Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

  1. Jessica E. Manning
  2. Jennifer A. Bohl
  3. Sreyngim Lay
  4. Sophana Chea
  5. Ly Sovann
  6. Yi Sengdoeurn
  7. Seng Heng
  8. Chan Vuthy
  9. Katrina Kalantar
  10. Vida Ahyong
  11. Michelle Tan
  12. Jonathan Sheu
  13. Cristina M. Tato
  14. Joseph L. DeRisi
  15. Laurence Baril
  16. Veasna Duong
  17. Philippe Dussart
  18. Erik A. Karlsson
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Abstract

Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia’s first case of COVID-2019.

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