Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 368, Issue 1614, 2013, Pages

  Stadler, Tanja ^a   Bonhoeffer, Sebastian ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Epidemiology; Heterogeneous population; Parameter inference; Phylogenetics

Indexed keywords

EPIDEMIC; EPIDEMIOLOGY; GENETIC ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS; MAXIMUM LIKELIHOOD ANALYSIS; PATHOGEN; PHYLOGENETICS; POPULATION STRUCTURE; SEXUALLY TRANSMITTED DISEASE; SUBPOPULATION;

LATVIA;

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DISEASE TRANSMISSION; GENETICS; HETEROSEXUALITY; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LATVIA; MALE; MALE HOMOSEXUALITY; PHYLOGENY; STATISTICAL MODEL; STATISTICS; SUBSTANCE ABUSE;

COMPUTER SIMULATION; HETEROSEXUALITY; HIV INFECTIONS; HIV-1; HOMOSEXUALITY, MALE; HOST-PATHOGEN INTERACTIONS; HUMANS; LATVIA; LIKELIHOOD FUNCTIONS; MALE; MODELS, BIOLOGICAL; MODELS, GENETIC; PHYLOGENY; SUBSTANCE ABUSE, INTRAVENOUS;

MLCS; MLOWN;

EID: 84880494351     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0198     Document Type: Article

References (34)

1. Pybus O, Charleston M, Gupta S, Rambaut A, Holmes E, Harvey P. 2001 The epidemic behavior of the hepatitis C virus. Science 292, 2323. (doi:10.1126/science.1058321)
2. Smith G et al. 2009 Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. Nature 459, 1122-1125. (doi:10.1038/ nature08182)
3. Bedford T, Cobey S, Beerli P, Pascual M, Ferguson N. 2010 Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog. 6, 1220-1228. (doi:10.1371/journal.ppat.1000918)
4. Raghwani J et al. 2011 Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathog. 7, e1002064. (doi:10.1371/journal.ppat.1002064)
5. Kouyos RD et al. 2010 Swiss HIV cohort study. Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J. Infect. Dis. 201, 1488-1497. (doi:10.1086/651951)
6. Siebenga J, Lemey P, Pond S, Rambaut A, Vennema H, Koopmans M. 2010 Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog. 6, e1000884. (doi:10.1371/journal.ppat.1000884)
7. Volz E, Pond S, Ward M, Brown A, Frost S. 2009 Phylodynamics of infectious disease epidemics. Genetics 183, 1421-1430. (doi:10.1534/genetics.109.106021)
8. Stadler T. 2012 The Swiss HIV Cohort study. Estimating the basic reproductive number from viral sequence data. Mol. Biol. Evol. 29, 347-357. (doi:10.1093/molbev/msr217)
9. Rasmussen D, Ratmann O, Koelle K. 2011 Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comput. Biol. 7, e1002136. (doi:10.1371/journal. pcbi.1002136)
10. Leventhal G, Kouyos R, Stadler T, von Wyl V, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard H., Bonhoeffer S. 2012 Inferring epidemic contact structure from phylogenetic trees. PLoS Comput. Biol. 8, e1002413. (doi:10.1371/journal.pcbi.1002413)
11. Balode D, Ferdats A, Dievberna I, Viksna L, Rozentale B, Kolupajeva T, Konicheva V, Leitner T. 2004 Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. AIDS Res. Hum. Retroviruses 20, 245-249. (doi:10.1089/088922204773004978)
12. Balode D, Skar H, Mild M, Kolupajeva T, Ferdats A, Rozentale B, Leitner T, Albert J. 2012 Phylogenetic analysis of the Latvian HIV-1 epidemic. AIDS Res. Hum. Retroviruses 28, 928-932. (doi:10.1089/AID.2011.0310)
13. Stadler T. 2011 Simulating trees with a fixed number of extant species. Syst. Biol. 60, 676-684. (doi:10.1093/sysbio/syr029)
14. Stadler T. 2011 Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl Acad. Sci. USA 108, 6187-6192. (doi:10.1073/pnas.1016876108)
15. Stadler T. 2010 Sampling-through-time in birth-death trees. J. Theor. Biol. 267, 396-404. (doi:10.1016/j.jtbi.2010.09.010)
16. Anderson R, May R. 1992 Infectious diseases of humans: dynamics and control. Cambridge, MA: Oxford University Press.
17. Keeling M, Rohani P. 2008 Modeling infectious diseases in humans and animals. Princeton, NJ: Princeton University Press.
18. Maddison W. 2007 Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56, 701-710. (doi:10.1080/10635150701607033)
19. Stadler T. In press. How can we improve accuracy of macroevolutionary rate estimates? Syst. Biol. (doi:10.1093/sysbio/sys073)
20. FitzJohn R, Maddison W, Otto S. 2009 Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58, 595-611. (doi:10.1093/sysbio/syp067)
21. Magnuson-Ford K, Otto S. 2012 Linking the investigations of character evolution and species diversification. Am. Nat. 180, 225-245. (doi:10.1086/666649)
22. Goldberg EE, Igić B. 2012 Tempo and mode in plant breeding system evolution. Evolution 66, 3701-3709. (doi:10.1111/j.1558-5646.2012.01730.x)
23. Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. 2013 Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc. Natl Acad. Sci. USA 110, 228-233. (doi:10.1073/pnas.1207965110)
24. Katoh K, Toh H. 2008 Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinformatics 9, 286-298. (doi:10.1093/bib/ bbn013)
25. Drummond A, Rambaut A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
26. Lipsitch M, Herre E, Nowak M. 1995 Host population structure and the evolution of virulence: a 'law of diminishing returns'. Evolution 49, 743-748. (doi:10.2307/2410327)
27. Boots M, Hudson P, Sasaki A. 2004 Large shifts in pathogen virulence relate to host population structure. Science 303, 842-844. (doi:10.1126/ science.1088542)
28. Keeling M. 2005 The implications of network structure for epidemic dynamics. Theor. Popul. Biol. 67, 1-8. (doi:10.1016/j.tpb.2004.08.002)
29. Graw F, Leitner T, Ribeiro RM. 2012 Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia. Epidemics 4, 104-116. (doi:10.1016/j.epidem.2012.04.002)
30. Lemey P, Rambaut A, Drummond A, Suchard M. 2009 Bayesian phylogeography finds its roots. PLoS Comput. Biol. 5, e1000520. (doi:10.1371/journal. pcbi.1000520)
31. Lemey P, Rambaut A, Welch J, Suchard M. 2010 Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 27, 1877-1885. (doi:10.1093/molbev/msq067)
32. Volz E. 2012 Complex population dynamics and the coalescent under neutrality. Genetics 190, 187-201. (doi:10.1534/genetics.111.134627)
33. Rabosky D. 2007 Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60, 1152-1164. (doi:10.1111/j.0014-3820.2006. tb01194.x)
34. Etienne R, Haegeman B, Stadler T, Aze T, Pearson P, Purvis A, Phillimore A. 2012 Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. B 279, 1300-1309. (doi:10.1098/rspb.2011.1439).