The creative energy and passion of our researchers exemplify what the VCDI is all about, from the development of a self-sampling protocol for routine SARS-CoV-2 screening to exploring innovative and cost-effective assays for COVID-19 surveillance in the population at large.
The VCDI has successfully passed the SARS-CoV-2 PCR external quality assessment of the Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA). The VCDI is now listed as a recommended laboratory of the Austrian ministry.
Developed a self-sampling protocol for routine SARS-CoV-2 screening.
We have developed a protocol for obtaining and handling throat wash samples using a simple gargling procedure, which can be performed at home. This minimizes the logistical burden and infection risk associated with centralized sampling. The protocol has been extensively validated using samples from COVID-19 patients and detects SARS-CoV-2 infections with similar sensitivity to conventional nasopharyngeal swab tests.
Benchmarked and optimized all key components of RT-qPCR-based SARS-CoV-2 testing.
We have performed extensive benchmarking of different (1) methods for sample- and RNA preparation, (2) primer/probe sets including all commonly used and newly designed primers, (3) RT-qPCR protocols, including various commercial kits as well as custom-made enzyme and reagents. Based on these analyses, we have (1) established experimental standards for benchmarking RT-qPCR protocols, (2) identified suitable primer/probe sets for ultra-sensitive and specific SARS-CoV-2 detection, (3) improved assays for internal sample quality control, and (4) established RT-qPCR protocols that substantially reduce the costs per assay (by about 80%).
Established a standardized assay for sensitive, scalable, and cost-effective SARS-CoV-2 testing.
We have implemented optimized primer/probe sets and protocols for automated sample processing, RNA extraction, and RT-qPCR into a standardized assay for high-throughput SARS-CoV-2 screening. In benchmark analyses on COVID-19 patient samples, our assay matches the sensitivity and specificity of clinical diagnostic tests (Pearson correlation of Ct values = 0.97). With our current automated setup we are capable of analyzing ~4000 samples/day. Furthermore, we have started to evaluate sample pooling in order to further increase the throughput of our setup. We have demonstrated that, with our ultra-sensitive approach, pooling of nine samples is generally possible without producing false-negative results.
Applied our SARS-CoV-2 RT-qPCR screening platform to first pilot studies.
Following the establishment of optimized, cost-effective assays and automated workflows, we have started to apply our SARS-CoV-2 testing platform in first screening projects, each involving several thousand gargle samples. For administrating samples and test results, we have also developed a database and user interface that allows for sample processing and result retrieval in a fully anonymized format.
Explored innovative assays for SARS-CoV-2 surveillance testing at population-scale.
We are developing innovative NGS, RT-LAMP, and CRISPR/Cas9 based RNA detection assays, which hold great promise for ramping up testing capacities to population-scale at markedly reduced cost.
Shared our knowledge and protocols with numerous institutions in Austria and world-wide.
In all activities and projects above, we have shared our knowledge and protocols with similar initiatives around the world. We follow the firm conviction that a broad alliance of basic researchers and medical doctors is required to effectively fight the COVID-19 pandemic.
Established a scalable, simple, rapid and highly sensitive isothermal SARS-CoV-2 detection assay for laboratory and home testing.
We have improved a 20-year old technology based on isothermal amplification of DNA (Loop-mediated isothermal amplification, RT-LAMP) to make it more robust, more sensitive and compatible with home-testing. Our assay uses a rapid upfront lysis step and the Magnesium indicator hydroxy-naphthol-blue (HNB) for colorimetric detection, which enables the robust SARS-CoV-2 detection from a variety of sample types within 30 minutes. By combining RT-LAMP with a simple, magnetic bead-based nucleic acid enrichment method (bead-LAMP), we profoundly increase assay sensitivity to RT-qPCR-like levels, thereby extending applications to large-scale pooled testing. Inclusion of a known cross-contamination prevention system (dUTP/UDG) makes the assay insensitive to carry-over contaminations. Finally, we developed HomeDip-LAMP for pipette-free SARS-CoV-2 detection for low-resource environments. Our combined optimizations set the stage for implementing RT-LAMP as SARS-CoV-2 diagnostics assay for population-wide and home-based testing.
Complete SOP for routine SARS-CoV-2 monitoring released
To enable routine monitoring for COVID-19 infections, the VCDI has established a technically robust, cost-effective, and scalable RT-qPCR testing pipeline based on standard laboratory equipment. To share our experience and current setup, we have compiled a complete standard operating procedure (SOP) describing all components of our pipeline.
VCDI leads Austrian SARS-CoV-2 monitoring initiatives at Austrian schools
To close the knowledge gap on the role of school children in the COVID-19 pandemics the VCDI has initiated large-scale monitoring projects at Austrian schools using gargling in combination with pooling and RT-qPCR.