Abstract
SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFY™) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs. 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.
Highlights
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to spread globally despite implementation of various public health measures
There was no significant difference in the positive rates and Ct values in SARS-CoV-2 Reverse transcription-polymerase chain reaction (RT-PCR) for pooled nasopharyngeal swab (NPS) or saliva specimens extracted using the liquid-based RNA extraction (LRE) and magnetic bead-based total nucleic acid extraction (MBTE) methods
We showed that the benefit of the LRE was most notable for pooled saliva specimens, in which the positive rate was higher for LRE than that of MBTE (88.3% vs. 81.7%)
Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to spread globally despite implementation of various public health measures. Rapid resurgence of cases occurred after partial relaxation of social distancing measures [1]. Aggressive diagnostic testing, together with prompt isolation and quarantine of close contacts, have successfully prevented further spread of the infection in some places [2,3]. Several gene regions have been evaluated as the target for RT-PCR, including the N, E, S, ORF1ab, nsp and nsp regions [5,6,7,8,9]. Novel SARS-CoV-2 variants may contain mutations at the primer sites which evade detection, such as the failure of the S gene RT-PCR in the detection of the UK variant B.1.1.7 lineage [10]
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