Volume 10,Issue 1
Fall 2025
A Case of Whole Genome Analysis of SARS-CoV-2 Using Oxford Nanopore MinION System
The application of whole genome sequencing on the 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 for 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, a nasopharyngeal specimen from one patient was subjected to whole-genome analysis using the nCoV-2019 sequencing protocol ARTIC V2 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 for cumbersome viral cultivation.
1. Uhteg K, Carroll KC, Mostafa HH. (2020). Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus? Clin Lab Med, 40: 459–472.
2. Burki T. (2021). Understanding Variants of SARS-CoV-2. Lancet, 397: 462.
3. Kim HM, Jeon S, Chung O, et al. (2021). Comparative Analysis of 7 Short-Read Sequencing Platforms using the Korean Reference Genome: MGI and Illumina Sequencing Benchmark for Whole-Genome Sequencing. Gigascience, 10: giab014.
4. Kim JM, Park SY, Lee D, et al. (2021). Genomic Investigation of the Coronavirus Disease-2019 Outbreak in the Republic of Korea. Sci Rep, 11: 1–10.
5. Hourdel V, Kwasiborski A, Baliere C, et al. (2020). Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100 TM System. Front Microbiol, 11: 571328.
6. Park AK, Kim IH, Kim J, et al. (2021). Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020. Osong Public Health Res Perspect, 12: 37–43.
7. Bull RA, Adikari TN, Ferguson JM, et al. (2020). Analytical Validity of Nanopore Sequencing for Rapid SARS-CoV-2 Genome Analysis. Nat Commun, 11: 6272.
8. Tyson JR, James P, Stoddart D, et al. (2020). Improvements to the ARTIC Multiplex PCR Method for SARS-CoV-2 Genome Sequencing using Nanopore. BioRxiv. https://doi.org/10.1101/2020.09.04.283077.
9. Tali SHS, LeBlanc JJ, Sadiq Z, et al. (2021). Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev, 34: e00228-20.
10. Park S, Kim DH, Lee WM, et al. (2020). Experience at Department of Laboratory Medicine During the COVID-19 Outbreak in Daegu. Ann Clin Microb, 23: 225–231.
11. Hong KH, In JW, Lee J, et al. (2022). Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Ann Lab Med, 42: 96–99.