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The article discusses a modified sequencing workflow using short tiling amplicons library preparation method and Illumina's iSeq100 desktop sequencer to identify gapped reads that capture characteristics of subgenomic RNA junctions in patient samples with COVID-19. Taqman assays were designed to accurately capture the quantity of subgenomic ORF5 and ORF7a RNA from patient samples and demonstrated utility in tracking subgenomic titres in patient samples when combined with a standard COVID-19 qRT-PCR assay. The workflow is described as versatile, small footprint, and decentralized, which can facilitate comprehensive genetics characterizations during outbreaks.
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