COVID-19 Sample Pooling: From RNA Extraction to Quantitative Real-time RT-PCR

Kenny Voon; Nur Alia Johari; Khai Lone Lim; Siew Tung Wong; Loke Tim Khaw; Shew Fung Wong; Elaine W L Chan; Kok Keong Chan; Boon Keat Tan; Nurul Hanis Ramzi; Patricia K C Lim; Lokman H Sulaiman

doi:10.21769/BioProtoc.4005

COVID-19 Sample Pooling: From RNA Extraction to Quantitative Real-time RT-PCR

Bio Protoc. 2021 May 5;11(9):e4005. doi: 10.21769/BioProtoc.4005.

Authors

Kenny Voon¹, Nur Alia Johari², Khai Lone Lim², Siew Tung Wong¹, Loke Tim Khaw¹, Shew Fung Wong^{1

3}, Elaine W L Chan², Kok Keong Chan⁴, Boon Keat Tan⁴, Nurul Hanis Ramzi², Patricia K C Lim^{1

2}, Lokman H Sulaiman^{5

3}

Affiliations

¹ Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia.
² Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia.
³ Centre for Environmental and Population Health Research, Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia.
⁴ Human Biology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia.
⁵ Department of Community Medicine, School of Medicine, International Medical University, Kuala Lumpur, Malaysia.

Abstract

The COVID-19 pandemic requires mass screening to identify those infected for isolation and quarantine. Individually screening large populations for the novel pathogen, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is costly and requires a lot of resources. Sample pooling methods improve the efficiency of mass screening and consume less reagents by increasing the capacity of testing and reducing the number of experiments performed, and are therefore especially suitable for under-developed countries with limited resources. Here, we propose a simple, reliable pooling strategy for COVID-19 testing using clinical nasopharyngeal (NP) and/or oropharyngeal (OP) swabs. The strategy includes the pooling of 10 NP/OP swabs for extraction and subsequent testing via quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), and may also be applied to the screening of other pathogens.

Keywords: COVID-19; Pooling strategy; RNA extraction; RT-qPCR; SARS-CoV-2; Sample pooling.