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Volume 26, Number 10—October 2020
Dispatch

Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2

Clinton R. Paden1, Ying Tao1, Krista Queen, Jing Zhang, Yan Li, Anna Uehara, and Suxiang TongComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (C. Paden, Y. Tao, K. Queen, Y. Li, S. Tong); IHRC, Atlanta (J. Zhang); Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (A. Uehara)

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Figure 1

Limits of detection for sequencing severe acute respiratory syndrome coronavirus 2. Triplicate serial dilutions of virus isolate A12 (J. Harcourt, unpub. data, https://doi.org/10.1101/2020.03.02.972935amplified by using the singleplex or multiplex primer set. Multiplex amplicons were barcoded, library-prepped, and sequenced on an Oxford MinION apparatus (https://nanoporetech.com) or an Illumina MiSeq apparatus (https://www.illumina.com). A) Percentage of reads that map to the virus genome for ea

Figure 1. Limits of detection for sequencing severe acute respiratory syndrome coronavirus 2. Triplicate serial dilutions of virus isolate A12 (8) were amplified by using the singleplex or multiplex primer set. Multiplex amplicons were barcoded, library-prepped, and sequenced on an Oxford MinION apparatus (https://nanoporetech.com) or an Illumina MiSeq apparatus (https://www.illumina.com). A) Percentage of reads that map to the virus genome for each sample. B) Percentage of virus genome that is covered at >20× depth by the multiplex amplicons on the MinION (black) or >100× depth on the MiSeq (orange), or covered by the nested, singleplex amplicons (gray) (measured by presence or absence on a gel). C) Real-time analysis of MinION sequencing data. Each data point represents the average 20× genome coverage of three replicates. NTC, nontemplate controls (human cell nucleic acid carried through the PCR and library preparation). Asterisk (*) indicates that samples were not analyzed at that dilution.

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1These authors contributed equally to this article.

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