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Manning JE, Bohl JA, Lay S, Chea S, Sovann L, Sengdoeurn Y, Heng S, Vuthy C, Kalantar K, Ahyong V, Tan M, Sheu J, Tato CM, DeRisi JL, Baril L, Duong V, Dussart P, Karlsson EA. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. bioRxiv 2020:2020.03.02.968818. [PMID: 32511296 PMCID: PMC7217139 DOI: 10.1101/2020.03.02.968818] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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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Affiliation(s)
- Jessica E. Manning
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jennifer A. Bohl
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sreyngim Lay
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Ly Sovann
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Yi Sengdoeurn
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Seng Heng
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | - Chan Vuthy
- Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jonathan Sheu
- Chan Zuckerberg Initiative, Redwood City, California, USA
| | | | | | | | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Erik A. Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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