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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.02.968818 doi: bioRxiv preprint genes for primary detection. This detection directly increased on-the-ground certainty in diagnostic sensitivity and specificity of available assays. 7 mNGS in field settings proved critical in development of countermeasures for the 2014-2016 Ebola virus epidemic in West Africa, just as ongoing sequencing of COVID-19 cases from lesser developed areas of Southeast Asia will contribute to overall understanding of pathogen transmission, origin, and evolution. 9,10 While COVID-19 cases are not limited to one remote region, as is often the case with viral hemorrhagic fever outbreaks, sequenced samples from all countries will be important for global disease containment. Instead of being limited to consensus Sanger sequencing, which may not detect high risk quasispecies, metagenomics is a powerful approach to detect variants of both novel and known species as epidemics evolve. 11 The clear limitation in an mNGS approach is that low viral titers or high levels of host material demand greater read depth than may be available on instruments such as the iSeq100. To overcome this barrier, our follow-up steps included a target enrichment of SARS-CoV-2 while keeping the comprehensiveness of our mNGS pipeline intact. 6 For an emerging threat, this strategy offers the flexibility to successfully recover the pathogen genome in question for subsequent phylogenetic analyses without compromising discovery. However, the other key factor in mNGS success is the accessibility to open-access, cloud-based metagenomics bioinformatics pipelines, such as IDseq which automates the process of separating host sequence characterizing the remaining non-host sequences. 12 As recent as the Ebola epidemic, bioinformatics analyses were still mainly completed in the Global North. 10 This newly available combination -more rugged, deployable sequencers plus user-friendly, globally accessible bioinformatics -represents an opportunity for responders in limited-resource settings; however, further proof-of-principle during outbreaks remains necessary.