A two minute liquid based sample preparation for rapid SARS-CoV2 real-time PCR screening: A multicentre evaluation

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This paper describes the application of a very rapid, novel sample preparation method that can be used for detection of viruses as SARS-coronavirus-2.

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Adding a 2 μL aliquot of the sample preparation buffer to 8 μL of nasopharyngeal swab in virus transport medium with a 2 min. incubation makes the sample ready for real-time PCR amplification.

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This simple procedure replaces nucleic acid extraction and was evaluated in four different microbiology laboratories in the Netherlands.

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Comparison to routine diagnostic method showed almost complete concordance for positive samples with C_T values up to 33. In addition, it was shown that the workflow could be automated.

Background

Apart from major health concerns associated to the SARS-coronavirus-2 (SARS-CoV-2) pandemic, also the diagnostic workflow encountered serious problems. Limited availability of kit components, buffers and even plastics has resulted in suboptimal testing procedures worldwide. Alternative workflows have been implemented to overcome these difficulties. Recently a liquid based sample prep has been launched as solution to overcome limitations in relation to nucleic acid extraction.

Objective

Multicenter evaluation of the QIAprep&amp Viral RNA UM kit (QIA P&A) for rapid sample preparation and real-time PCR detection of SARS-CoV-2 in comparison to standardized laboratory testing methods.

Study design

Selected samples of the routine diagnostic workflow at Clinical Microbiology Laboratories of four Dutch hospitals have been subjected to the rapid QIA P&A protocol and the results have been compared to routine diagnostic data.

Results

Combining results of manual and automated procedures, a total of 377 clinical samples of which 202 had been tested positive with a wide range of C_T values, showed almost complete concordance in the QIA P&A assay for samples up to C_T values of 33 with one exception of C_T 31. Prospectively 60 samples were tested and also showed 100 % concordance with 5 positives. The method has been automated by two centres.

Conclusions

Despite an input of only 8 μL of clinical sample, the QIA P&A kit showed good performance for sample preparation and amplification of SARS-CoV-2 and can contribute as a rapid molecular testing strategy in managing the CoV-2 pandemic.