. 2021 Apr 2;13(4):615.
doi: 10.3390/v13040615.
Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Allen Wing-Ho Chu 1 , Cyril Chik-Yan Yip 2 , Wan-Mui Chan 1 , Anthony Chin-Ki Ng 1 , Dream Lok-Sze Chan 3 , Ryan Ho-Ping Siu 3 , Cheuk Yiu Tenny Chung 3 , Jessica Pui-Ling Ng 3 , Harsha Kittur 3 , Garrett Lee Mosley 3 , Rosana Wing-Shan Poon 2 , Ricky Yin-To Chiu 3 , Kelvin Kai-Wang To 1 2



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.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; diagnostics; liquid-based nucleic acid extraction; mass screening; nasopharyngeal swab; pooled specimens; saliva.