A Case of Whole Genome Analysis of SARS-CoV-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

Corresponding author : jaeseok@hallym.ac.kr

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