Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 48, 2011, Pages 19359-19364

  Bahl, Justin ^a,b   Nelson, Martha I ^c   Chan, Kwok H ^a   Chen, Rubing ^d   Vijaykrishna, Dhanasekaran ^a,b   Halpin, Rebecca A ^e   Stockwell, Timothy B ^e   Lin, Xudong ^e   Wentworth, David E ^e   Ghedin, Elodie ^e,f   Guan, Yi ^a   Peiris, J S Malik ^a,g   Riley, Steven ^h,i   Rambaut, Andrew ^c,j   Holmes, Edward C ^c,k   Smith, Gavin J D ^a,b  

^a THE UNIVERSITY OF HONG KONG   (Hong Kong)

^b DUKE NUS MEDICAL SCHOOL   (Singapore)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

^e J CRAIG VENTER INSTITUTE   (United States)

^f UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^g HKU PASTEUR RESEARCH CENTRE   (Hong Kong)

^h UNIVERSITY OF HONG KONG   (Hong Kong)

ⁱ IMPERIAL COLLEGE LONDON   (United Kingdom)

^j UNIVERSITY OF EDINBURGH   (United Kingdom)

^k PENNSYLVANIA STATE UNIVERSITY   (United States)

more..

Author keywords

Evolution; Molecular epidemiology; Phylogeography; Source sink

Indexed keywords

ARTICLE; AUSTRALIA; BAYES THEOREM; DISEASE SURVEILLANCE; EPIDEMIC; EUROPE; GENE SEQUENCE; HONG KONG; HUMAN; INFLUENZA; INFLUENZA VIRUS A H3N2; JAPAN; METAPOPULATION; MIGRATION; NEW ZEALAND; NONHUMAN; PHYLOGEOGRAPHY; PRIORITY JOURNAL; SEASONAL POPULATION DYNAMICS; SEROPREVALENCE; SOUTHEAST ASIA; UNITED STATES; VIRUS ISOLATION; VIRUS TRANSMISSION;

ASIA; AUSTRALASIA; BASE SEQUENCE; BAYES THEOREM; DEMOGRAPHY; DISEASE OUTBREAKS; EUROPE; EVOLUTION, MOLECULAR; GENETIC VARIATION; HUMANS; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; MODELS, BIOLOGICAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NEW YORK; PHYLOGEOGRAPHY; POPULATION DYNAMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEASONS; SEQUENCE ANALYSIS, DNA;

EID: 82755190600     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1109314108     Document Type: Article

References (27)

1. Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8:196-205.
2. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC (2007) Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 3:1220-1228. (Pubitemid 47510275)
3. Rambaut A, et al. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615-619. (Pubitemid 351769300)
4. Koelle K, Cobey S, Grenfell B, Pascual M (2006) Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314:1898-1903. (Pubitemid 46026107)
5. Nelson MI, et al. (2006) Stochastic processes are key determinants of short-term evolution in influenza A virus. PLoS Pathog 2(12):e125.
6. Viboud C, Alonso WJ, Simonsen L (2006) Influenza in tropical regions. PLoS Med 3(4):e89.
7. Population Division of the Department of Economic and Social Affairs of the United Nations Secretariat. (2009) World Urbanization Prospects: The 2009 Revision Population Database. http://esa.un.org/wup2009/unup/. Accessed October 25, 2011.
8. Wong CM, et al. (2006) Influenza-associated hospitalization in a subtropical city. PLoS Med 3(4):e121.
9. Chew FT, Doraisingham S, Ling AE, Kumarasinghe G, Lee BW (1998) Seasonal trends of viral respiratory tract infections in the tropics. Epidemiol Infect 121:121-128. (Pubitemid 28423337)
10. Lee VJ, et al. (2007) Influenza pandemics in Singapore, a tropical, globally connected city. Emerg Infect Dis 13:1052-1057. (Pubitemid 47048078)
11. Russell CA, et al. (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science 320:340-346. (Pubitemid 351555652)
12. Bedford T, Cobey S, Beerli P, Pascual M (2010) Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog 6:e1000918.
13. World Health Organization (2003) Severe acute respiratory syndrome (SARS): Status of the outbreak and lessons for the immediate future. Available at http://www.who.int/csr/media/sars-wha.pdf. Accessed October 25, 2011.
14. Hufnagel L, Brockmann D, Geisel T (2004) Forecast and control of epidemics in a globalized world. Proc Natl Acad Sci USA 101:15124-15129. (Pubitemid 39391729)
15. Parker J, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty. Infect Genet Evol 8:239-246. (Pubitemid 351597657)
16. Smith GJD, et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-1125.
17. Minin VN, Bloomquist EW, Suchard MA (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25:1459-1471. (Pubitemid 351882020)
18. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLOS Comput Biol 5(9):e1000520.
19. Shaman J, Kohn M (2009) Absolute humidity modulates influenza survival, transmission, and seasonality. Proc Natl Acad Sci USA 106:3243-3248.
20. Tamerius J, et al. (2010) Global influenza seasonality: Reconciling patterns across temperate and tropical regions. Environ Health Perspect 119:439-445.
21. Lipsitch M, Viboud C (2009) Influenza seasonality: Lifting the fog. Proc Natl Acad Sci USA 106:3645-3646.
22. Pulliam HR (1988) Sources, sinks and population regulation. Am Nat 132:652-661.
23. Barr IG, et al. (2010) Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: Basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season. Vaccine 28:1156-1167.
24. Bao Y, et al. (2008) The influenza virus resource at the National Center for Biotechnology Information. J Virol 82:596-601.
25. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4(5):e88.
26. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
27. Shapiro B, Rambaut A, Drummond AJ (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23:7-9. (Pubitemid 41785947)