1887
Rapid communication Open Access

Abstract

Genomic surveillance during ebolavirus outbreaks to elucidate transmission chains and develop diagnostic tests is delayed by the laborious development of variant-specific laboratory assays. We developed a new protocol combining 31 parallel PCR assays with Illumina/MinION-based sequencing, allowing generic ebolavirus genomic surveillance, validated using cell culture-derived Ebola, Reston, Sudan and Taï Forest virus at concentrations compatible with patient viral loads. Our approach enables pre-emptive genomic surveillance of ongoing and future ebolavirus outbreaks irrespective of variant divergence.

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/content/10.2807/1560-7917.ES.2020.25.3.1900765
2020-01-23
2020-02-21
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2020.25.3.1900765
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References

  1. World Health Organization (WHO). Ebola virus disease – Democratic Republic of the Congo - 18 July 2019. Geneva: WHO; 2019. Available from: https://www.who.int/csr/don/18-july-2019-ebola-drc/en/
  2. Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics. 2019;20(1):155.  https://doi.org/10.1186/s12864-019-5543-2  PMID: 30808306 
  3. Houldcroft CJ, Beale MA, Breuer J. Clinical and biological insights from viral genome sequencing. Nat Rev Microbiol. 2017;15(3):183-92.  https://doi.org/10.1038/nrmicro.2016.182  PMID: 28090077 
  4. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345(6202):1369-72.  https://doi.org/10.1126/science.1259657  PMID: 25214632 
  5. Dietzel E, Schudt G, Krähling V, Matrosovich M, Becker S. Functional characterization of adaptive mutations during the West African Ebola virus outbreak. J Virol. 2017;91(2):e01913-6.  https://doi.org/10.1128/JVI.01913-16  PMID: 27847361 
  6. Moran-Gilad J. How do advanced diagnostics support public health policy development? Euro Surveill. 2019;24(4):1900068.  https://doi.org/10.2807/1560-7917.ES.2019.24.4.1900068  PMID: 30696524 
  7. Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530(7589):228-32.  https://doi.org/10.1038/nature16996  PMID: 26840485 
  8. Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evol. 2016;2(1):vew016.  https://doi.org/10.1093/ve/vew016  PMID: 28694998 
  9. Meredith L, Quick J. Ebola virus sequencing kit-list. ARCTICNetwork; 2018. Available from: http://artic.network/ebov/ebov-seq-kit.html
  10. Sozhamannan S, Holland MY, Hall AT, Negrón DA, Ivancich M, Koehler JW, et al. Evaluation of signature erosion in Ebola virus due to genomic drift and its impact on the performance of diagnostic assays. Viruses. 2015;7(6):3130-54.  https://doi.org/10.3390/v7062763  PMID: 26090727 
  11. Corman VM, Rasche A, Baronti C, Aldabbagh S, Cadar D, Reusken CB, et al. Assay optimization for molecular detection of Zika virus. Bull World Health Organ. 2016;94(12):880-92.  https://doi.org/10.2471/BLT.16.175950  PMID: 27994281 
  12. Fischer C, de Lamballerie X, Drexler JF. Enhanced molecular surveillance of chikungunya virus. MSphere. 2019;4(4):e00295-19.  https://doi.org/10.1128/mSphere.00295-19  PMID: 31270168 
  13. Li J, Duan H-J, Chen H-Y, Ji Y-J, Zhang X, Rong Y-H, et al. Age and Ebola viral load correlate with mortality and survival time in 288 Ebola virus disease patients. Int J Infect Dis. 2016;42:34-9.  https://doi.org/10.1016/j.ijid.2015.10.021  PMID: 26523640 
  14. de La Vega M-A, Caleo G, Audet J, Qiu X, Kozak RA, Brooks JI, et al. Ebola viral load at diagnosis associates with patient outcome and outbreak evolution. J Clin Invest. 2015;125(12):4421-8.  https://doi.org/10.1172/JCI83162  PMID: 26551677 
  15. Forbes KM, Webala PW, Jääskeläinen AJ, Abdurahman S, Ogola J, Masika MM, et al. Bombali virus in Mops condylurus bat, Kenya. Emerg Infect Dis. 2019;25(5):955.  https://doi.org/10.3201/eid2505.181666  PMID: 31002301 
  16. Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, et al. Evolution and spread of Ebola virus in Liberia, 2014-2015. Cell Host Microbe. 2015;18(6):659-69.  https://doi.org/10.1016/j.chom.2015.11.008  PMID: 26651942 
  17. Tong Y-G, Shi W-F, Liu D, Qian J, Liang L, Bo X-C, et al. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature. 2015;524(7563):93-6.  https://doi.org/10.1038/nature14490  PMID: 25970247 
  18. Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, et al. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. 2015;524(7563):97-101.  https://doi.org/10.1038/nature14594  PMID: 26083749 
  19. Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, et al. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell. 2015;161(7):1516-26.  https://doi.org/10.1016/j.cell.2015.06.007  PMID: 26091036 
  20. Quick J, Loman N, Duraffour S, Cowley L, Rambaut A, Simpson J, et al. Real-time sequencing and data release for Ebolavirus genomic surveillance in Guinea. 2015. Available from: http://virological.org/t/real-time-sequencing-and-data-release-for-ebolavirus-genomic-surveillance-in-guinea/37
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