Pre-emptive genomic surveillance of emerging ebolaviruses

Euro Surveill. 2020 Jan;25(3):1900765. doi: 10.2807/1560-7917.ES.2020.25.3.1900765.


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.

Keywords: Ebolavirus; PCR; genomic surveillance; nested PCR.

MeSH terms

  • Base Sequence
  • Communicable Diseases, Emerging
  • DNA, Viral / analysis*
  • Ebolavirus / classification
  • Ebolavirus / genetics*
  • Ebolavirus / isolation & purification*
  • Genome, Viral / genetics*
  • Hemorrhagic Fever, Ebola / diagnosis*
  • Humans
  • Polymerase Chain Reaction / methods*
  • RNA, Viral / genetics*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA


  • DNA, Viral
  • RNA, Viral