A Case of Whole Genome Analysis of SARS-CoV-2 Using Oxford Nanopore MinION System
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
Figures & Tables
Table 1. Genomic and amino acid changes of the SARS-CoV-2 positive specimen
Genomic change |
Amino acid change |
Gene/region |
241 C -> T |
|
5′-UTR |
1059 C -> T |
T265I |
orf1ab |
3037 C -> T |
F924 |
orf1ab |
11916 C -> T |
Y3884L |
orf1ab |
14408 C -> T |
P4715L |
orf1ab |
16650 C -> T |
L5462 |
orf1ab |
20675 A -> T |
Q6804L |
orf1ab |
23403 A -> G |
D614G |
S |
25563 G -> T |
Q57H |
orf3a |
29179 G -> T |
P302 |
N |
29779 G -> T |
|
3′-UTR |