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

Manning, J. E.; Bohl, J. A.; Lay, S.; Chea, S.; Ly, S.; Sengdoeurn, Y.; Heng, S.; Vuthy, C.; Kalantar, K.; Ahyong, V.; Tan, M.; Sheu, J.; Tato, C. M.; DeRisi, J.; Baril, L.; Dussart, P.; Duong, V.; Karlsson, E. A.

doi:10.1101/2020.03.02.968818

bioRxiv · 10.1101/2020.03.02.968818

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

Manning, J. E.·Bohl, J. A.·Lay, S.·Chea, S.·Ly, S.·Sengdoeurn, Y.·Heng, S.·Vuthy, C.·Kalantar, K.·Ahyong, V.·Tan, M.·Sheu, J.·Tato, C. M.·DeRisi, J.·Baril, L.·Dussart, P.·Duong, V.·Karlsson, E. A.

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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 Cambodias first case of COVID-2019.

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Manning, J. E., Bohl, J. A., Lay, S., Chea, S., Ly, S., Sengdoeurn, Y., Heng, S., Vuthy, C., Kalantar, K., Ahyong, V., Tan, M., Sheu, J., Tato, C. M., DeRisi, J., Baril, L., Dussart, P., Duong, V., Karlsson, E. A.. 2020-03-05. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. https://doi.org/10.1101/2020.03.02.968818

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