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. 2020 Jun 19;2(25):447-452.
doi: 10.46234/ccdcw2020.088.

Sequencing the Complete Genome of COVID-19 Virus from Clinical Samples Using the Sanger Method

Roujian Lu  1 , Peihua Niu  1 , Li Zhao  1 , Huijuan Wang  1 , Wenling Wang  1 , Wenjie Tan  1
Affiliations

Sequencing the Complete Genome of COVID-19 Virus from Clinical Samples Using the Sanger Method

Roujian Lu et al. China CDC Wkly. .

Abstract

What is already known on this topic?

Coronavirus disease 2019 (COVID-19), a disease caused by a novel human coronavirus named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 virus, was reported in December 2019. Complete genomes of the COVID-19 virus from clinical samples using next generation sequencing (NGS) have been reported.

What is added by this report?

Here we provide the technical data for sequencing complete genome of COVID-19 virus from clinical samples using the Sanger method. Two complete COVID-19 virus genome sequences (named WH19004-S and GX0002) were obtained from clinical samples of COVID-19 patients, and two single nucleotide polymorphisms (SNPs) in ORF7a (T/C, nt 27,493) and ORF8 (T/C, nt 28,253) of WH19004-S were identified by Sanger sequencing.

What are the implications for public health practice?

The COVID-19 virus genome sequencing by Sanger method reported here could be used to generate data of high enough quality without requirement for expensive NGS equipment, which support sequencing complete genomes from clinical samples and monitoring of viral genetic variations of COVID-19 infections.

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Conflict of interest statement

Conflict of interest: No conflicts of interest were reported.

Figures

Figure 1
Figure 1
COVID-19 virus genome fragment amplification by RT-PCR. A: Schematic representation of the amplificatory fragments of the genome. B: Capillary electrophoresis profiles of RT-PCR products of the obtained partial fragment. a to k: RT-PCR products of the fragment 1–11; l to m: RT-PCR products of the end of 5’ and 3’ of the genome.
Figure 2
Figure 2
Sequence comparison and Sanger sequencing diagram of COVID-19 virus in this study. (A) Sequence alignment of 4 whole-length genomes of COVID-19 virus. (B) Sanger sequencing diagram of WH19004-S by reverse primers 29R and 30R, which shows the SNPs in ORF7 and ORF8 of WH19004-S.
See this image and copyright information in PMC

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