Projection of seasonal influenza severity from sequence and serological data

PLoS Currents

Volumn , Issue DEC, 2010, Pages 1-20

  Wolf, Yuri ^a   Nikolskaya, Anastasia ^b   Cherry, Joshua L ^b   Viboud, Cecile ^a   Koonin, Eugene ^b   Lipman, David J ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873430970     PISSN: None     EISSN: 21573999     Source Type: Journal    
DOI: 10.1371/currents.RRN1200     Document Type: Article

References (56)

1. Kilbourne ED. The molecular epidemiology of influenza. J Infect Dis. 1973 Apr;127(4):478-87. PubMed PMID: 4121053.
2. Torrens J. Influenza: its sequelae and treatment. Br Med J. 1934 Feb 17;1(3815):274-276. PubMed PMID: 20778073; PubMed Central PMCID: PMC2444160.
3. Francis T Jr, Salk JJ, Quilligan JJ Jr. Experience with vaccination against influenza in the spring of 1947; a preliminary report. Am J Public Health. 1947 Aug;37(8):1013-6. PubMed PMID: 20256594.
4. Salk JE, Suriano PC. Importance of antigenic composition of influenza virus vaccine in protecting against the natural disease; observations during the winter of 1947-1948. Am J Public Health Nations Health. 1949 Mar;39(3):345-55. PubMed PMID: 18124075; PubMed Central PMCID: PMC1527846.
5. Langmuir AD, Henderson DA, Serfling RE. The epidemiological basis for the control of influenza. Am J Public Health Nations Health. 1964 Apr;54:563-71. PubMed PMID: 14136320; PubMed Central PMCID: PMC1254817.
6. McLaren C, Potter CW, Jennings R. Immunity to influenza in ferrets. XI. Cross-immunity between A/Hong Kong/68 and A/England/72 viruses: serum antibodies produced by infection or immunization. J Hyg (Lond). 1974 Dec;73(3):389-99. PubMed PMID: 4531448; PubMed Central PMCID: PMC2130465.
7. Park AW, Daly JM, Lewis NS, Smith DJ, Wood JL, Grenfell BT. Quantifying the impact of immune escape on transmission dynamics of influenza. Science. 2009 Oct 30;326(5953):726-8. PubMed PMID: 19900931.
8. Potter CW, Jennings R, Nicholson K, Tyrrell DA, Dickinson KG. Immunity to attenuated influenza virus WRL 105 infection induced by heterologous, inactivated influenza A virus vaccines. J Hyg (Lond). 1977 Dec;79(3):321-32. PubMed PMID: 270523; PubMed Central PMCID: PMC2129958.
9. Larson HE, Tyrrell DA, Bowker CH, Potter CW, Schild GC. Immunity to challenge in volunteers vaccinated with an inactivated current or earlier strain of influenza A(H3N2). J Hyg (Lond). 1978 Apr;80(2):243-8. PubMed PMID: 632564; PubMed Central PMCID: PMC2129992.
10. Jefferson T, Smith S, Demicheli V, Harnden A, Rivetti A, Di Pietrantonj C. Assessment of the efficacy and effectiveness of influenza vaccines in healthy children: systematic review. Lancet. 2005 Feb 26-Mar 4;365(9461):773-80. Review. PubMed PMID: 15733718.
11. Basta NE, Halloran ME, Matrajt L, Longini IM Jr. Estimating influenza vaccine efficacy from challenge and community-based study data. Am J Epidemiol. 2008 Dec 15;168(12):1343-52. Epub 2008 Oct 29. Review. PubMed PMID: 18974084; PubMed Central PMCID: PMC2638553.
12. Gupta V, Earl DJ, Deem MW. Quantifying influenza vaccine efficacy and antigenic distance. Vaccine. 2006 May 1;24(18):3881-8. Epub 2006 Jan 19. PubMed PMID: 16460844.
13. Gill PW, Murphy AM. Naturally acquired immunity to influenza type A: a further prospective study. Med J Aust. 1977 Dec 3;2(23):761-5. PubMed PMID: 611373.
14. Wu A, Peng Y, Du X, Shu Y, Jiang T. Correlation of influenza virus excess mortality with antigenic variation: application to rapid estimation of influenza mortality burden. PLoS Comput Biol. 2010 Aug 12;6(8). pii: e1000882. PubMed PMID: 20711361; PubMed Central PMCID: PMC2920844.
15. Simonsen L, Clarke MJ, Williamson GD, Stroup DF, Arden NH, Schonberger LB. The impact of influenza epidemics on mortality: introducing a severity index. Am J Public Health. 1997 Dec;87(12):1944-50. Epidemiology. 1997 Jul;8(4):390-5.
16. United States Centers for Disease Control
17. Simonsen L, Reichert TA, Viboud C, Blackwelder WC, Taylor RJ, Miller MA. Impact of influenza vaccination on seasonal mortality in the US elderly population. Arch Intern Med. 2005 Feb 14;165(3):265-72. PubMed PMID: 15710788.
18. Viboud C, Bjørnstad ON, Smith DL, Simonsen L, Miller MA, Grenfell BT. Synchrony, waves, and spatial hierarchies in the spread of influenza. Science. 2006 Apr 21;312(5772):447-51. Epub 2006 Mar 30. PubMed PMID: 16574822.
19. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. The influenza virus resource at the National Center for Biotechnology Information. J Virol. 2008 Jan;82(2):596-601. Epub 2007 Oct 17. PubMed PMID: 17942553; PubMed Central PMCID: PMC2224563.
20. Supp1_USA. H3N2. Isolates. Used. txt
21. Supp2_HK. H3N2. Isolates. Used. txt
22. SH. Isolates. Used. txt
23. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004 Aug 19;5:113. PubMed PMID: 15318951; PubMed Central PMCID: PMC517706.
24. Wiley DC, Wilson IA, Skehel JJ. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature. 1981 Jan 29;289(5796):373-8. PubMed PMID: 6162101.
25. Muñoz ET, Deem MW. Epitope analysis for influenza vaccine design. Vaccine. 2005 Jan 19;23(9):1144-8. PubMed PMID: 15629357.
26. Supp3__for_HI_Assay_Data
27. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Fouchier RA. Mapping the antigenic and genetic evolution of influenza virus. Science. 2004 Jul 16;305(5682):371-6. Epub 2004 Jun 24. PubMed PMID: 15218094.
28. Efron B. The Jackknife, the Bootstrap, and Other Resampling Plans. CBMS-NSF Regional Conference Series in Applied Mathematics 38, Society for Industrial Mathematics, ISBN: 978-0898711790, 1987
29. Hong Kong Centre for Health Protection
30. Shu YL, Fang LQ, de Vlas SJ, Gao Y, Richardus JH, Cao WC. Dual seasonal patterns for influenza, China. Emerg Infect Dis. 2010 Apr;16(4):725-6. PubMed PMID: 20350403.
31. Leo YS, Lye DC, Chow A. Influenza in the tropics. Lancet Infect Dis. 2009 Aug;9(8):457-8. PubMed PMID: 19628167.
32. Projection. Panama. for2003. Isolates. Used. txt
33. Projection. Fujian. for2003. Isolates. Used. txt
34. HA1. H3N2.2009. Tree. txt
35. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct. 2006 Oct 26;1:34. PubMed PMID: 17067369; PubMed Central PMCID: PMC1647279.
36. Season. Series. Data. xls
37. Shaman J, Pitzer V, Viboud C, Lipsitch M, Grenfell B. Absolute humidity and the seasonal onset of influenza in the continental US. PLoS Curr. 2009 Dec 18:RRN1138. Update in: PLoS Biol. 2010 Feb;8(2):e1000316. PubMed PMID: 20066155; PubMed Central PMCID: PMC2803311.
38. Tellier R. Aerosol transmission of influenza A virus: a review of new studies. J R Soc Interface. 2009 Dec 6;6 Suppl 6:S783-90. Epub 2009 Sep 22. Review. PubMed PMID: 19773292; PubMed Central PMCID: PMC2843947.
39. Shaman J, Kohn M. Absolute humidity modulates influenza survival, transmission, and seasonality. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3243-8. Epub 2009 Feb 9. PubMed PMID: 19204283; PubMed Central PMCID: PMC2651255.
40. du Prel JB, Puppe W, Gröndahl B, Knuf M, Weigl JA, Schaaff F, Schmitt HJ. Are meteorological parameters associated with acute respiratory tract infections? Clin Infect Dis. 2009 Sep 15;49(6):861-8. PubMed PMID: 19663691.
41. Anestad G, Nordbo SA. Interference between outbreaks of respiratory viruses. Euro Surveill. 2009 Oct 15;14(41):19359. Erratum in: Euro Surveill. 2009;14(42). pii: 19367. PubMed PMID: 19883536.
42. Greer RM, McErlean P, Arden KE, Faux CE, Nitsche A, Lambert SB, Nissen MD, Sloots TP, Mackay IM. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections? J Clin Virol. 2009 May;45(1):10-5. Epub 2009 Apr 18. PubMed PMID: 19376742.
43. Glezen WP, Paredes A, Taber LH. Influenza in children. Relationship to other respiratory agents. JAMA. 1980 Apr 4;243(13):1345-9. PubMed PMID: 6244421.
44. Anestad G. Interference between outbreaks of respiratory syncytial virus and influenza virus infection. Lancet. 1982 Feb 27;1(8270):502. PubMed PMID: 6121154.
45. Sonoguchi T, Sakoh M, Kunita N, Satsuta K, Noriki H, Fukumi H. Reinfection with influenza A (H2N2, H3N2, and H1N1) viruses in soldiers and students in Japan. J Infect Dis. 1986 Jan;153(1):33-40. PubMed PMID: 3941288.
46. Sonoguchi T, Naito H, Hara M, Takeuchi Y, Fukumi H. Cross-subtype protection in humans during sequential, overlapping, and/or concurrent epidemics caused by H3N2 and H1N1 influenza viruses. J Infect Dis. 1985 Jan;151(1):81-8. PubMed PMID: 3965596.
47. Epstein SL. Prior H1N1 influenza infection and susceptibility of Cleveland Family Study participants during the H2N2 pandemic of 1957: an experiment of nature. J Infect Dis. 2006 Jan 1;193(1):49-53. Epub 2005 Nov 21. PubMed PMID: 16323131.
48. Finkelman BS, Viboud C, Koelle K, Ferrari MJ, Bharti N, Grenfell BT. Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: viral coexistence and latitudinal gradients. PLoS One. 2007 Dec 12;2(12):e1296. PubMed PMID: 18074020; PubMed Central PMCID: PMC2117904.
49. Shen J, Ma J, Wang Q. Evolutionary trends of A(H1N1) influenza virus hemagglutinin since 1918. PLoS One. 2009 Nov 17;4(11):e7789. PubMed PMID: 19924230; PubMed Central PMCID: PMC2773012.
50. Memoli MJ, Jagger BW, Dugan VG, Qi L, Jackson JP, Taubenberger JK. Recent human influenza A/H3N2 virus evolution driven by novel selection factors in addition to antigenic drift. J Infect Dis. 2009 Oct 15;200(8):1232-41. PubMed PMID: 19743921; PubMed Central PMCID: PMC2778484.
51. Hensley SE, Das SR, Bailey AL, Schmidt LM, Hickman HD, Jayaraman A, Viswanathan K, Raman R, Sasisekharan R, Bennink JR, Yewdell JW. Hemagglutinin receptor binding avidity drives influenza A virus antigenic drift. Science. 2009 Oct 30;326(5953):734-6. PubMed PMID: 19900932; PubMed Central PMCID: PMC2784927.
52. Chen Z, Zhou H, Jin H. The impact of key amino acid substitutions in the hemagglutinin of influenza A (H3N2) viruses on vaccine production and antibody response. Vaccine. 2010 May 28;28(24):4079-85. PubMed PMID: 20399830.
53. Asaoka N, Tanaka Y, Sakai T, Fujii Y, Ohuchi R, Ohuchi M. Low growth ability of recent influenza clinical isolates in MDCK cells is due to their low receptor binding affinities. Microbes Infect. 2006 Feb;8(2):511-9. Epub 2005 Oct 18. PubMed PMID: 16300986.
54. Liao YC, Lee MS, Ko CY, Hsiung CA. Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus. Bioinformatics. 2008 Feb 15;24(4):505-12. Epub 2008 Jan 10. PubMed PMID: 18187440.
55. http://edition.cnn.com/2003/HEALTH/12/13/sprj.flu03.vaccine/index.html
56. MMWR report; Influenza Activity--United States and Worldwide, 13 Jun-25 Sep 2010