Rapid High Throughput Whole Genome Sequencing of SARS-CoV-2 by using One-step RT-PCR Amplification with Integrated Microfluidic System and Next-Gen Sequencing

Tao Li; Hye Kyung Chung; Papa K. Pireku; Brett F. Beitzel; Mark A. Sanborn; Cynthia Y. Tang; Richard Hammer; Detlef G. Ritter; Xiu‐Feng Wan; Irina Maljkovic Berry; Jun Hang

doi:10.1128/jcm.02784-20

Molecular BiologyJournal of Clinical MicrobiologyMar 3, 2021

Peer-reviewed journal article

Rapid High Throughput Whole Genome Sequencing of SARS-CoV-2 by using One-step RT-PCR Amplification with Integrated Microfluidic System and Next-Gen Sequencing

Tao Li iD, Hye Kyung Chung iD, Papa K. Pireku, Brett F. Beitzel iD, Mark A. Sanborn iD, Cynthia Y. Tang iD, Richard Hammer iD, Detlef G. Ritter iD, Xiu‐Feng Wan iD, Irina Maljkovic Berry iD, Jun Hang iD

Abstract

The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here we report a simple and efficient workflow for whole genome sequencing utilizing one-step RT-PCR amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm IFC and instruments to amplify 48 samples with 39 pairs of primers in a single step. Application of this method on RNA samples from both viral isolate and clinical specimens demonstrate robustness and efficiency of this method in obtaining the full genome sequence of SARS-CoV-2.

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