Modelling seasonal influenza: The role of weather and punctuated antigenic drift

Journal of the Royal Society Interface

Volumn 10, Issue 84, 2013, Pages

  Yaari, R ^a   Katriel, G ^a,b   Huppert, A ^c   Axelsen, J B ^a   Stone, L ^a,d  

^a TEL AVIV UNIVERSITY   (Israel)

^b ORT BRAUDE COLLEGE   (Israel)

^c GERTNER INSTITUTE FOR EPIDEMIOLOGY AND HEALTH POLICY RESEARCH   (Israel)

^d RMIT UNIVERSITY   (Australia)

Author keywords

Antigenic drift; Epidemic modelling; Maximum likelihood; Model fitting; Seasonal influenza; Weather

Indexed keywords

DIGITAL STORAGE; MAXIMUM LIKELIHOOD; PARAMETER ESTIMATION; VIRUSES;

ABSOLUTE HUMIDITY; ANTIGENIC DRIFT; INFLUENZA TRANSMISSIONS; INTERANNUAL VARIABILITY; LIKELIHOOD FUNCTIONS; MODEL FITTING; SEASONAL INFLUENZA; WEATHER;

ANTIGENS;

ARTICLE; HUMAN; HUMIDITY; IMMUNITY; MODEL; SEASONAL INFLUENZA; SEASONAL VARIATION; TEMPERATURE; WEATHER; ANTIGENIC DRIFT; ANTIGENIC VARIATION; EPIDEMIC; EPIDEMIC MODELLING; GENETICS; IMMUNOLOGY; INFLUENZA; ISRAEL; MAXIMUM LIKELIHOOD METHOD; MODEL FITTING; MOLECULAR EVOLUTION; SEASON; SPECIES DIFFERENCE; STATISTICAL MODEL; STATISTICS; THEORETICAL MODEL;

ORTHOMYXOVIRIDAE;

ANTIGENIC DRIFT; EPIDEMIC MODELLING; MAXIMUM LIKELIHOOD; MODEL FITTING; SEASONAL INFLUENZA; WEATHER;

ANTIGENIC VARIATION; DISEASE OUTBREAKS; EVOLUTION, MOLECULAR; HUMANS; INFLUENZA, HUMAN; ISRAEL; LIKELIHOOD FUNCTIONS; MODELS, THEORETICAL; SEASONS; SPECIES SPECIFICITY; WEATHER;

EID: 84878632785     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2013.0298     Document Type: Article

References (50)

1. Simonsen L. 1999 The global impact of influenza on morbidity and mortality. Vaccine 17(Suppl. 1), S3-S10. (doi:10.1016/S0264-410X(99)00099-7)
2. Cox NJ, Subbarao K. 2000 Global epidemiology of nfluenza: past and present. Annu. Rev. Med. 51, 407-421. (doi:10.1146/annurev.med.51.1.407)
3. Earn D. 2002 Ecology and evolution of the flu. Trends Ecol. Evol. 17, 334-340. (doi:10.1016/S0169-5347(02)02502-8)
4. Huppert A, Barnea O, Katriel G, Yaari R, Roll U, Stone L. 2012 Modeling and statistical analysis of the spatio-temporal patterns of seasonal influenza in Israel. PLoS ONE 7, e45107. (doi:10.1371/journal.pone.0045107)
5. Finkenstädt BF, Morton A, Rand DA. 2005 Modelling antigenic drift in weekly flu incidence. Stat. Med. 24, 3447-3461. (doi:10.1002/sim.2196)
6. Xia Y, Gog JR, Grenfell BT. 2005 Semiparametric estimation of the duration of immunity from infectious disease time series: influenza as a case-study. J. R. Stat. Soc. C (Appl. Stat.) 54, 659-672. (doi:10.1111/j.1467- 9876.2005.05383.x)
7. Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M. 2010 Absolute humidity and the seasonal onset of influenza in the continental United States. PLoS Biol. 8, e1000316. (doi:10.1371/journal.pbio.1000316)
8. Edlund S et al. 2011 A spatiotemporal model for influenza. electronic. J. Health Inform. 6, 1-7.
9. Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly CA, Ghani A, Ferguson N. 2012 Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. J. R. Soc. Interface 9, 304-312. (doi:10.1098/rsif.2011.0309)
10. van Noort SP, Águas R, Ballesteros S, Gomes MGM. 2012 The role of weather on the relation between influenza and influenza-like illness. J. Theor. Biol. 298, 131-137. (doi:10.1016/j.jtbi.2011.12.020)
11. Nelson MI, Holmes EC. 2007 The evolution of epidemic influenza. Nat. Rev. Genet. 8, 196-205. (doi:10.1038/nrg2053)
12. Lipsitch M, Viboud C. 2009 Influenza seasonality: lifting the fog. Proc. Natl Acad. Sci. USA 106, 3645-3646. (doi:10.1073/pnas.0900933106)
13. Cauchemez S, Valleron AJ, Boëlle PY, Flahault A, Ferguson NM. 2008 Estimating the impact of school closure on influenza transmission from sentinel data. Nature 452, 750-754. (doi:10.1038/nature06732)
14. Heymann AD, Hoch I, Valinsky L, Kokia E, Steinberg DM. 2009 School closure may be effective in reducing transmission of respiratory viruses in the community. Epidemiol. Infect. 137, 1369-1376. (doi:10.1017/S0950268809002556)
15. Earn D, He D, Loeb M, Fonseca K. 2012 Effects of school closure on incidence of pandemic influenza in Alberta, Canada. Ann. Intern. Med. 156, 173-181. (doi:10.7326/0003-4819-156-3-201202070-00005)
16. Eames KTD, Tilston NL, Brooks-Pollock E, Edmunds WJ. 2012 Measured dynamic social contact patterns explain the spread of H1N1v influenza. PLoS Comput. Biol. 8, e1002425. (doi:10.1371/journal.pcbi.1002425)
17. Dowell SF. 2001 Seasonal variation in host susceptibility and cycles of certain infectious diseases. Emerg. Infect. Dis. 7, 369-374.
18. Nelson RJ, Demas GE, Klein SL, Kriegsfeld LJ, Bronson F. 2002 Seasonal patterns of stress, immune function, and disease. Cambridge, UK: Cambridge University Press.
19. Cannell JJ, Vieth R, Umhau JC, Holick MF, Grant WB, Madronich S, Garland CF, Giovannucci E. 2006 Epidemic influenza and vitamin D. Epidemiol. Infect. 134, 1129-1140. (doi:10.1017/S0950268806007175)
20. Harper GJ. 1961 Airborne micro-organisms: survival tests with four viruses. J. Hygiene 59, 479-486. (doi:10.1017/S0022172400039176)
21. Schulman JL. 1961 Experimental transmission of influenza virus infection in mice. Epidemiol. Infect. 59, 479-488.
22. Lowen A, Mubareka S, Steel J, Palese P. 2007 Influenza virus transmission is dependent on relative humidity and temperature. PLoS Pathog. 3, e151. (doi:10.1371/journal.ppat.0030151)
23. Lowen AC, Steel J, Mubareka S, Palese P. 2008 High temperature (308C) blocks aerosol but not contact transmission of influenza virus. J. Virol. 82, 5650-5652. (doi:10.1128/JVI.00325-08)
24. Shaman J, Kohn M. 2009 Absolute humidity modulates influenza survival, transmission, and seasonality. Proc. Natl Acad. Sci. USA 106, 3243-3248. (doi:10.1073/pnas.0806852106)
25. McDevitt J, Rudnick S, First M, Spengler J. 2010 Role of absolute humidity in the inactivation of influenza viruses on stainless steel surfaces at elevated temperatures. Appl. Environ. Microbiol. 76, 3943-3947. (doi:10.1128/AEM.02674-09)
26. Barreca AI, Shimshack JP. 2012 Absolute humidity, temperature, and influenza mortality: 30 years of county-level evidence from the United States. Am. J. Epidemiol. 176(Suppl. 7), S114-S122. (doi:10.1093/aje/kws259)
27. Earn DJ, Rohani P, Bolker BM, Grenfell BT. 2000 A simple model for complex dynamical transitions in epidemics. Science 287, 667-670. (doi:10.1126/science.287.5453.667)
28. Stone L, Olinky R, Huppert A. 2007 Seasonal dynamics of recurrent epidemics. Nature 446, 533-536. (doi:10.1038/nature05638)
29. Finkelman BS, Viboud C, Koelle K, Ferrari MJ, Bharti N, Grenfell BT. 2007 Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: viral coexistence and latitudinal gradients. PLoS ONE 2, e1296. (doi:10.1371/journal.pone.0001296)
30. Gog JR, Grenfell BT. 2002 Dynamics and selection of many-strain pathogens. Proc. Natl Acad. Sci. USA 99, 17 209-17 214. (doi:10.1073/pnas. 252512799)
31. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM. 2004 Mapping the antigenic and genetic evolution of influenza virus. Science 305, 371-376. (doi:10.1126/science.1097211)
32. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. 2006 Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol. Direct. 1, 34. (doi:10.1186/1745-6150-1-34)
33. Pease CM. 1987 An evolutionary epidemiological mechanism, with applications to type A influenza. Theor. Popul. Biol. 31, 422-452. (doi:10.1016/0040-5809(87)90014-1)
34. Cobey S, Koelle K. 2008 Capturing escape in infectious disease dynamics. Trends Ecol. Evol. 23, 572-577. (doi:10.1016/j.tree.2008.06.008)
35. Ionides EL, Bretó C, King AA. 2006 Inference for nonlinear dynamical systems. Proc. Natl Acad. Sci. USA 103, 18 438-18 443. (doi:10.1073/pnas.0603181103)
36. King AA, Ionides EL, Pascual M, Bouma MJ. 2008 Inapparent infections and cholera dynamics. Nature 454, 877-880. (doi:10.1038/nature07084)
37. He D, Ionides EL, King AA. 2010 Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. J. R. Soc. Interface 7, 271-283. (doi:10.1098/rsif.2009.0151)
38. Israel Center for Disease Control (ICDC). 2007 Preceding report - influenza like illness surveillance . See http://www.old.health.gov.il/Download/ pages/flu-makdim2007.pdf.
39. Israeli Meteorological Service (IMS) database. See http://data.gov.il/ ims.
40. Israel Ministry of the Environment. Air resources manager. See http://www.svivaaqm.net/Default.rtl.aspx.
41. Katriel G, Yaari R, Huppert A, Roll U, Stone L. 2011 Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study. J. R. Soc. Interface 8, 856-867. (doi:10.1098/rsif.2010.0515)
42. Katriel G. 2012 Stochastic discrete-time age-of-infection epidemic models. Int. J. Biomath. 6, 1250066. (doi:10.1142/S1793524512500660)
43. Israel Central Bureau of Statistics. 2012 Statistical abstract of Israel 2012, table 3.1. See http://www.cbs.gov.il/shnaton63/st03-01.pdf.
44. Hilborn R, Mangel M. 1997 The ecological detective: confronting models with data. Princeton, NJ: Princeton University Press.
45. Johonson JB, Omland KS. 2004 Model selection in ecology and evolution. Trends Ecol. Evol. 19, 101-108. (doi:10.1016/j.tree.2003.10.013)
46. Anderson RM, May RM. 1992 Infectious diseases of humans: dynamics and control. Oxford, UK: Oxford University Press.
47. Paget WJ, Meerhoff TJMA. 2005 Epidemiological and virological assessment of influenza activity in Europe during the 2003-2004 season. Eurosurveillance 10, 107-111.
48. Health Protection Agency (HPA). 2005 Influenza and other respiratory viruses surveillance in the United Kingdom: October 2003 to May 2004. See http://www.hpa.org.uk/cdr/archives/2005/cdr0305.pdf.
49. Centers for Disease Control and Prevention (CDC). 2004 2003-04 U.S. influenza season summary. See http://www.cdc.gov/flu/weekly/weeklyarchives2003- 2004/03-04summary.htm.
50. Shaman J, Karspeck A. 2012 Forecasting seasonal outbreaks of influenza. Proc. Natl Acad. Sci. USA 109, 20 425-20 430. (doi:10.1073/pnas.1208772109)