Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

http://www.sciencemag.org/content/345/6202/1369.full#F1
ABSTRACT
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

Note:
– diverged from central African lineages around 2004. NO outbreaks in Zaire or between Zaire and West Africa to account for 2014 outbreak in West Africa??
– no evidence of additional zoonotic sources. No fruit bats or green monkeys then
– 7 of the researchers have since died (Mostly Ebola, 1 of stroke)

EDITOR’S SUMMARY
Evolution of Ebola virus over time
The high rate of mortality in the current Ebola epidemic has made it difficult for researchers to collect samples of the virus and study its evolution. Gire et al. describe Ebola epidemiology on the basis of 99 whole-genome sequences, including samples from 78 affected individuals. The authors analyzed changes in the viral sequence and conclude that the current outbreak probably resulted from the spread of the virus from central Africa in the past decade. The outbreak started from a single transmission event from an unknown animal reservoir into the human population. Two viral lineages from Guinea then spread from person to person into Sierra Leone.

Science, this issue p. 1369

Researchers:

  1. Stephen K. Gire1,2,*, 
  2. Augustine Goba3,*,, 
  3. Kristian G. Andersen1,2,*,, 
  4. Rachel S. G. Sealfon2,4,*, 
  5. Daniel J. Park2,*,
  6. Lansana Kanneh3, 
  7. Simbirie Jalloh3, 
  8. Mambu Momoh3,5, 
  9. Mohamed Fullah3,5,, 
  10. Gytis Dudas6, 
  11. Shirlee Wohl1,2,7,
  12. Lina M. Moses8, 
  13. Nathan L. Yozwiak1,2, 
  14. Sarah Winnicki1,2, 
  15. Christian B. Matranga2, 
  16. Christine M. Malboeuf2,
  17. James Qu2, 
  18. Adrianne D. Gladden2, 
  19. Stephen F. Schaffner1,2, 
  20. Xiao Yang2, 
  21. Pan-Pan Jiang1,2, 
  22. Mahan Nekoui1,2,
  23. Andres Colubri1, 
  24. Moinya Ruth Coomber3, 
  25. Mbalu Fonnie3,, 
  26. Alex Moigboi3,, 
  27. Michael Gbakie3, 
  28. Fatima K. Kamara3,
  29. Veronica Tucker3, 
  30. Edwin Konuwa3, 
  31. Sidiki Saffa3,, 
  32. Josephine Sellu3, 
  33. Abdul Azziz Jalloh3, 
  34. Alice Kovoma3,,
  35. James Koninga3, 
  36. Ibrahim Mustapha3, 
  37. Kandeh Kargbo3, 
  38. Momoh Foday3, 
  39. Mohamed Yillah3, 
  40. Franklyn Kanneh3,
  41. Willie Robert3, 
  42. James L. B. Massally3, 
  43. Sinéad B. Chapman2, 
  44. James Bochicchio2, 
  45. Cheryl Murphy2, 
  46. Chad Nusbaum2,
  47. Sarah Young2, 
  48. Bruce W. Birren2, 
  49. Donald S. Grant3, 
  50. John S. Scheiffelin8, 
  51. Eric S. Lander2,7,9, 
  52. Christian Happi10,
  53. Sahr M. Gevao11, 
  54. Andreas Gnirke2,§, 
  55. Andrew Rambaut6,12,13,§, 
  56. Robert F. Garry8,§, 
  57. S. Humarr Khan3,§,
  58. Pardis C. Sabeti1,2,§

Author Affiliations


  1. 1Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

  2. 2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

  3. 3Kenema Government Hospital, Kenema, Sierra Leone.

  4. 4Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

  5. 5Eastern Polytechnic College, Kenema, Sierra Leone.

  6. 6Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.

  7. 7Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

  8. 8Tulane University Medical Center, New Orleans, LA 70112, USA.

  9. 9Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

  10. 10Redeemer’s University, Ogun State, Nigeria.

  11. 11University of Sierra Leone, Freetown, Sierra Leone.

  12. 12Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.

  13. 13Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK.

Author Notes

  •  Deceased.

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