tetano
Editor, Senior Moderator
Viruses
. 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[SUP] 1 [/SUP], Cyril Chik-Yan Yip[SUP] 2 [/SUP], Wan-Mui Chan[SUP] 1 [/SUP], Anthony Chin-Ki Ng[SUP] 1 [/SUP], Dream Lok-Sze Chan[SUP] 3 [/SUP], Ryan Ho-Ping Siu[SUP] 3 [/SUP], Cheuk Yiu Tenny Chung[SUP] 3 [/SUP], Jessica Pui-Ling Ng[SUP] 3 [/SUP], Harsha Kittur[SUP] 3 [/SUP], Garrett Lee Mosley[SUP] 3 [/SUP], Rosana Wing-Shan Poon[SUP] 2 [/SUP], Ricky Yin-To Chiu[SUP] 3 [/SUP], Kelvin Kai-Wang To[SUP] 1 2 [/SUP]
Affiliations
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[SUP]?[/SUP] easyMAG[SUP]?[/SUP]). 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.
. 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[SUP] 1 [/SUP], Cyril Chik-Yan Yip[SUP] 2 [/SUP], Wan-Mui Chan[SUP] 1 [/SUP], Anthony Chin-Ki Ng[SUP] 1 [/SUP], Dream Lok-Sze Chan[SUP] 3 [/SUP], Ryan Ho-Ping Siu[SUP] 3 [/SUP], Cheuk Yiu Tenny Chung[SUP] 3 [/SUP], Jessica Pui-Ling Ng[SUP] 3 [/SUP], Harsha Kittur[SUP] 3 [/SUP], Garrett Lee Mosley[SUP] 3 [/SUP], Rosana Wing-Shan Poon[SUP] 2 [/SUP], Ricky Yin-To Chiu[SUP] 3 [/SUP], Kelvin Kai-Wang To[SUP] 1 2 [/SUP]
Affiliations
- PMID: 33918447
- DOI: 10.3390/v13040615
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[SUP]?[/SUP] easyMAG[SUP]?[/SUP]). 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.