Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

PLoS Computational Biology

Volumn 11, Issue 12, 2015, Pages

  Hall, Matthew ^a   Woolhouse, Mark ^a   Rambaut, Andrew ^a,b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; EPIDEMIOLOGY; MARKOV PROCESSES; TREES (MATHEMATICS);

FULLY COMPATIBLE; GENETIC DATA; INFECTIOUS DISEASE; NODE SETS; PATHOGEN POPULATIONS; PHYLOGENETIC INFERENCE; PHYLOGENETICS; PHYLOGENY RECONSTRUCTION; TRANSMISSION TREES; TREE RECONSTRUCTION;

PHYLOGENETIC;

ARTICLE; CONTROLLED STUDY; DISEASE TRANSMISSION; EPIDEMIC; INFLUENZA A (H7N7); MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MONTE CARLO METHOD; NETHERLANDS; PHYLOGENETIC TREE; PHYLOGENY; PROBABILITY; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; GENETICS; INFLUENZA A VIRUS (H7N7); INFLUENZA IN BIRDS; MARKOV CHAIN; POULTRY; PROCEDURES; SOFTWARE; VIROLOGY;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; EPIDEMICS; INFLUENZA A VIRUS, H7N7 SUBTYPE; INFLUENZA IN BIRDS; MARKOV CHAINS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; PHYLOGENY; POULTRY; SOFTWARE;

EID: 84953268887     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004613     Document Type: Article

References (54)

1. Liu J, Lim SL, Ruan Y, Ling AE, Ng LFP, Drosten C, et al. SARS transmission pattern in Singapore reassessed by viral sequence variation analysis. PLOS Med. 2005;2:e43. doi: 10.1371/journal.pmed.0020043 15736999
2. Spada E, Sagliocca L, Sourdis J, Garbuglia AR, Poggi V, Fusco CD, et al. Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection. J Clin Microbiol. 2004;42:4230–4236. doi: 10.1128/JCM.42.9.4230-4236.2004 15365016
3. Aldrin M, Lyngstad TM, Kristoffersen AB, Storvik B, Borgan Ø, Jansen PA, Modelling the spread of infectious salmon anaemia among salmon farms based on seaway distances between farms and genetic relationships between infectious salmon anaemia virus isolates. J Roy Soc Interface. 2011;8:1346–1356. doi: 10.1098/rsif.2010.0737
4. Jombart T, Eggo RM, Dodd PJ, Balloux F, Reconstructing disease outbreaks from genetic data: a graph approach. Heredity. 2011;106:383–390. doi: 10.1038/hdy.2010.78 20551981
5. Cottam EM, Thébaud G, Wadsworth J, Gloster J, Mansley L, Paton DJ, et al. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. P Roy Soc B. 2008;275:887–895. doi: 10.1098/rspb.2007.1442
6. Ypma RJF, Bataille AMA, Stegeman A, Koch G, Wallinga J, van Ballegooijen WM, Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data. P Roy Soc B. 2011;279:444–450. doi: 10.1098/rspb.2011.0913
7. Morelli MJ, Thébaud G, Chadœuf J, King DP, Haydon DT, Soubeyrand S, A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data. PLOS Comput Biol. 2012;8:e1002768. doi: 10.1371/journal.pcbi.1002768 23166481
8. Ypma RJF, Ballegooijen WMv, Wallinga J, Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics. 2013;195:1055–1062. doi: 10.1534/genetics.113.154856 24037268
9. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N, Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLOS Comput Biol. 2014;10:e1003457. doi: 10.1371/journal.pcbi.1003457
10. Didelot X, Gardy J, Colijn C, Bayesian inference of infectious disease transmission from whole genome sequence data. Mol Biol Evol. 2014;31:1869–1879. doi: 10.1093/molbev/msu121 24714079
11. Mollentze N, Nel LH, Townsend S, Roux Kl, Hampson K, Haydon DT, et al. A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data. P Roy Soc B. 2014;281:20133251. doi: 10.1098/rspb.2013.3251
12. Worby CJ, Chang HH, Hanage WP, Lipsitch M, The distribution of pairwise genetic distances: a tool for investigating disease transmission. Genetics. 2014;198:1395–1404. doi: 10.1534/genetics.114.171538 25313129
13. Stadler T, Kouyos R, von Wyl V, Yerly S, Böoni J, Bürgisser P, et al. Estimating the basic reproductive number from viral sequence data. Mol Biol Evol. 2011;29:347–357. doi: 10.1093/molbev/msr217 21890480
14. Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ, Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). P Natl Acad Sci USA 2013;110:228–233. doi: 10.1073/pnas.1207965110
15. Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T, Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol. 2014;31:6–17. doi: 10.1093/molbev/mst172 24085839
16. Kühnert D, Stadler T, Vaughan TG, Drummond AJ, Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model. J Roy Soc Interface. 2014;11:20131106. doi: 10.1098/rsif.2013.1106
17. Volz EM, Pond SLK, Ward MJ, Brown AJL, Frost SDW, Phylodynamics of infectious disease epidemics. Genetics. 2009;183:1421–1430. doi: 10.1534/genetics.109.106021 19797047
18. Bataille A, van der Meer F, Stegeman A, Koch G, Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. PLOS Pathog. 2011;7:e1002094. doi: 10.1371/journal.ppat.1002094 21731491
19. Gibson GJ, Austin EJ, Fitting and testing spatio-temporal stochastic models with application in plant epidemiology. Plant Pathol. 1996;45:172–184. doi: 10.1046/j.1365-3059.1996.d01-116.x
20. Keeling MJ, Woolhouse MEJ, Shaw DJ, Matthews L, Chase-Topping M, Haydon DT, et al. Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science. 2001;294:813–817. doi: 10.1126/science.1065973 11679661
21. Deardon R, Brooks SP, Grenfell BT, Keeling MJ, Tildesley MJ, Savill NJ, et al. Inference for individual-level models of infectious diseases in large populations. Statistica Sinica. 2010;20:239–261. 26405426
22. Drummond AJ, Suchard MA, Xie D, Rambaut A, Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–1973. doi: 10.1093/molbev/mss075 22367748
23. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002;161:1307–1320. 12136032
24. Hohna S, Defoin-Platel M, Drummond A, Clock-constrained tree proposal operators in Bayesian phylogenetic inference. 8th IEEE International Conference on BioInformatics and BioEngineering, 2008. BIBE 2008; 2008. p. 1–7.
25. Wilson IJ, Balding DJ, Genealogical inference from microsatellite data. Genetics. 1998;150:499–510. 9725864
26. Hasegawa M, Kishino H, Yano Ta, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J of Mol Evol. 1985;22:160–174. doi: 10.1007/BF02101694
27. Rodriguez F, Oliver JL, Marin A, Medina JR, The general stochastic model of nucleotide substitution. J Theor Biol. 1990;142:485–501. doi: 10.1016/S0022-5193(05)80104-3 2338834
28. Felsenstein J, Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–376. doi: 10.1007/BF01734359 7288891
29. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A, Relaxed phylogenetics and dating with confidence. PLOS Biology. 2006;4:e88. doi: 10.1371/journal.pbio.0040088 16683862
30. Slatkin M, Hudson RR, Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991;129:555–562. 1743491
31. Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH, The epidemic behavior of the hepatitis C virus. Science. 2001;292:2323–2325. doi: 10.1126/science.1058321 11423661
32. Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA, πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics. 2014;15:133. doi: 10.1186/1471-2105-15-133 24885610
33. Minin VN, Bloomquist EW, Suchard MA, Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008;25:1459–1471. doi: 10.1093/molbev/msn090 18408232
34. Whidden C, Zeh N, Beiko RG, Supertrees based on the subtree prune-and-regraft distance. Syst Biol. 2014;63:566–581. doi: 10.1093/sysbio/syu023 24695589
35. Elbers ARW, Fabri THF, Vries TSd, Wit JJd, Pijpers A, Koch G, The highly pathogenic avian influenza A (H7N7) virus epidemic in the Netherlands in 2003: lessons learned from the first five outbreaks. Avian Dis. 2004;48:691–705. doi: 10.1637/7149 15529997
36. Stegeman A, Bouma A, Elbers ARW, De Jong MCM, Nodelijk G, De Klerk F, et al. Avian influenza A virus (H7N7) epidemic in the Netherlands in 2003: course of the epidemic and effectiveness of control measures. J Infect Dis. 2004;190:2088–2095. doi: 10.1086/425583 15551206
37. Boender GJ, Hagenaars TJ, Bouma A, Nodelijk G, Elbers ARW, de Jong MCM, et al. Risk maps for the spread of highly pathogenic avian influenza in poultry. PLOS Comput Biol. 2007;3:e71. doi: 10.1371/journal.pcbi.0030071 17447838
38. Jonges M, Bataille A, Enserink R, Meijer A, Fouchier RAM, Stegeman A, et al. Comparative analysis of avian influenza virus diversity in poultry and humans during a highly pathogenic avian influenza A (H7N7) virus outbreak. J Virol. 2011;85:10598–10604. doi: 10.1128/JVI.05369-11 21849451
39. Van Borm S, Jonges M, Lambrecht B, Koch G, Houdart P, van den Berg T, Molecular epidemiological analysis of the transboundary transmission of 2003 highly pathogenic avian influenza H7N7 outbreaks between the Netherlands and Belgium. Transbound Emerg Dis. 2014;61:86–90. doi: 10.1111/tbed.12009 22994451
40. Ypma RJF, Jonges M, Bataille A, Stegeman A, Koch G, Boven Mv, et al. Genetic data provide evidence for wind-mediated transmission of highly pathogenic avian influenza. J Infect Dis. 2013;207:730–735. doi: 10.1093/infdis/jis757 23230058
41. Bogner P, Capua I, Lipman DJ, Cox NJ, et al. A global initiative on sharing avian flu data. Nature. 2006;442:981–981. doi: 10.1038/442981a
42. Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340 15034147
43. Shapiro B, Rambaut A, Drummond AJ, Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 2006;23:7–9. doi: 10.1093/molbev/msj021 16177232
44. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T, Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–2504. doi: 10.1101/gr.1239303 14597658
45. White LF, Pagano M, A likelihood-based method for real-time estimation of the serial interval and reproductive number of an epidemic. Stat Med. 2008;27:2999–3016. doi: 10.1002/sim.3136 18058829
46. Bos MEH, Boven MV, Nielen M, Bouma A, Elbers ARW, Nodelijk G, et al. Estimating the day of highly pathogenic avian influenza (H7N7) virus introduction into a poultry flock based on mortality data. Vet Res. 2007;38:493–504. doi: 10.1051/vetres:2007008 17425936
47. Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, et al. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLOS Comput Biol. 2014;10:e1003505. doi: 10.1371/journal.pcbi.1003505 24699231
48. Numminen E, Chewapreecha C, Sirén J, Turner C, Turner P, Bentley SD, et al. Two-phase importance sampling for inference about transmission trees P Roy Soc B. 2014;281:20141324. doi: 10.1098/rspb.2014.1324
49. Green PJ, Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika. 1995;82:711–732. doi: 10.1093/biomet/82.4.711
50. Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, et al. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLOS Pathog. 2012 Dec;8:e1003081. doi: 10.1371/journal.ppat.1003081 23308065
51. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. P Natl Acad Sci USA. 2008;105:7552–7557. doi: 10.1073/pnas.0802203105
52. Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, et al. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLOS Pathog. 2011 Sep;7:e1002243. doi: 10.1371/journal.ppat.1002243 21912520
53. Heled J, Drummond AJ, Calibrated tree priors for relaxed phylogenetics and divergence time estimation Syst Biol. 2012;61:138–149. doi: 10.1093/sysbio/syr087 21856631
54. Frost SDW, Volz EM, Viral phylodynamics and the search for an ‘effective number of infections’ Philos T Roy Soc B. 2010;365:1879–1890. doi: 10.1098/rstb.2010.0060