PMC:7033720 / 11963-13139 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7033720","sourcedb":"PMC","sourceid":"7033720","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7033720","text":"On 7th January 2020, the sequencing results were obtained in less than 24 h, with 7,369,020 and 4,522,558 reads generated for the samples of patient 1 and 2, respectively. To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline based on individual reads was carried out on sequenced data. Aside from those belonged to PhiX genome (in-library control), a majority of the viral reads (99.9% and 99.7% respectively for sample 1 and 2) were associated with coronaviruses. The raw sequence data minus human genomic information was uploaded to Sequence Read Archive (SRA) database (Bioproject accession PRJNA601736). On the other hand, bacterial pathogen identification was carried out by using the Metaphlan2 program, which revealed Capnocytophaga sp and Veillonella sp in sample 2 and none in sample 1, and both bacteria identified were not known for their pathogenicity. Collectively, coronavirus is likely to be the main microbial pathogen within these samples. The reads were assembled de novo using Megahit to form a ∼30 kb contigs with sequence homology to CoV. After confirmation with read mapping, the final CoV genome was 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