Fig. 3

One-step direct detection without RNA extraction. a Analysis of extracted RNA or direct UTM from a panel of patients using the BGI or Norgen (N1 and N2 primers) detection systems. b Comparison of Ct values from original clinical diagnosis with extracted RNA (Seegene Allplex RdRp and N genes) to data obtained for direct analysis with the BGI detection system. c Patient samples in UTM were left untreated, or treated with the RNase inhibitor RNaseOUT with or without heating at 95 °C for 15 min, or treated with the indicated lysis buffers/detergents and then directly analyzed using the BGI or Norgen (N1/N2 primers) RT-qPCR detection systems. Note sample L020 (clinical negative) was also tested under these conditions and was confirmed as SARS-CoV-2 negative. d Comparison of Ct values from original clinical diagnosis (Seegene Allplex RdRp and N genes) and data obtained with the BGI or Norgen detection systems in the larger cohort of 30 positive samples. Horizontal dotted line indicates Ct threshold for positive clinical detection and vertical dotted line indicates Ct threshold for positive detection using the BGI system. Note, that R² and slope calculations include only samples that were detected with Ct < 40. e ROC curve for direct analysis using the BGI RT-qPCR detection system including all 37 positive and 31 negative sample analyzed. f Cost analysis comparing Norgen, BGI, Qiagen and SYBR green systems. Price is in USD at the time these studies were initiated (late March/early April 2020) for 10 µl RT-qPCR reactions and include relevant processing and shipping fees, and would be influenced by regional pricing. *BGI RNA extraction module is based on the 96-sample format, price can be reduced ~ 15% by purchasing the 1728-sample format, and bulk pricing with a ~ 25% discount of the detection module is available for > 10,000 samples. **Pricing for the Norgen detection module is based on the 50-sample format running three separate wells (N1, N2 and RNaseP) per sample, pricing can be reduced if purchasing the larger 500-sample format. ***Pricing for SYBR green detection is based on the 200 reaction size LUNA Universal One-Step RT-qPCR Kit (NEB) running three separate wells/sample (two viral genes and one human control gene). Pricing can be reduced up to 30% with larger kit sizes. N/A: not applicable