Caldwell N, Shaw R, Maurer-Stroh S. A new pandemic influenza A(H1N1) genetic variant predominated in the winter 2010 influenza season in Australia, New Zealand and Singapore. Euro Surveill 2010; 15:19692; PMID: 21034722
   PubMedGoogle Scholar
• Gupta V, Earl DJ, Deem MW. Quantifying influenza vaccine efficacy and antigenic distance. Vaccine 2006; 24:3881 - 8; http://dx.doi.org/10.1016/j.vaccine.2006.01.010; PMID: 16460844
   PubMed Web of Science ®Google Scholar
• http://www.nimr.mrc.ac.uk/who-influenza-centre/annual-and-interim-reports/
   Google Scholar
• Morens DM, Taubenberger JK, Fauci AS. The 2009 H1N1 pandemic influenza virus: what next?. MBio 2010; 1:e00211 - 10; http://dx.doi.org/10.1128/mBio.00211-10; PMID: 20877580
   PubMedGoogle Scholar
• Pajak B, Stefanska I, Łepek K, Donevski S, Romanowska M, Szeliga M, Brydak LB, Szewczyk B, Kucharczyk K. Rapid differentiation of mixed influenza A/H1N1 virus infections with seasonal and pandemic variants by multitemperature single-stranded conformational polymorphism analysis. J Clin Microbiol 2011; 49:2216 - 21; http://dx.doi.org/10.1128/JCM.02567-10; PMID: 21471335
   PubMed Web of Science ®Google Scholar
• Deem MW, Pan K. The epitope regions of H1-subtype influenza A, with application to vaccine efficacy. Protein Eng Des Sel 2009; 22:543 - 6; http://dx.doi.org/10.1093/protein/gzp027; PMID: 19578121
   PubMed Web of Science ®Google Scholar
• Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol 2008; 9:1 - 15; http://dx.doi.org/10.1186/1471-2172-9-1; PMID: 18211710
   PubMed Web of Science ®Google Scholar
• Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, et al. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses 2012; 6:404 - 16; http://dx.doi.org/10.1111/j.1750-2659.2011.00331.x; PMID: 22260278
   PubMed Web of Science ®Google Scholar
• Corti D, Voss J, Gamblin SJ, Codoni G, Macagno A, Jarrossay D, Vachieri SG, Pinna D, Minola A, Vanzetta F, et al. A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 2011; 333:850 - 6; http://dx.doi.org/10.1126/science.1205669; PMID: 21798894
   PubMed Web of Science ®Google Scholar
• Fleury D, Daniels RS, Skehel JJ, Knossow M, Bizebard T. Structural evidence for recognition of a single epitope by two distinct antibodies. Proteins 2000; 40:572 - 8; http://dx.doi.org/10.1002/1097-0134(20000901)40:4<572::AID-PROT30>3.0.CO;2-N; PMID: 10899782
   PubMed Web of Science ®Google Scholar
• Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 2006; 7:339; http://dx.doi.org/10.1186/1471-2105-7-339; PMID: 16836757
   PubMed Web of Science ®Google Scholar
• Gigant B, Fleury D, Bizebard T, Skehel JJ, Knossow M. Crystallization and preliminary X-ray diffraction studies of complexes between an influenza hemagglutinin and Fab fragments of two different monoclonal antibodies. Proteins 1995; 23:115 - 7; http://dx.doi.org/10.1002/prot.340230113; PMID: 8539243
   PubMed Web of Science ®Google Scholar
• Knossow M, Skehel JJ. Variation and infectivity neutralization in influenza. Immunology 2006; 119:1 - 7; http://dx.doi.org/10.1111/j.1365-2567.2006.02421.x; PMID: 16925526
   PubMed Web of Science ®Google Scholar
• Fleury D, Barrère B, Bizebard T, Daniels RS, Skehel JJ, Knossow M. A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site. Nat Struct Biol 1999; 6:530 - 4; http://dx.doi.org/10.1038/9299; PMID: 10360354
   PubMedGoogle Scholar
• Fleury D, Wharton SA, Skehel JJ, Knossow M, Bizebard T. Antigen distortion allows influenza virus to escape neutralization. Nat Struct Biol 1998; 5:119 - 23; http://dx.doi.org/10.1038/nsb0298-119; PMID: 9461077
   PubMedGoogle Scholar
• Zhou H, Pophale R, Deem MW. Chapter 10: Computer-associated vaccine design. Influenza: Molecular Virology, Caister Academic Press 2009; 173-191.
   Google Scholar
• Pan K, Subieta KC, Deem MW. A novel sequence-based antigenic distance measure for H1N1, with application to vaccine effectiveness and the selection of vaccine strains. Protein Eng Des Sel 2011; 24:291 - 9; http://dx.doi.org/10.1002/1522-2683(200109)22:16<3539::AID-ELPS3539>3.0.CO;2-T; PMID: 11669539
   PubMed Web of Science ®Google Scholar
• Kaczanowski R, Trzeciak L, Kucharczyk K. Multitemperature single-strand conformation polymorphism. Electrophoresis 2001; 22:3539 - 45; http://dx.doi.org/10.1002/1522-2683(200109)22:16<3539::AID-ELPS3539>3.0.CO;2-T; PMID: 11669539
   PubMed Web of Science ®Google Scholar
• Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74:5463 - 7; http://dx.doi.org/10.1073/pnas.74.12.5463; PMID: 271968
   PubMed Web of Science ®Google Scholar
• Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 2006; 7:339; http://dx.doi.org/10.1186/1471-2105-7-339; PMID: 16836757
   PubMed Web of Science ®Google Scholar