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

Jessica E. Manning, Jennifer A. Bohl, Sreyngim Lay, Sophana Chea, Ly Sovann, Yi Sengdoeurn, Seng Heng, Chan Vuthy, Katrina Kalantar, Vida Ahyong, Michelle Tan, Jonathan Sheu, Cristina M. Tato, View ORCID ProfileJoseph L. DeRisi, Laurence Baril, Veasna Duong, Philippe Dussart, View ORCID ProfileErik A. Karlsson
doi: https://doi.org/10.1101/2020.03.02.968818
Jessica E. Manning
1Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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  • For correspondence: jessica.manning@nih.gov
Jennifer A. Bohl
1Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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Sreyngim Lay
1Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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Sophana Chea
1Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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Ly Sovann
2Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
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Yi Sengdoeurn
2Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
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Seng Heng
2Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
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Chan Vuthy
2Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
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Katrina Kalantar
3Chan Zuckerberg Initiative, Redwood City, California, USA
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Vida Ahyong
4Chan Zuckerberg Biohub, San Francisco, California, USA
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Michelle Tan
4Chan Zuckerberg Biohub, San Francisco, California, USA
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Jonathan Sheu
3Chan Zuckerberg Initiative, Redwood City, California, USA
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Cristina M. Tato
4Chan Zuckerberg Biohub, San Francisco, California, USA
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Joseph L. DeRisi
4Chan Zuckerberg Biohub, San Francisco, California, USA
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  • ORCID record for Joseph L. DeRisi
Laurence Baril
5Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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Veasna Duong
6Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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Philippe Dussart
6Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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Erik A. Karlsson
6Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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  • ORCID record for Erik A. Karlsson
  • For correspondence: ekarlsson@pasteur-kh.org
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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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Posted March 05, 2020.
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Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
Jessica E. Manning, Jennifer A. Bohl, Sreyngim Lay, Sophana Chea, Ly Sovann, Yi Sengdoeurn, Seng Heng, Chan Vuthy, Katrina Kalantar, Vida Ahyong, Michelle Tan, Jonathan Sheu, Cristina M. Tato, Joseph L. DeRisi, Laurence Baril, Veasna Duong, Philippe Dussart, Erik A. Karlsson
bioRxiv 2020.03.02.968818; doi: https://doi.org/10.1101/2020.03.02.968818
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Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
Jessica E. Manning, Jennifer A. Bohl, Sreyngim Lay, Sophana Chea, Ly Sovann, Yi Sengdoeurn, Seng Heng, Chan Vuthy, Katrina Kalantar, Vida Ahyong, Michelle Tan, Jonathan Sheu, Cristina M. Tato, Joseph L. DeRisi, Laurence Baril, Veasna Duong, Philippe Dussart, Erik A. Karlsson
bioRxiv 2020.03.02.968818; doi: https://doi.org/10.1101/2020.03.02.968818

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