Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2

Xin Xie; Tamara Gjorgjieva; Zaynoun Attieh; Mame Massar Dieng; Marc Arnoux; Mostafa Khair; Yasmine Moussa; Fatima Al Jallaf; Nabil Rahiman; Christopher A. Jackson; Lobna El Messery; Khristine Pamplona; Zyrone Victoria; Mohammed Zafar; Raghib Ali; Fabio Piano; Kristin C. Gunsalus; Youssef Idaghdour

LAPSE

Living Archive for Process Systems Engineering

LAPSE:2021.0426

Published Article

LAPSE:2021.0426

Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2

Xin Xie, Tamara Gjorgjieva, Zaynoun Attieh, Mame Massar Dieng, Marc Arnoux, Mostafa Khair, Yasmine Moussa, Fatima Al Jallaf, Nabil Rahiman, Christopher A. Jackson, Lobna El Messery, Khristine Pamplona, Zyrone Victoria, Mohammed Zafar, Raghib Ali, Fabio Piano, Kristin C. Gunsalus, Youssef Idaghdour

May 25, 2021

A major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. In this study, we implemented a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification, and nano-scale qPCR based on a commercially available microfluidic chip. Using SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of this microfluidic RT-qPCR by 1000-fold, enabling detection below 1 copy/µL. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible and quantitative detection of SARS-CoV-2 over five orders of magnitude (<1 to 106 viral copies/µL). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/µL) in 17 samples with negative clinical diagnosis, indicating a potential false-negative rate of 18.7% by clinical diagnostic procedures. In summary, this three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (<1 viral copy/µL) and has the potential to reduce the false-negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.

Record ID

LAPSE:2021.0426

Keywords

COVID-19, detection, microfluidics, nano-qPCR, SARS-CoV-2, ultra-sensitive, viral load, viral RNA

Subject

Biosystems

Suggested Citation

Xie X, Gjorgjieva T, Attieh Z, Dieng MM, Arnoux M, Khair M, Moussa Y, Al Jallaf F, Rahiman N, Jackson CA, Messery LE, Pamplona K, Victoria Z, Zafar M, Ali R, Piano F, Gunsalus KC, Idaghdour Y. Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2. (2021). LAPSE:2021.0426

Author Affiliations

Xie X: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE [ORCID]
Gjorgjieva T: Program in Biology, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Public Health Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE [ORCID]
Attieh Z: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Dieng MM: Program in Biology, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Arnoux M: Core Technology Platforms, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Khair M: Core Technology Platforms, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Moussa Y: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Al Jallaf F: Program in Biology, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Public Health Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Rahiman N: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Jackson CA: Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
Messery LE: Proficiency Healthcare Diagnostics, Electra Street, Abu Dhabi 51133, UAE
Pamplona K: Proficiency Healthcare Diagnostics, Electra Street, Abu Dhabi 51133, UAE
Victoria Z: Proficiency Healthcare Diagnostics, Electra Street, Abu Dhabi 51133, UAE
Zafar M: Proficiency Healthcare Diagnostics, Electra Street, Abu Dhabi 51133, UAE
Ali R: Public Health Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE
Piano F: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
Gunsalus KC: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Public Health Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Department of Biology and Center for Genomi
Idaghdour Y: Program in Biology, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE; Public Health Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi 51133, UAE [ORCID]

Journal Name

Processes

Volume

8

Issue

11

Article Number

E1425

Year

2020

Publication Date

2020-11-09