Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence
Zoe Patterson Ross, Naomi Komadina, Yi-Mo Deng, Natalie Spirason, Heath A Kelly, Sheena G Sullivan, Ian G Barr, Edward C Holmes, Zoe Patterson Ross, Naomi Komadina, Yi-Mo Deng, Natalie Spirason, Heath A Kelly, Sheena G Sullivan, Ian G Barr, Edward C Holmes
Abstract
The factors that determine the characteristic seasonality of influenza remain enigmatic. Current models predict that occurrences of influenza outside the normal surveillance season within a temperate region largely reflect the importation of viruses from the alternate hemisphere or from equatorial regions in Asia. To help reveal the drivers of seasonality we investigated the origins and evolution of influenza viruses sampled during inter-seasonal periods in Australia. To this end we conducted an expansive phylogenetic analysis of 9912, 3804, and 3941 hemagglutinnin (HA) sequences from influenza A/H1N1pdm, A/H3N2, and B, respectively, collected globally during the period 2009-2014. Of the 1475 viruses sampled from Australia, 396 (26.8% of Australian, or 2.2% of global set) were sampled outside the monitored temperate influenza surveillance season (1 May - 31 October). Notably, rather than simply reflecting short-lived importations of virus from global localities with higher influenza prevalence, we documented a variety of more complex inter-seasonal transmission patterns including "stragglers" from the preceding season and "heralds" of the forthcoming season, and which included viruses sampled from clearly temperate regions within Australia. We also provide evidence for the persistence of influenza B virus between epidemic seasons, in which transmission of a viral lineage begins in one season and continues throughout the inter-seasonal period into the following season. Strikingly, a disproportionately high number of inter-seasonal influenza transmission events occurred in tropical and subtropical regions of Australia, providing further evidence that climate plays an important role in shaping patterns of influenza seasonality.
Conflict of interest statement
The authors have declared that no competing interests exist.
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References
- Nelson MI, Holmes EC. The evolution of epidemic influenza. Nat Rev Genet. 2007; 8: 196–205.
- Viboud C, Alonso WJ, Simonsen L. Influenza in tropical regions. PLoS Med. 2006; 3: e89
- 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
- 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 10.1371/journal.pone.0006118
- 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 10.1371/journal.pone.0054445
- 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. 10.1289/ehp.1002383
- Dowell SF. Seasonal variation in host susceptibility and cycles of certain infectious diseases. Emerg Infect Dis. 2001; 7: 369–374.
- 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.
- Lofgren E, Fefferman NH, Naumov YN, Gorski J, Naumova EN. Influenza seasonality: underlying causes and modeling theories. J Virol. 2007; 81: 5429–5436.
- 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. 10.1038/nature06732
- Lowen AC, Steel J. Roles of humidity and temperature in shaping influenza seasonality. J Virol. 2014; 88: 7692–7695. 10.1128/JVI.03544-13
- Lowen AC, Mubareka S, Steel J, Palese P. Influenza virus transmission is dependent on relative humidity and temperature. PLoS Pathog. 2007; 3: e151.
- Shaman J, Kohn M. Absolute humidity modulates influenza survival, transmission, and seasonality. Proc Natl Acad Sci. 2009; 106: 3243–3248. 10.1073/pnas.0806852106
- 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
- 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. 10.1111/irv.12057
- 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. 10.1126/science.1154137
- 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. 10.1038/nature06945
- 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.
- 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. 10.3201/eid1911.130349
- 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. 10.3201/eid2008.130910
- 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.
- 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.
- 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. 10.1128/JVI.00018-10
- 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 10.1371/journal.pone.0077244
- Bureau of Meteorology. Climate classification maps: Australian Government; 2012 Available at: . Accessed 03/06/2014.
- Australian Bureau of Statistics. ABS Catalogue No. 1301.0, Year Book Australia. In: Pink B, editor. Canberra, Australia: Australian Bureau of Statistics; 2012.
- Deng YM, Caldwell N, Barr IG. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing. PLoS One. 2011; 6: e23400 10.1371/journal.pone.0023400
- 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.
- Stamatakis A. RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30: 1312–1313. 10.1093/bioinformatics/btu033
- 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. 10.1093/sysbio/syq010
- Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 1993; 42: 182–192.
- 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
- World Health Organization. Manual for the laboratory diagnosis and virological surveillance of influenza. Available at: . Accessed 13/08/2014.
- 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.
- Hufnagel L, Brockmann D, Geisel T. Forecast and control of epidemics in a globalized world. Proc Natl Acad Sci. 2004; 101: 15124–15129.
- 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; 10.1371/currents.RRN1126
- Shaman J, Goldstein E, Lipsitch M. Absolute humidity and pandemic versus epidemic influenza. Am J Epidemiol. 2010; 173: 127–135. 10.1093/aje/kwq347
- 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 10.1371/journal.pbio.1000316
- 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 10.1371/journal.ppat.1003194
- 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.
- 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. 10.1073/pnas.1109314108
- 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.
- Sullivan SG, Tay EL, Kelly H. Variable definitions of the influenza season and their impact on vaccine effectiveness estimates. Vaccine. 2013; 31: 4280–4283. 10.1016/j.vaccine.2013.06.103
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