Extraction-free diagnostic platforms a faster, cheaper way to detect SARS-CoV-2

Diagnostic platforms that omit the conventional nucleic acid extraction step in the detection of SARS-CoV-2 in nasopharyngeal swab samples help reduce the turnaround time and the overall testing costs, as reported in a study.

Researchers used two commercial kits for molecular detection of SARS-CoV-2 (Allplex SARS-CoV-2 assay [ALLPLEX-COV] and Allplex SARS-CoV-2/FluA/FluB/RSV assay [ALLPLEX-COV-FLU]) in nasopharyngeal swabs in order to assess the performance of extraction-free protocols that involve simple dilution of the specimen in sterile RNAse free water (with or without a heating step) as compared with standard RNA extraction protocols.

A total of 139 nasopharyngeal swab samples were evaluated using ALLPLEX-COV with three different methods: 1) RNA extraction followed by PCR set-up and cycling, 2) direct PCR set-up after dilution of the sample in sterile RNase-free water (EX-FREE protocol), and 3) direct PCR set-up after dilution of the sample in sterile RNase-free water and heating at 98 °C for 3 minutes (EX-FREE-HEAT protocol). A second group of 69 samples was evaluated using ALLPLEX-COV-FLU.

Extraction-free protocols based on sample dilution without a heating step had a lower analytical sensitivity than conventional protocols74 percent with ALLPLEX-COV and 82 percent with ALLPLEX-COV-FLU, with a mean increase in Ct values of 2.04 and 1.32, respectively).

Most false negative results were obtained using samples with low viral load. The inclusion of a step of heat exposure did not improve but actually reduced the analytical sensitivity of the assay.