Sequencing the viral genome as the outbreak progresses is important, particularly the identification of new variants and to identify whether any changes in the genome will impair clinical testing. Using the MinION/GridIONS platform, we developed a sensitive protocol to rapidly sequence the viral genome. With this study, we showed that amplicon-based detection and subsequent sequencing are feasible for identifying the SARS-CoV-2 genome or nucleic acid in samples from patients with COVID-19.