Genomic investigation of SARS-CoV-2 using microfluidics | Tao Li, MS

The global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Genomic surveillance has become a critical measure for identification of new SARS-CoV-2 variants, providing vital information for infection control strategies and vaccine development. In contrast to the massive capacity of next-generation sequencing (NGS), conventional methods for whole genome amplification of RNA viruses are often time-consuming, a big hurdle for amplification of large 30 Kb genomic RNA such as that of SARS-CoV-2. Using the Fluidigm integrated fluidic circuit (IFC) and Access Array™ instruments, we built a robust workflow for sequencing, utilizing one-step whole-genome reverse transcription PCR (RT-PCR) amplification, followed by amplicon sequencing using Illumina® NGS systems MiSeq™, NextSeq™ or NovaSeq™. The 48.48 Access Array™ IFC was used to amplify 48 extracted RNA samples with up to 48 individual pairs of primers. Only 1 to 1.45 µL of RNA was needed for each sample with minimal hands-on time and lower risks of contamination. The yields of RT-PCR and genome assembly coverage were highly correlated with Ct values or viral titers of the samples. The method has been successfully used in a number of projects on RNA samples from both viral isolates and clinical specimens, with demonstrated robustness and efficiency in obtaining the full genome sequence of SARS-CoV-2.

→ABOUT THE SPEAKER:
Tao Li, MS
Research Scientist
Viral Diseases Branch,
Center of Infectious Diseases Research
Walter Reed Army Institute of Research

For Research Use Only. Not for use in diagnostic procedures.
Information in this publication is subject to change without notice. Patent and license information: fluidigm.com/legal/notices. Trademarks: Fluidigm, the Fluidigm logo, Access Array, Biomark, Delta Gene, Dynamic Array, EPI, Juno and SNP Type are trademarks and/or registered trademarks of Fluidigm Corporation in the United States and/or other countries. All other trademarks are the sole property of their respective owners. © 2021 Fluidigm Corporation. All rights reserved. 06/2021