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Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification

Published: March 31st, 2021



1Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 2International College, University of Chinese Academy of Sciences, 3Sino-Africa Joint Research Center, 4CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 5Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute

This work summarizes steps on developing different assays for SARS-CoV-2 detection using a two color ddPCR system. The steps are elaborate and notes have been included on how to improve the assays and experiment performance. These assays may be used for multiple SARS-CoV-2 RT-ddPCR applications.

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) is the gold standard for SARS-CoV-2 diagnosis as no permanent solution is available. However effective this technique may be, research has emerged showing its limitations in detection and diagnosis especially when it comes to low abundant targets. In contrast, droplet digital PCR (ddPCR), a recent emerging technology with superior advantages over qPCR, has been shown to overcome the challenges of RT-qPCR in diagnosis of SARS-CoV-2 from low abundant target samples. Prospectively, in this article, the capabilities of RT-ddPCR are further expanded by showing steps on how to develop simplex, duplex, triplex probe mix, and quadruplex assays using a two-color detection system. Using primers and probes targeting specific sites of the SARS-CoV-2 genome (N, ORF1ab, RPP30, and RBD2), the development of these assays is shown to be possible. Additionally, step by step detailed protocols, notes, and suggestions on how to improve the assays workflow and analyze data are provided. Adapting this workflow in future works will ensure that the maximum number of targets can be sensitively detected in a small sample significantly improving on cost and sample throughput.

Polymerase chain reaction (PCR), a well-recognized technique, has undergone several transformations since its advent to become a powerful technique capable of providing answers to nucleic acid research. These transformations have been a constant improvement of the old technique. These transformations can be summarized into three generations1. The first generation is conventional PCR that relies on gel electrophoresis to quantify and detect amplified targets. The second generation is quantitative real time PCR (qPCR) that can detect samples in real time and rely on a standard curve to directly quantify targets in a sample. The third generation, ....

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Ethical statement
Wuhan Institute of Virology (WHIOV) is among the labs and institutes approved by China CDC of Wuhan city to conduct research on SARS-CoV-2 and detect COVID-19 from clinical samples. Research on developing new diagnostic techniques for COVID-19 using clinical samples has also been approved by the ethical committee of Wuhan Institute of Virology (2020FCA001).

1. Sample processing workflow (Figure 1A)

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In a proof-of-concept study, the multiplex assays analytical performance was tested on clinical and research samples19. The performance of the multiplex assays was superior to that of an RT-PCR19. Since low numbers of droplets may indicate a problem during droplet generation, in this article a cutoff of 10,000 droplets per well was set based on empirical data.

A good separation between positive and negative droplets with minimal rain interference.......

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Few resources are available on how to develop RT-ddPCR assays for SARS-CoV-2 detection. Though not used in this article, standard samples with known copies may be used to develop and optimize assays. In this work however, SARS-CoV-2 samples grown in Vero-E6 cells were spiked in a background of human genomic RNA and used as standard samples to develop the assays. Proper primer and probe sequences are essential when developing assays. Since most preliminary work on SARS-CoV-2 RT-ddPCR used the China CDC primer and probes t.......

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This research was funded by Megaproject of Infectious Disease Control from Ministry of Health of China, grant number 2017ZX10302301-005 and Sino-Africa Joint Research Center, grant number SAJC201605.


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Name Company Catalog Number Comments
32-channel fully automatic nucleic acid extractor Purifier 32 Genfine Biotech FHT101-32 Automated extractor for RNA
AutoDG Oil for Probes BioRad 12003017 QX200 AutoDG consumable
ddPCR 96-Well Plates BioRad 12003185
ddPCR Supermix for Probes (No dUTP) BioRad 1863024 Making ddPCR assay mastermix
DG32 AutoDG Cartridges BioRad 1864108 QX200 AutoDG consumable
Electronic thermostatic water bath pot Beijing Changfeng Instrument and Meter Company XMTD-8000 Heat inactivation of samples
FineMag Rapid Bead Virus DNA/RNA Extraction Kit Genfine Biotech FMY502T5 Magnetic bead extraction of inactivated RNA samples
Pierceable Foil Heat Seals BioRad 1814040
Pipet Tips for the AutoDG BioRad 1864120 QX200 AutoDG consumable
Pipet Tip Waste Bins for the AutoDG BioRad 1864125 QX200 AutoDG consumable
PrimeScript RT Master Mix (Perfect Real Time) TaKaRa RR036A cDNA generation
PX1 PCR Plate Sealer BioRad 1814000 Seal the droplet plate from AutoDG
QuantaSoft 1.7 Software BioRad 10026368 Data acquisition and analysis
QuantaSoft Analysis Pro 1.0 BioRad N/A Data analysis
QX200 Automated Droplet Gererator (AutoDG) BioRad 1864101 QX200 AutoDG consumable
QX200 Droplet Reader BioRad 1864003 Droplet reading and data acquisition
T100 Thermal Cycler BioRad 1861096 Droplet target amplification (PCR) and cDNA generation

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