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

Jessica E. Manning (1) , Jennifer A. Bohl (1) , Sreyngim Lay (1) , Sophana Chea (1) , Ly Sovann (2) , Yi Sengdoeurn (2) , Seng Heng (2) , Chan Vuthy (2) , Katrina Kalantar (3) , Vida Ahyong (4) , Michelle Tan (4) , Jonathan Sheu (3) , Cristina M. Tato (4) , Joseph L. Derisi (4) , Laurence Baril (5) , Veasna Duong (6) , Philippe Dussart (6) , Erik A. Karlsson (6)

1 NIAID - National Institute of Allergy and Infectious Diseases [Phnom Penh, Cambodia]
2 Ministry of Health [Phnom Penh]
3 CZI - Chan Zuckerberg Initiative [Redwood City, CA]
4 Chan Zuckerberg BioHub [San Francisco, CA]
5 Institut Pasteur du Cambodge
6 Unité de Virologie / Virology Unit [Phnom Penh]

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.

Keywords: metagenomics; sequencing; coronavirus; COVID-19; SARS-CoV-2; unbiased metagenomics

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Virology

Jessica E. Manning, Jennifer A. Bohl, Sreyngim Lay, Sophana Chea, Ly Sovann, et al.. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. 2021. ⟨pasteur-03221716⟩