Novel RT-ddPCR assays for determining the transcriptional profile of SARS-CoV-2

The exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics. HighlightsO_LIWe developed a novel panel of 7 quantitative RT-ddPCRs assays for SARS-Cov-2 C_LIO_LIOur panel targets nongenic and genic regions in genomic and subgenomic RNAs C_LIO_LIAll assays detect 1-10 copies and are linear over 3-4 orders of magnitude C_LIO_LIAll assays correlated with the clinical Abbott SARS-CoV-2 Viral Load Assay C_LIO_LIClinical samples showed higher copy numbers for targets at the 3 end of the genome C_LI