Genomic analysis of emerging pathogens: Methods, application and future trends

Genome Biology

Volumn 15, Issue 11, 2014, Pages

  Li, Lucy M ^a   Grassly, Nicholas C ^a   Fraser, Christophe ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CORONAVIRUS INFECTION; DISEASE TRANSMISSION; EBOLA HEMORRHAGIC FEVER; EBOLA VIRUS; EPIDEMIC; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME ANALYSIS; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INFECTION; INFECTION RISK; INFLUENZA VIRUS A H3N2; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NONHUMAN; PANDEMIC INFLUENZA; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION SIZE; REVIEW; RISK FACTOR; SEASONAL INFLUENZA; SEQUENCE ALIGNMENT; VIRUS GENOME; VIRUS STRAIN; VIRUS VIRULENCE; BACTERIAL GENOME; BACTERIUM; COMMUNICABLE DISEASE; GENETICS; GENOMICS; MICROBIOLOGY; PATHOGENICITY; VIROLOGY; VIRUS;

BACTERIA; COMMUNICABLE DISEASES; COMMUNICABLE DISEASES, EMERGING; GENOME, BACTERIAL; GENOME, VIRAL; GENOMICS; HUMANS; VIRUSES;

EID: 84924574262     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0541-9     Document Type: Review

References (75)

1. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P: Global trends in emerging infectious diseases. Nature 2008, 451:990-993.
2. Pulliam JR, Epstein JH, Dushoff J, Rahman SA, Bunning M, Jamaluddin AA, Hyatt AD, Field HE, Dobson AP, Daszak P: Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis. J R Soc Interface 2012, 9:89-101.
3. Wilder-Smith A, Gubler DJ: Geographic expansion of dengue: the impact of international travel. Med Clin North Am 2008, 92:1377-1390.
4. Khan K, Arino J, Hu W, Raposo P, Sears J, Calderon F, Heidebrecht C, Macdonald M, Liauw J, Chan A, Gardam M: Spread of a novel influenza A (H1N1) virus via global airline transportation. New Engl J Med 2009, 361:212-214.
5. Le Guenno B, Camprasse MA, Guilbaut JC, Lanoux P, Hoen B: Hantavirus epidemic in Europe, 1993. Lancet 1994, 343:114-115.
6. Velayati AA, Masjedi MR, Farnia P, Tabarsi P, Ghanavi J, Ziazarifi AH, Hoffner SE: Emergence of new forms of totally drug-resistant tuberculosis bacilli: super extensively drug-resistant tuberculosis or totally drug-resistant strains in Iran. Chest 2009, 136:420-425.
7. Ohnishi M, Golparian D, Shimuta K, Saika T, Hoshina S, Iwasaku K, Nakayama S, Kitawaki J, Unemo M: Is Neisseria gonorrhoeae initiating a future era of untreatable gonorrhea?: Detailed characterization of the first strain with high-level resistance to ceftriaxone. Antimicrob Agents Chemother 2011, 55:3538-3545.
8. Anderson RM, May RM: Infectious Diseases of Humans: Dynamics and Control, Volume 28. Oxford: Oxford University Press; 1991.
9. Grassly NC, Fraser C: Mathematical models of infectious disease transmission. Nat Rev Microbiol 2008, 6:477-487.
10. Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A: Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009, 459:1122-1125.
11. Cottam EM, Haydon DT, Paton DJ, Gloster J, Wilesmith JW, Ferris NP, Hutchings GH, King DP: Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. J Virology 2006, 80:11274-11282.
12. Kingman JF: On the genealogy of large populations. J Appl Probability 1982, 19:27-43.
13. Drummond AJ, Rambaut A, Shapiro B, Pybus OG: Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005, 22:1185-1192.
14. Stadler T: Sampling-through-time in birth-death trees. J Theor Biol 2010, 267:396-404.
15. Stadler T, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond AJ, Bonhoeffer S, Swiss HIV Cohort Study: Estimating the basic reproductive number from viral sequence data. Mol Biol Evol 2012, 29:347-357.
16. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC: Unifying the epidemiological and evolutionary dynamics of pathogens. Science 2004, 303:327-332.
17. Rasmussen DA, Ratmann O, Koelle K: Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comput Biol 2011, 7:1002136.
18. Ypma RJ, van Ballegooijen WM, Wallinga J: Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics 2013, 195:1055-1062.
19. Felsenstein J: Inferring Phylogenies. Sunderland, MA: Sinauer Associates; 2004.
20. Cottam EM, Thébaud G, Wadsworth J, Gloster J, Mansley L, Paton DJ, King DP, Haydon DT: Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc Biol Sci 2008, 275:887-895.
21. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P: Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. New Engl J Med 2011, 364:730-739.
22. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG: Measurably evolving populations. Trends Ecol Evol 2003, 18:481-488.
23. Ho SY, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A: Time-dependent rates of molecular evolution. Mol Ecol 2011, 20:3087-3101.
24. Thorne JL, Kishino H, Painter IS: Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 1998, 15:1647-1657.
25. Yoder AD, Yang Z: Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol 2000, 17:1081-1090.
26. Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214.
27. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012, 61:539-542.
28. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC: The genomic and epidemiological dynamics of human influenza A virus. Nature 2008, 453:615-619.
29. Volz EM, Ionides E, Romero-Severson EO, Brandt M-G, Mokotoff E, Koopman JS: HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis. PLoS Med 2013, 10:1001568.
30. Rasmussen DA, Boni MF, Koelle K: Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Mol Biol Evol 2014, 31:258-271.
31. 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 R Soc Interface 2014, 11:20131106.
32. Volz EM: Complex population dynamics and the coalescent under neutrality. Genetics 2012, 190:187-201.
33. Frost SD, Volz EM: Modelling tree shape and structure in viral phylodynamics. Philos Trans R Soc London B Biol Sci 2013, 368:20120208.
34. Rasmussen DA, Volz EM, Koelle K: Phylodynamic inference for structured epidemiological models. PLoS Comput Biol 2014, 10:1003570.
35. Volz EM, Pond SLK, Ward MJ, Brown AJL, Frost SD: Phylodynamics of infectious disease epidemics. Genetics 2009, 183:1421-1430.
36. Volz EM, Koopman JS, Ward MJ, Brown AL, Frost SD: Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol 2012, 8:1002552.
37. Koelle K, Rasmussen DA: Rates of coalescence for common epidemiological models at equilibrium. J R Soc Interface 2012, 9:997-1007.
38. Stadler T, Bonhoeffer S: Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci 2013, 368:20120198.
39. Stadler T, Yang Z: Dating phylogenies with sequentially sampled tips. Syst Biol 2013, 62:674-688.
40. Stadler T, Kuhnert D, Bonhoeffer S, Drummond AJ: Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc Natl Acad Sci U S A 2013, 110:228-233.
41. Magiorkinis G, Sypsa V, Magiorkinis E, Paraskevis D, Katsoulidou A, Belshaw R, Fraser C, Pybus OG, Hatzakis A: Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics. PLoS Comput Biol 2013, 9:1002876.
42. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz W: Superspreading and the effect of individual variation on disease emergence. Nature 2005, 438:355-359.
43. Wallinga J, Lipsitch M: How generation intervals shape the relationship between growth rates and reproductive numbers. Proc R Soc Biol Sci 2007, 274:599-604.
44. Svensson Å: A note on generation times in epidemic models. Math Biosci 2007, 208:300-311.
45. Kenah E, Lipsitch M, Robins JM: Generation interval contraction and epidemic data analysis. Math Biosci 2008, 213:71-79.
46. Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P: HIV epidemiology. The early spread and epidemic ignition of hiv-1 in human populations. Science 2014, 346:56-61.
47. Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD: Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biol 2014, 12:49.
48. Bedford T, Cobey S, Beerli P, Pascual M: Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog 2010, 6:1000918.
49. Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JS, Riley S, Rambaut A, Holmes EC, Smith GJ: Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci U S A 2011, 108:19359-19364.
50. Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SY, Shapiro B, Pybus OG, Allain J-P, Hatzakis A: The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med 2009, 6:1000198.
51. Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, et al: A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res 2013, 23:653-664.
52. Didelot X, Gardy J, Colijn C: Bayesian inference of infectious disease transmission from whole genome sequence data. Mol Biol Evol 2014, 31:1869-1879.
53. Grassly NC, Harvey PH, Holmes EC: Population dynamics of hiv-1 inferred from gene sequences. Genetics 1999, 151:427-438.
54. 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.
55. Strimmer K, Pybus OG: Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 2001, 18:2298-2305.
56. Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keïta S, De Clerck H, Tiffany A, Dominguez G, Loua M, Traoré A, Kolié M, Malano ER, Heleze E, Bocquin A, Mély S, Raoul H, Caro V, Cadar D, Gabriel M, Pahlmann M, Tappe D, Schmidt-Chanasit J, Impouma B, Diallo AK, Formenty P, Van Herp M, et al: Emergence of Zaire Ebola virus disease in Guinea-preliminary report. New Engl J Med 2014, 371:1418-1425.
57. Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang P-P, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, et al: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014, 345:1369-1372.
58. Dudas G, Rambaut A: Phylogenetic analysis of Guinea 2014 EBOV Ebolavirus outbreak. PLoS Curr 2014, 6
59. Center for Disease Control and Prevention: Middle East Respiratory Virus (MERS). 2014, [ http://www.cdc.gov/coronavirus/mers/ ]
60. Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enou V, van der Werf S, Ferguson NM: Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. Lancet Infect Dis 2014, 14:50-56.
61. Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, Alhakeem R, Durosinloun A, Al Asmari M, Islam A, Kapoor A, Briese T, Daszak P, Al Rabeeah AA, Lipkin WI: Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerg Infect Dis 2013, 19:1819-1823.
62. Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R, Godeke GJ, Jonges M, Farag E, Diab A, Ghobashy H, Alhajri F, Al-Thani M, Al-Marri SA, Al Romaihi HE, Al Khal A, Bermingham A, Osterhaus AD, AlHajri MM, Koopmans MP: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014, 14:140-145.
63. Azhar EI, Hashem AM, El-Kafrawy SA, Sohrab SS, Aburizaiza AS, Farraj SA, Hassan AM, Al-Saeed MS, Jamjoom GA, Madani TA: Detection of the Middle East respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient. Mbio 2014, 5:e01450-14.
64. Corman VM, Ithete NL, Richards LR, Schoeman MC, Preiser W, Drosten C, Drexler JF: Rooting the phylogenetic tree of Middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat. J Virol 2014, 88:11297-11303.
65. Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Alpuche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C, WHO Rapid Pandemic Assessment Collaboration: Pandemic potential of a strain of influenza A (H1N1): early findings. Science 2009, 324:1557-1561.
66. Hedge J, Lycett S, Rambaut A: Real-time characterization of the molecular epidemiology of an influenza pandemic. Biol Lett 2013, 9:20130331.
67. Wilson DJ: Insights from genomics into bacterial pathogen populations. PLoS Pathog 2012, 8:1002874.
68. Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ: Whole-genome sequencing for analysis of an outbreak of methicillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 2013, 13:130-136.
69. Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme A-M, Van Laethem K, Lemey P: The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates. PLoS Comput Biol 2014, 10:1003505.
70. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E: Equation of state calculations by fast computing machines. J Chem Phys 2004, 21:1087-1092.
71. Fisher RA: The Genetical Theory of Natural Selection. Oxford: Clarendon; 1930.
72. Wright S: Evolution in Mendelian populations. Genetics 1931, 16:97-159.
73. Griffiths RC, Tavare S: Sampling theory for neutral alleles in a varying environment. Phil Trans R Soc Lond Biol Sci 1994, 344:403-410.
74. Pybus OG, Rambaut A, Harvey PH: An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 2000, 155:1429-1437.
75. 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.