Investigation of SARS-CoV-2 lineages and mutations circulating in a university-affiliated hospital in South Korea analyzed using Oxford Nanopore MinION sequencing.
Hyaekang Kim, Sung Hee Chung, Hyun Soo Kim, Han-Sung Kim, Wonkeun Song, Ki Ho Hong, Jae-Seok Kim
Author Information
Hyaekang Kim: Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea.
Sung Hee Chung: Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea.
Hyun Soo Kim: Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea.
Han-Sung Kim: Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea.
Wonkeun Song: Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea.
Ki Ho Hong: Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
Jae-Seok Kim: Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea.
OBJECTIVES: Despite the introduction of vaccines, treatments, and massive diagnostic testing, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to overcome barriers that had slowed its previous spread. As the virus evolves towards increasing fitness, it is critical to continue monitoring the occurrence of new mutations that could evade human efforts to control them. METHODS: We performed whole-genome sequencing using Oxford Nanopore MinION sequencing on 58 SARS-CoV-2 isolates collected during the ongoing coronavirus disease 2019 pandemic at a tertiary hospital in South Korea and tracked the emergence of mutations responsible for massive spikes in South Korea. RESULTS: The differences among lineages were more pronounced in the spike gene, especially in the receptor-binding domain (RBD), than in other genes. Those RBD mutations could compromise neutralization by antibodies elicited by vaccination or previous infections. We also reported multiple incidences of Omicron variants carrying mutations that could impair the diagnostic sensitivity of reverse transcription-polymerase chain reaction-based testing. CONCLUSION: These results provide an understanding of the temporal changes of variants and mutations that have been circulating in South Korea and their potential impacts on antigenicity, therapeutics, and diagnostic escape of the virus. We also showed that the utilization of the nanopore sequencing platform and the ARTIC workf low can provide convenient and accurate SARS-CoV-2 genomic surveillance even at a single hospital.
