Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

•Detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing.•Direct metatranscritptome sequencing from nasopharyngeal swab of a COVID-19 patient.•Depletion of human rRNA and in-house bioinformatics strategy for Ion torrent sequencing. Herein, we describe the detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing directly from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil. Depletion of human ribosomal RNA and use of an optimized in-house developed bioinformatics strategy contributed to successful detection of the virus.