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Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

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 n...

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Autores principales: Chu, Allen Wing-Ho, Yip, Cyril Chik-Yan, Chan, Wan-Mui, Ng, Anthony Chin-Ki, Chan, Dream Lok-Sze, Siu, Ryan Ho-Ping, Chung, Cheuk Yiu Tenny, Ng, Jessica Pui-Ling, Kittur, Harsha, Mosley, Garrett Lee, Poon, Rosana Wing-Shan, Chiu, Ricky Yin-To, To, Kelvin Kai-Wang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067048/
https://www.ncbi.nlm.nih.gov/pubmed/33918447
http://dx.doi.org/10.3390/v13040615
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author Chu, Allen Wing-Ho
Yip, Cyril Chik-Yan
Chan, Wan-Mui
Ng, Anthony Chin-Ki
Chan, Dream Lok-Sze
Siu, Ryan Ho-Ping
Chung, Cheuk Yiu Tenny
Ng, Jessica Pui-Ling
Kittur, Harsha
Mosley, Garrett Lee
Poon, Rosana Wing-Shan
Chiu, Ricky Yin-To
To, Kelvin Kai-Wang
author_facet Chu, Allen Wing-Ho
Yip, Cyril Chik-Yan
Chan, Wan-Mui
Ng, Anthony Chin-Ki
Chan, Dream Lok-Sze
Siu, Ryan Ho-Ping
Chung, Cheuk Yiu Tenny
Ng, Jessica Pui-Ling
Kittur, Harsha
Mosley, Garrett Lee
Poon, Rosana Wing-Shan
Chiu, Ricky Yin-To
To, Kelvin Kai-Wang
author_sort Chu, Allen Wing-Ho
collection PubMed
description 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.
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spelling pubmed-80670482021-04-25 Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR Chu, Allen Wing-Ho Yip, Cyril Chik-Yan Chan, Wan-Mui Ng, Anthony Chin-Ki Chan, Dream Lok-Sze Siu, Ryan Ho-Ping Chung, Cheuk Yiu Tenny Ng, Jessica Pui-Ling Kittur, Harsha Mosley, Garrett Lee Poon, Rosana Wing-Shan Chiu, Ricky Yin-To To, Kelvin Kai-Wang Viruses Article 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. MDPI 2021-04-02 /pmc/articles/PMC8067048/ /pubmed/33918447 http://dx.doi.org/10.3390/v13040615 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chu, Allen Wing-Ho
Yip, Cyril Chik-Yan
Chan, Wan-Mui
Ng, Anthony Chin-Ki
Chan, Dream Lok-Sze
Siu, Ryan Ho-Ping
Chung, Cheuk Yiu Tenny
Ng, Jessica Pui-Ling
Kittur, Harsha
Mosley, Garrett Lee
Poon, Rosana Wing-Shan
Chiu, Ricky Yin-To
To, Kelvin Kai-Wang
Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title_full Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title_fullStr Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title_full_unstemmed Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title_short Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR
title_sort evaluation of an automated high-throughput liquid-based rna extraction platform on pooled nasopharyngeal or saliva specimens for sars-cov-2 rt-pcr
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067048/
https://www.ncbi.nlm.nih.gov/pubmed/33918447
http://dx.doi.org/10.3390/v13040615
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