Human influenza virus commonly causes disease in the winter months of temperate countries, but exhibits more complex patterns in tropical localities. Most studies of this complex seasonality have only considered viruses sampled within the “normal” influenza season. To help reveal the drivers of influenza seasonality we utilized viruses sampled outside of the normal influenza season, focusing on Australia which is characterized by a wide range of climates. Using a phylogenetic approach we revealed more complex patterns of influenza transmission than previously anticipated, particularly that the virus is able to transmit for extended periods and even persist locally within Australia throughout the virus “off-season”. In addition, we found that inter-seasonal influenza was more frequent in tropical and sub-tropical than temperate regions, adding weight to theories that climate likely plays an important role in influenza seasonality.
Vyšlo v časopise: Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence. PLoS Pathog 11(6): e32767. doi:10.1371/journal.ppat.1004991 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004991
1. Nelson MI, Holmes EC. The evolution of epidemic influenza. Nat Rev Genet. 2007; 8 : 196–205. 17262054
2. Viboud C, Alonso WJ, Simonsen L. Influenza in tropical regions. PLoS Med. 2006; 3: e89. 16509764
3. Wong CM, Yang L, Chan KP, Leung GM, Chan KH, Guan Y, et al. Influenza-associated hospitalization in a subtropical city. PLoS Med. 2006; 3: e121. 16515368
4. Laguna-Torres VA, Gómez J, Ocaña V, Aguilar P, Saldarriaga T, Chavez E, et al. Influenza-like illness sentinel surveillance in Peru. PLoS One. 2009; 4: e6118. doi: 10.1371/journal.pone.0006118 19568433
5. Bloom-Feschbach K, Alonso WJ, Charu V, Tamerius J, Simonsen L, Miller MA, Viboud C. Latitudinal variations in seasonal activity of influenza and respiratory syncytial virus (RSV): a global comparative review. PLoS One. 2013; 8: e54445. doi: 10.1371/journal.pone.0054445 23457451
6. Tamerius J, Nelson MI, Zhou SZ, Viboud C, Miller MA, Alonso WJ. Global influenza seasonality: Reconciling patterns across temperate and tropical regions. Environ Health Perspect. 2011; 119 : 439–445. doi: 10.1289/ehp.1002383 21097384
7. Dowell SF. Seasonal variation in host susceptibility and cycles of certain infectious diseases. Emerg Infect Dis. 2001; 7 : 369–374. 11384511
8. Viboud C, Boëlle P-Y, Cauchemez S, Lavenu A, Valleron A-J, Flahault A, Carrat F. Risk factors of influenza transmission in households. Brit J Gen Prac. 2004; 54 : 684–689.
9. Lofgren E, Fefferman NH, Naumov YN, Gorski J, Naumova EN. Influenza seasonality: underlying causes and modeling theories. J Virol. 2007; 81 : 5429–5436. 17182688
10. Cauchemez S, Valleron A-J, Boelle P-Y, Flahault A, Ferguson NM. Estimating the impact of school closure on influenza transmission from sentinel data. Nature. 2008; 452 : 750–754. doi: 10.1038/nature06732 18401408
11. Lowen AC, Steel J. Roles of humidity and temperature in shaping influenza seasonality. J Virol. 2014; 88 : 7692–7695. doi: 10.1128/JVI.03544-13 24789791
12. Lowen AC, Mubareka S, Steel J, Palese P. Influenza virus transmission is dependent on relative humidity and temperature. PLoS Pathog. 2007; 3: e151.
13. Shaman J, Kohn M. Absolute humidity modulates influenza survival, transmission, and seasonality. Proc Natl Acad Sci. 2009; 106 : 3243–3248. doi: 10.1073/pnas.0806852106 19204283
14. Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, et al. Stochastic processes are key determinants of short-term evolution in influenza A virus. PLoS Pathog. 2006; 2: e125. 17140286
15. Kelly HA, Grant KA, Tay EL, Franklin L, Hurt AC. The significance of increased influenza notifications during spring and summer of 2010–11 in Australia. Influenza Other Respir Viruses. 2013; 7 : 1136–1141. doi: 10.1111/irv.12057 23176174
16. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, et al. The global circulation of seasonal influenza A (H3N2) viruses. Science. 2008; 320 : 340–346. doi: 10.1126/science.1154137 18420927
17. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature. 2008; 453 : 615–659. doi: 10.1038/nature06945 18418375
18. Nelson MI, Njouom R, Viboud C, Niang MND, Kadjo H, Ampofo W, et al. Multiyear persistence of 2 pandemic A/H1N1 influenza virus lineages in West Africa. J Infect Dis. 2014; 210 : 121–125. 24446525
19. Le MQ, Lam HM, Cuong VD, Lam TTY, Halpin RA, Wentworth DE, et al. Migration and persistence of human influenza A viruses, Vietnam, 2001–2008. Emerg Infect Dis. 2013; 19 : 1756–1765. doi: 10.3201/eid1911.130349 24188643
20. Li X, Zhang Z, Yu A, Ho SYW, Carr MJ, Zheng W, et al. Global and local persistence of influenza A(H5N1) virus. Emerg Infect Dis. 2014; 20 : 1287–1295. doi: 10.3201/eid2008.130910 25061965
21. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog. 2007; 3 : 1220–8. 17941707
22. Fitch WM, Bush RM, Bender CA, Cox NJ. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci. 1997; 94 : 7712–7718. 9223253
23. Ghedin E, Wentworth DE, Halpin RA, Lin X, Bera J, DePasse J, et al. Unseasonal transmission of H3N2 influenza A virus during the swine-origin H1N1 pandemic. J Virol. 2010; 84 : 5715–5718. doi: 10.1128/JVI.00018-10 20237080
24. Tay EL, Grant K, Kirk M, Mounts A, Kelly H. Exploring a proposed WHO method to determine thresholds for seasonal influenza surveillance. PLoS One. 2013; 8: e77244. doi: 10.1371/journal.pone.0077244 24146973
25. Bureau of Meteorology. Climate classification maps: Australian Government; 2012 Available at: http://www.bom.gov.au/jsp/ncc/climate_averages/climate-classifications/index.jsp?maptype=kpngrp-glance. Accessed 03/06/2014.
26. Australian Bureau of Statistics. ABS Catalogue No. 1301.0, Year Book Australia. In: Pink B, editor. Canberra, Australia: Australian Bureau of Statistics; 2012.
27. Deng YM, Caldwell N, Barr IG. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing. PLoS One. 2011; 6: e23400. doi: 10.1371/journal.pone.0023400 21886790
28. Katoh K, Misawa K, Kuma Ki, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acid Res. 2002; 30 : 3059–3066.
29. Stamatakis A. RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30 : 1312–1313. doi: 10.1093/bioinformatics/btu033 24451623
30. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59 : 307–321. doi: 10.1093/sysbio/syq010 20525638
31. Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 1993; 42 : 182–192.
32. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, George KS, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 2005; 3: e300. 16026181
33. World Health Organization. Manual for the laboratory diagnosis and virological surveillance of influenza. Available at: http://whqlibdoc.who.int/publications/2011/9789241548090_eng.pdf. Accessed 13/08/2014.
34. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature. 2005; 437 : 1162–1166. 16208317
35. Hufnagel L, Brockmann D, Geisel T. Forecast and control of epidemics in a globalized world. Proc Natl Acad Sci. 2004; 101 : 15124–15129. 15477600
36. Nelson MI, Spiro DJ, Wentworth DE, Fan J, Beck ET, St. George K, et al. The early diversification of influenza A/H1N1pdm. PLoS Currents: Influenza. 2009; doi: 10.1371/currents.RRN1126
37. Shaman J, Goldstein E, Lipsitch M. Absolute humidity and pandemic versus epidemic influenza. Am J Epidemiol. 2010; 173 : 127–135. doi: 10.1093/aje/kwq347 21081646
38. Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M. Absolute humidity and the seasonal onset of influenza in the continental United States. PLoS Biol. 2010 : 8: e1000316. doi: 10.1371/journal.pbio.1000316 20186267
39. Tamerius JD, Shaman J, Alonso WJ, Bloom-Feshbach K, Uejio CK, Comrie A, Viboud C. Environmental predictors of seasonal influenza epidemics across temperate and tropical climates. PLoS Pathog. 2013; 9:e1003194. doi: 10.1371/journal.ppat.1003194 23505366
40. Chowell G, Miller MA, Viboud C. Seasonal influenza in the United States, France, and Australia: transmission and prospects for control. Epidemiol Infect. 2008; 136 : 852–864. 17634159
41. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, et al. Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci USA. 2011; 108 : 19359–19364. doi: 10.1073/pnas.1109314108 22084096
42. Sullivan SG, Chilver MB-N, Higgins G, Cheng AC, Stocks NP. Influenza vaccine effectiveness in Australia: results from the Australian Sentinel Practices Research Network. Med J Aus. 2014; 201 : 109–111.
43. Sullivan SG, Tay EL, Kelly H. Variable definitions of the influenza season and their impact on vaccine effectiveness estimates. Vaccine. 2013; 31 : 4280–4283. doi: 10.1016/j.vaccine.2013.06.103 23850417
Zvýšte si kvalifikáciu online z pohodlia domova
Nemáte účet? Registrujte sa
Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
