Development and implementation of a RT-qPCR extraction-free protocol for the detection of SARS-CoV-2 and impact on the turn-around-time.

Blairon, Laurent; Piteüs, Sébastien; Beukinga, Ingrid; Tré-Hardy, Marie

The occurrence of the COVID-19 second wave outbreak in Europe has pushed laboratories performing molecular SARS-CoV-2 tests to increase their throughput and decrease the result rendering time. In this evaluation, we tested for the first time a new, extraction-free, protocol with the Allplex™ SARS-CoV-2 Assay RT-qPCR kit on a Nimbus platform. Ninety one samples, of which 71 previously tested positive with RT-qPCR with extraction were immediately analyzed without extraction, using only a dilution and thermal shock protocol. The positive and negative percentage agreements were respectively 97.2% (95% CI: 0.90-0.99) and 95.0% (95% IC: 0.76-0.99). The 2 false negatives observed were very weakly positive with the comparison method. Moderate variations in Ct of the targeted genes were observed (median ±95% CI): E gene, +2.49 ±0.44; N gene, +0.98 ±0.54; RdRP/S genes, +2.64 ±0.48. On the other hand, the number of tests performed within 24 hours raised from 86.4% to 97.8%, the turn-around time decreased from 19:18 to 09:03 (P<0.0001) and the number of tests that can be performed per day doubled since this technique was introduced routinely in our laboratory. This article is protected by copyright. All rights reserved.