SPRINT platform - fightCOVID@DKFZ

Contributing groups:
Banito, Boutros, Kraemer, Hübschmann, Lichter, Odom, Rippe, Stegle, Teleman

A significant fraction of SARS-CoV-2 infections occur from pre- and asymptomatic carriers that are not included in the current clinical diagnostics schemes. It is becoming clear that detecting these carriers early on is essential to control virus spreading within the population. However, this goal cannot be achieved by simple upscaling current testing methods because the following challenging requirements need to be fulfilled simultaneously: (i) Cost-efficient high-throughput workflows so that large cohorts of people can be tested that possibly contain a small number of infected carriers. (ii) High detection sensitivity as virus loads in pre- and asymptomatic carriers are low. (iii) High specificity to minimize the numbers of false positive results that would otherwise create unnecessary further follow-up work in the clinic.

The DKFZ Functional and Structural Genomics Program, together with other DKFZ units, is developing a screening platform for SARS-CoV-2 infection identification (SPRINT) to address these unmet needs. This will be achieved by harnessing our expertise and instrumentation for automated high-throughput RNA isolation and processing, developed for large-scale cancer genomics efforts. SPRINT is being built up as an open source reference platform in close collaboration with local and regional partners. SPRINT benefits from the tight interactions with Departments of the Heidelberg University Medical Centers and will support their diagnostics work when possible and if needed. The current SPRINT activities focus on the following main three areas:

SPRINT explicitly aims to identify and produce alternative reagents to those currently used in clinics for SARS-CoV-2 diagnostics. This serves to both avoid placing further demand on clinically relevant materials and increase throughput. More specifically, SPRINT groups are working on developing and testing (i) alternative buffers, PCR reaction mixes and enzymes such as RTX reverse transcriptase, (ii) increased sample processing throughput by automated liquid-handling systems, (iii) sample pooling strategies, and (iv) optimized RT-qPCR workflows with respect to target RNA detection, multiplexing and quantitative data analysis. SPRINT reagents are readily available to regional diagnostics should the need arise.

To increase throughput, sensitivity and specificity over the currently used RT-qPCR assays, we are developing a sequencing-based method termed Cov-seq. It employs molecular barcode technologies from single cell sequencing methods to analyze thousands of samples in one sequencing run. The method can be further upscaled as needed and will include an automated bioinformatic data analysis pipeline to allow delivery of results within 24 hours.

SPRINT participates in cohort studies of asymptomatic SARS-CoV-2 carriers at collaborating institutions with respect to virus detection as well as sample management and tracking via an integrated database.