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Nature. 2021 Sep;597(7877):539-543. doi: 10.1038/s41586-021-03901-9. Epub 2021 Sep 15.

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks.

Nature

Alpha Kabinet Keita, Fara R Koundouno, Martin Faye, Ariane Düx, Julia Hinzmann, Haby Diallo, Ahidjo Ayouba, Frederic Le Marcis, Barré Soropogui, Kékoura Ifono, Moussa M Diagne, Mamadou S Sow, Joseph A Bore, Sebastien Calvignac-Spencer, Nicole Vidal, Jacob Camara, Mamadou B Keita, Annick Renevey, Amadou Diallo, Abdoul K Soumah, Saa L Millimono, Almudena Mari-Saez, Mamadou Diop, Ahmadou Doré, Fodé Y Soumah, Kaka Kourouma, Nathalie J Vielle, Cheikh Loucoubar, Ibrahima Camara, Karifa Kourouma, Giuditta Annibaldis, Assaïtou Bah, Anke Thielebein, Meike Pahlmann, Steven T Pullan, Miles W Carroll, Joshua Quick, Pierre Formenty, Anais Legand, Karla Pietro, Michael R Wiley, Noel Tordo, Christophe Peyrefitte, John T McCrone, Andrew Rambaut, Youssouf Sidibé, Mamadou D Barry, Madeleine Kourouma, Cé D Saouromou, Mamadou Condé, Moussa Baldé, Moriba Povogui, Sakoba Keita, Mandiou Diakite, Mamadou S Bah, Amadou Sidibe, Dembo Diakite, Fodé B Sako, Fodé A Traore, Georges A Ki-Zerbo, Philippe Lemey, Stephan Günther, Liana E Kafetzopoulou, Amadou A Sall, Eric Delaporte, Sophie Duraffour, Ousmane Faye, Fabian H Leendertz, Martine Peeters, Abdoulaye Toure, N' Faly Magassouba

Affiliations

  1. Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea. [email protected].
  2. TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France. [email protected].
  3. Laboratoire du Projet des Fièvres Hémorragiques de Guinée (PFHG), Conakry, Guinea.
  4. Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.
  5. Institut Pasteur de Dakar (IPD), Dakar, Senegal.
  6. Robert Koch Institute (RKI), Berlin, Germany.
  7. German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
  8. UK Health Security Agency, National Infection Service, Porton Down, Salisbury, UK.
  9. Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea.
  10. TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France.
  11. Ecole Nationale Supérieure de Lyon, Lyon, France.
  12. Hôpital National Donka, Service des Maladies Infectieuses et Tropicales, Conakry, Guinea.
  13. Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  14. Institut National de Santé Publique de Guinée (INSP), Conakry, Guinea.
  15. World Health Organization (WHO), Conakry, Guinea.
  16. Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  17. Health Emergencies Program, World Health Organization (WHO), Geneva, Switzerland.
  18. PraesensBio, Lincoln, NE, USA.
  19. University of Nebraska Medical Center, Omaha, NE, USA.
  20. Institut Pasteur de Guinée, Conakry, Guinea.
  21. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  22. Hôpital Régional de Nzérékoré, Nzérékoré, Guinea.
  23. Agence Nationale de Sécurité Sanitaire, Conakry, Guinea.
  24. Direction Nationale des Laboratoires, Ministère de la Santé, Conakry, Guinea.
  25. Université Gamal Abdel Nasser de Conakry, Conakry, Guinea.
  26. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
  27. Infectious Diseases Departement, University Hospital Montpellier, Montpellier, France.

PMID: 34526718 DOI: 10.1038/s41586-021-03901-9

Abstract

Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak-between 14 February and 19 June 2021-near the epicentre of the previous epidemic

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

References

  1. Baize, S. et al. Emergence of Zaire Ebola virus disease in Guinea. N. Engl. J. Med. 371, 1418–1425 (2014). - PubMed
  2. World Health Organization. 2016 Situation Report: Ebola Virus Disease (World Health Organization, 2016). - PubMed
  3. Malvy, D., McElroy, A. K., de Clerck, H., Günther, S. & van Griensven, J. Ebola virus disease. Lancet 393, 936–948 (2019). - PubMed
  4. Mbala-Kingebeni, P. et al. Rapid confirmation of the Zaire Ebola virus in the outbreak of the Equateur Province in the Democratic Republic of Congo: implications for public health interventions. Clin. Infect. Dis. 68, 330–333 (2019). - PubMed
  5. Mbala-Kingebeni, P. et al. 2018 Ebola virus disease outbreak in Equateur Province, Democratic Republic of the Congo: a retrospective genomic characterization. Lancet Infect. Dis. 19, 641–647 (2019). - PubMed
  6. Pigott, D. M. et al. Mapping the zoonotic niche of Ebola virus disease in Africa. eLife 3, e04395 (2014). - PubMed
  7. Diallo, B. et al. Resurgence of Ebola virus disease in Guinea linked to a survivor with virus persistence in seminal fluid for more than 500 days. Clin. Infect. Dis. 63, 1353–1356 (2016). - PubMed
  8. Sissoko, D. et al. Ebola virus persistence in breast milk after no reported illness: a likely source of virus transmission from mother to child. Clin. Infect. Dis. 64, 513–516 (2017). - PubMed
  9. Keita, A. K. et al. A 40-month follow-up of Ebola virus disease survivors in Guinea (PostEbogui) reveals long-term detection of Ebola viral ribonucleic acid in semen and breast milk. Open Forum Infect. Dis. 6, ofz482 (2019). - PubMed
  10. Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016). - PubMed
  11. Diehl, W. E. et al. Ebola virus glycoprotein with increased infectivity dominated the 2013–2016 epidemic. Cell 167, 1088–1098.e6 (2016). - PubMed
  12. Urbanowicz, R. A. et al. Human adaptation of Ebola virus during the West African outbreak. Cell 167, 1079–1087.e5 (2016). - PubMed
  13. Blackley, D. J. et al. Reduced evolutionary rate in reemerged Ebola virus transmission chains. Sci. Adv. 2, e1600378 (2016). - PubMed
  14. Diallo, M. S. K. et al. Understanding the long-term evolution and predictors of sequelae of Ebola virus disease survivors in Guinea: a 48-month prospective, longitudinal cohort study (PostEboGui). Clin. Infect. Dis. https://doi.org/10.1093/cid/ciab168 (2021). - PubMed
  15. Etard, J. F. et al. Multidisciplinary assessment of post-Ebola sequelae in Guinea (PostEboGui): an observational cohort study. Lancet Infect. Dis. 17, 545–552 (2017). - PubMed
  16. PREVAIL III Study Group. A longitudinal study of Ebola sequelae in Liberia. N. Engl. J. Med. 380, 924–934 (2019). - PubMed
  17. Diallo, M. S. K. et al. Prevalence of infection among asymptomatic and paucisymptomatic contact persons exposed to Ebola virus in Guinea: a retrospective, cross-sectional observational study. Lancet Infect. Dis. 19, 308–316 (2019). - PubMed
  18. Glynn, J. R. et al. Asymptomatic infection and unrecognised Ebola virus disease in Ebola-affected households in Sierra Leone: a cross-sectional study using a new non-invasive assay for antibodies to Ebola virus. Lancet Infect. Dis. 17, 645–653 (2017). - PubMed
  19. Camara, I. et al. Unrecognized Ebola virus infection in Guinea: complexity of surveillance in a health crisis situation: case report. Pan Afr. Med. J. 36, 201 (2020). - PubMed
  20. Thorson, A. E. et al. Persistence of Ebola virus in semen among Ebola virus disease survivors in Sierra Leone: a cohort study of frequency, duration, and risk factors. PLoS Med. 18, e1003273 (2021). - PubMed
  21. Fischer, W. A. et al. Ebola virus ribonucleic acid detection in semen more than two years after resolution of acute Ebola virus infection. Open Forum Infect. Dis. 4, ofx155 (2017). - PubMed
  22. Sissoko, D. et al. Persistence and clearance of Ebola virus RNA from seminal fluid of Ebola virus disease survivors: a longitudinal analysis and modelling study. Lancet Glob. Health 5, e80–e88 (2017). - PubMed
  23. Mate, S. E. et al. Molecular evidence of sexual transmission of Ebola virus. N. Engl. J. Med. 373, 2448–2454 (2015). - PubMed
  24. Dokubo, E. K. et al. Persistence of Ebola virus after the end of widespread transmission in Liberia: an outbreak report. Lancet Infect. Dis. 18, 1015–1024 (2018). - PubMed
  25. Liu, W. J. et al. Comprehensive clinical and laboratory follow-up of a female patient with Ebola virus disease: Sierra Leone Ebola virus persistence study. Open Forum Infect. Dis. 6, ofz068 (2019). - PubMed
  26. Wiedemann, A. et al. Long-lasting severe immune dysfunction in Ebola virus disease survivors. Nat. Commun. 11, 3730 (2020). - PubMed
  27. Adaken, C. et al. Ebola virus antibody decay–stimulation in a high proportion of survivors. Nature 590, 468–472 (2021). - PubMed
  28. Thom, R. et al. Longitudinal antibody and T cell responses in Ebola virus disease survivors and contacts: an observational cohort study. Lancet Infect. Dis. 21, 507–516 (2021). - PubMed
  29. Mbala Kingebeni, P. et al. Ebola virus transmission initiated by relapse of systemic Ebola virus disease. N. Engl. J. Med. 384, 1240–1247 (2021). - PubMed
  30. Muyembe-Tamfum, J. J. et al. Two Ebola virus variants circulating during the 2020 Equateur Province outbreak. https://virological.org/t/two-ebola-virus-variants-circulating-during-the-2020-equateur-province-outbreak/538 (2020). - PubMed
  31. Leroy, E. M. et al. Human Ebola outbreak resulting from direct exposure to fruit bats in Luebo, Democratic Republic of Congo, 2007. Vector Borne Zoonotic Dis. 9, 723–728 (2009). - PubMed
  32. Grard, G. et al. Emergence of divergent Zaire Ebola virus strains in Democratic Republic of the Congo in 2007 and 2008. J. Infect. Dis. 204 (Suppl 3), S776–S784 (2011). - PubMed
  33. Enria, L. What Crisis Produces: Dangerous Bodies, Ebola Heroes and Resistance in Sierra Leone' 'BathPapers in International Development and Wellbeing, Centre for Development Studies, University of Bath no. 53 (2017). - PubMed
  34. Ronse, M. et al. What motivates Ebola survivors to donate plasma during an emergency clinical trial? The case of Ebola-Tx in Guinea. PLoS Negl. Trop. Dis. 12, e0006885 (2018). - PubMed
  35. Sow, S., Desclaux, A., Taverne, B. & Groupe d’étude PostEboGui. Ebola en Guinée: formes de la stigmatisation des acteurs de sante survivants. Bull. Soc. Pathol. Exot. 109, 309–313 (2016). - PubMed
  36. Farmer, P. Aids and Accusation. Haiti and the Geography of Blame (Univ. California Press, 2006). - PubMed
  37. Wilkinson, A. & Fairhead, J. Comparison of social resistance to Ebola response in Sierra Leone and Guinea suggests explanations lie in political configurations not culture. Crit. Public Health 27, 14–27 (2017). - PubMed
  38. Gire, S. K. et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369–1372 (2014). - PubMed
  39. Arias, A. et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evol. 2, vew016 (2016). - PubMed
  40. Pini, A. et al. Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015. Euro Surveill. 23, 17-00140 (2018). - PubMed
  41. Mbala-Kingebeni, P. et al. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment. Lancet Infect. Dis. 19, 648–657 (2019). - PubMed
  42. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010). - PubMed
  43. Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015). - PubMed
  44. Bolger A. M., Lohse M. & Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). - PubMed
  45. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). - PubMed
  46. Weidmann, M., Mühlberger, E. & Hufert, F. T. Rapid detection protocol for filoviruses. J. Clin. Virol. 30, 94–99 (2004). - PubMed
  47. Katoh, K., Asimenos, G. & Toh, H. Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol. 537, 39–64 (2009). - PubMed
  48. Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309–315 (2017). - PubMed
  49. Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020). - PubMed
  50. Rambaut, A., Lam, T. T., Max Carvalho, L. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2, vew007 (2016). - PubMed
  51. Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018). - PubMed
  52. Worobey, M., Han, G. Z. & Rambaut, A. A. Synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508, 254–257 (2014). - PubMed
  53. Gill, M. S. et al. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol. Biol. Evol. 30, 713–724 (2013). - PubMed
  54. Duchene, S., et al. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. 6, veaa061 (2020). - PubMed

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