Influenza a H1N1 pandemic strain evolution - Divergence and the potential for antigenic drift variants

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Klein, Eili Y ^a,b   Serohijos, Adrian W R ^c   Choi, Jeong Mo ^c   Shakhnovich, Eugene I ^c   Pekosz, Andrew ^d  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Center for Disease Dynamics Economics and Policy   (United States)

^c HARVARD UNIVERSITY   (United States)

^d JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; EPITOPE; HEMAGGLUTININ; NUCLEOPROTEIN; NUCLEOTIDE; SIALIDASE; VIRUS ANTIGEN;

AMINO ACID SEQUENCE; ANTIGENICITY; ARTICLE; GENETIC CONSERVATION; GENETIC DRIFT; GENETIC VARIABILITY; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; VIRUS ISOLATION; VIRUS MUTATION; VIRUS STRAIN; EVOLUTION; GENETICS; HUMAN; IMMUNOLOGY; INFLUENZA, HUMAN; ISOLATION AND PURIFICATION; UNITED STATES; VIROLOGY;

ANTIGENS, VIRAL; BIOLOGICAL EVOLUTION; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; UNITED STATES;

EID: 84899463545     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093632     Document Type: Article

References (35)

1. Shinde V, Bridges CB, Uyeki TM, Shu B, Balish A, et al. (2009) Triple-Reassortant Swine Influenza A (H1) in Humans in the United States, 2005-2009. New England Journal of Medicine 360: 2616-2625.
2. Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team (2009) Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans. New England Journal of Medicine 360: 2605-2615.
3. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, et al. (2009) Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans. Science 325: 197-201.
4. Jegaskanda S, Laurie KL, Amarasena TH, Winnall WR, Kramski M, et al. (2013) Age-Associated Cross-reactive Antibody-Dependent Cellular Cytotoxicity Toward 2009 Pandemic Influenza A Virus Subtype H1N1. Journal of Infectious Diseases 208: 1051-1061.
5. Deem MW, Pan K (2009) The epitope regions of H1-subtype influenza A, with application to vaccine efficacy. Protein Engineering Design and Selection 22: 543-546.
6. Park AW, Daly JM, Lewis NS, Smith DJ, Wood JLN, et al. (2009) Quantifying the Impact of Immune Escape on Transmission Dynamics of Influenza. Science 326: 726-728.
7. Smith CB, Cox NJ, Subbarao K, Taber LH, Glezen WP (2002) Molecular Epidemiology of Influenza A(H3N2) Virus Reinfections. Journal of Infectious Diseases 185: 980-985. (Pubitemid 34274442)
8. Strengell M, Ikonen N, Ziegler T, Julkunen I (2011) Minor Changes in the Hemagglutinin of Influenza A(H1N1)2009 Virus Alter Its Antigenic Properties. PLoS ONE 6: e25848.
9. Shrestha SS, Swerdlow DL, Borse RH, Prabhu VS, Finelli L, et al. (2011) Estimating the burden of 2009 pandemic influenza A (H1N1) in the United States (April 2009-April 2010). Clinical Infectious Diseases 52: S75-S82.
10. Centers for Disease Control and Prevention (2011) Final estimates for 2009-10 Seasonal Influenza and Influenza A (H1N1) 2009 Monovalent Vaccination Coverage - United States, August 2009 through May, 2010.
11. Khandaker I, Suzuki A, Kamigaki T, Tohma K, Odagiri T, et al. (2013) Molecular evolution of the hemagglutinin and neuraminidase genes of pandemic (H1N1) 2009 influenza viruses in Sendai, Japan, during 2009-2011. Virus Genes: 1-11.
12. Makkoch J, Suwannakarn K, Payungporn S, Prachayangprecha S, Cheiocharnsin T, et al. (2012) Whole Genome Characterization, Phylogenetic and Genome Signature Analysis of Human Pandemic H1N1 Virus in Thailand, 2009-2012. PLoS ONE 7: e51275.
13. de la Rosa-Zamboni D, Vázquez-Pérez JA, Ávila-Ríos S, Carranco-Arenas AP, Ormsby CE, et al. (2012) Molecular Characterization of the Predominant Influenza A(H1N1)pdm09 Virus in Mexico, December 2011-February 2012. PLoS ONE 7: e50116.
14. Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, et al. (2012) Molecular Evolutionary Analysis of pH1N1 2009 Influenza Virus in Reunion Island, South West Indian Ocean Region: A Cohort Study. PLoS ONE 7: e43742.
15. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, et al. (2008) The Influenza Virus Resource at the National Center for Biotechnology Information. J Virol 82: 596-601.
16. Katoh K, Standley DM (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30: 772-780.
17. Katoh K, Misawa K, Kuma Ki, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066. (Pubitemid 34851225)
18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. (Pubitemid 350162903)
19. Plotkin JB, Dushoff J, Levin SA (2002) Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proceedings of the National Academy of Sciences 99: 6263-6268. (Pubitemid 34493300)
20. R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria.
21. Bush RM, Fitch WM, Bender CA, Cox NJ (1999) Positive selection on the H3 hemagglutinin gene of human influenza virus A. Molecular Biology and Evolution 16: 1457-1465. (Pubitemid 29510888)
22. Gupta V, Earl DJ, Deem MW (2006) Quantifying influenza vaccine efficacy and antigenic distance. Vaccine 24: 3881-3888. (Pubitemid 44308221)
23. Huang J-W, Lin W-F, Yang J-M (2012) Antigenic sites of H1N1 influenza virus hemagglutinin revealed by natural isolates and inhibition assays. Vaccine 30: 6327-6337.
24. Caton AJ, Brownlee GG, Yewdell JW, Gerhard W (1982) The antigenic structure of the influenza virus A/PR/8/34 hemagglutinin (H1 subtype). Cell 31: 417-427. (Pubitemid 13178866)
25. Muñoz ET, Deem MW (2005) Epitope analysis for influenza vaccine design. Vaccine 23: 1144-1148. (Pubitemid 40052010)
26. World Health Organization (2013) Recommended composition of influenza virus vaccines for use in the 2013-2014 northern hemisphere influenza season.
27. World Health Organization (2013) Recommended composition of influenza virus vaccines for use in the 2014 southern hemisphere influenza season.
28. Guarnaccia T, Carolan LA, Maurer-Stroh S, Lee RTC, Job E, et al. (2013) Antigenic Drift of the Pandemic 2009 A(H1N1) Influenza Virus in a Ferret Model. PLoS Pathog 9: e1003354.
29. Wilson IA, Cox NJ (1990) Structural basis of immune recognition of influenza virus hemagglutinin. Annual review of immunology 8: 737-787.
30. Wolf YI, Nikolskaya A, Cherry JL, Viboud C, Koonin E, et al. (2010) Projection of seasonal influenza severity from sequence and serological data. PLoS currents 2.
31. Wu A, Peng Y, Du X, Shu Y, Jiang T (2010) Correlation of influenza virus excess mortality with antigenic variation: application to rapid estimation of influenza mortality burden. PLoS computational biology 6: e1000882.
32. Centers for Disease Control and Prevention (2013) Health Advisory. Notice to Clinicians: Early Reports of pH1N1-Associated Illnesses for the 2013-14 Influenza Season. CDC Health Alert Network. December 24, 2013.
33. Ndifon W, Wingreen NS, Levin SA (2009) Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines. Proceedings of the National Academy of Sciences 106: 8701-8706.
34. Skowronski D, Chambers C, Sabaiduc S, De Serres G, Dickinson J, et al. (2014) Interim estimates of 2013/14 vaccine effectiveness against influenza A(H1N1)pdm09 from Canada's sentinel surveillance network, January 2014. Euro Surveill 19: 20690.
35. Catania J, Que LG, Govert JA, Hollingsworth JW, Wolfe CR (2014) High ICU admission rate for 2013-2014 Influenza is associated with a low rate of vaccination. American Journal of Respiratory and Critical Care Medicine.