Annals of Clinical Microbiology, The official Journal of the Korean Society of Clinical Microbiology

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pISSN 2288-0585 eISSN 2288-6850

A Case of Whole Genome Analysis of SARSCoV-2 Using Oxford Nanopore MinION System

Original article

Annals of Clinical Microbiology (Ann Clin Microbiol) 2021 March, Volume 24, Issue 1, pages 135-140.

https://doi.org/10.5145/ACM.2021.24.4.4

A Case of Whole Genome Analysis of SARSCoV-2 Using Oxford Nanopore MinION System

Jae-Seok Kim, Sung Hee Chung, Jung-Min Kim, Hyun Soo Kim, Han-Sung Kim, Wonkeun Song

Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea

Abstract

The application of whole genome sequencing on SARS-CoV-2 viral genome is essential for our understanding of the molecular epidemiology and spread of viruses in the community. The portable whole genome sequencer MinION (Oxford Nanopore Technologies, ONT, UK) could be feasibly used in a clinical microbiology laboratory without the need of vast resources or stringent operating conditions. We used the MinION sequencer to analyze the viral genome sequence of one SARS-CoV-2 strain. In June 2020, nasopharyngeal specimen from one patient was subjected to whole-genome analysis using the nCoV-2019 sequencing protocol v2 of ARTIC using the MinION sequencer. The ONT MinKNOW software, RAMPART tool, and Genome Workbench were used. We identified 11 nucleotide variants using the Wuhan-Hu-1 isolate (NC_045512.2) as the reference sequence. There were six nucleotide variants (T265I, F924, Y3884L, P4715L, L5462, and Q6804L) in the ORF1ab region, one variant (D614G) in the S gene, one variant (Q57H) in ORF3a, one variant (P302) in the N gene, and two variants in each the 5′UTR and 3′-UTR. In this prolonged coronavirus disease 2019 (COVID-19) pandemic season, the MinION system that operates an amplicon-based whole-genome sequencing protocol could be a rapid and reliable sequencer without the need of cumbersome viral cultivation.

Keywords

Nanopore sequencing, SARS-CoV-2, COVID-19, Whole genome sequencing