Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR

medRxiv

Abstract

Abstract Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Here we compare qRT-PCR with DETECTR to diagnose COVID-19 on 378 patient samples and report a 95% reproducibility. Patient sample dilution assays suggest a higher analytical sensitivity of DETECTR compared to qRT-PCR, however, this was not confirmed in a large patient cohort. The data showed that both techniques are equally sensitive in detecting SARS-CoV-2 providing an added value of DETECTR to the currently used qRT-PCR platforms. For DETECTR, different gRNAs can be used simultaneously to obviate negative results due to mutations in N-gene. Lateral flow strips, suitable as a point of care test (POCT), showed a 100% correlation to the high-throughput DETECTR assay. Importantly, DETECTR was 100% specific for SARS-CoV-2 and did not detect other human coronaviruses. As there is no need for specialized equipment, DETECTR could be rapidly implemented as a complementary technically independent approach to qRT-PCR thereby increasing the testing capacity of medical microbiological laboratories and relieving the existent PCR-platforms for routine non-SARS-CoV-2 diagnostic testing.

Authors 6

1. Eelke T. Brandsma corresponding

   Sanquin · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Sanquin Research, Department of Hematopoiesis, Amsterdam, The Netherlands, and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands

2. Han J. M. P. Verhagen corresponding

   Sanquin · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Sanquin Research, Department of Hematopoiesis, Amsterdam, The Netherlands, and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands

3. Thijs J. W. van de Laar

   Sanquin · OLVG · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Medical Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands

   Sanquin Research, Department of Donor Medicine Research, Amsterdam, The Netherlands and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands

4. Eric C. J. Claas Aachen Department of Medical Microbiology

   Leiden University Medical Center

   Affiliation as printed

   Department of Medical microbiology, Leiden University Medical Center, Leiden, The Netherlands

5. Marion T. E. Cornelissen

   Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers

   Affiliation as printed

   Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands

6. Emile van den Akker

   Sanquin · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Sanquin Research, Department of Hematopoiesis, Amsterdam, The Netherlands, and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands