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

Raw fastq files were uploaded to the IDseq portal, a cloud-based, open-source bioinformatics platform to identify microbes from metagenomic data (https://idseq.net). The filter steps and microbial data are accessible at http://public.idseq.net/covid-19?utm_source=bioarxiv&utm_medium=paper&utm_campaign=covid-19. Potential pathogens were distinguished from commensal flora and contaminating microbial sequences from the environment and reagents by establishing a Z-score metric based on a background distribution derived from four non-templated "water-only" control libraries. Data were normalized to unique reads mapped per million input reads for each microbe at both species and genus levels. Taxa with Z-score less than 1, base pair alignment less than 50 base pairs, and reads per million (rpM) less than 10 were removed from analysis. Geneious Prime 2020.0.5 was used for separate de novo assembly and annotation of the draft SARS-CoV-2 genome. In subsequent runs to achieve higher coverage of the viral genome, two additional steps were taken: 1) the subsampling filter of the nonhost reads was removed and 2) targeted enrichment of the SARS-CoV-2 sequence using author/funder. All rights reserved. No reuse allowed without permission.