Journal Article

Long-Term Genomic Surveillance and Immune Escape of SARS-CoV-2 in the Republic of Korea, with a Focus on JN.1-Derived Variants

No, Jin Sun, Kim, Eun-Jin, Noh, Ji Yeong, Kim, Jeong-Ah, O, Sang Won, Nam, Jeong-Hyun, Kim, Jeong-Min, Choi, Yong Jun, An, Bo Min, Kim, Il-Hwan, Lee, Eun Ju, Lee, Chae Young, Rhee, Jee Eun

2025

Overview

Since the onset of the COVID-19 pandemic, the Republic of Korea has experienced continuous waves of SARS-CoV-2 variants. The current study aimed to analyze the long-term trends of variant prevalence and associated changes in immune responses within the country. Whole-genome sequencing was performed on confirmed patient samples collected from December 2020 to May 2025, and variant distribution, genetic diversity, and neutralization were compared. As a result of analyzing a total of 157,962 gene sequences, various Omicron sub-lineages, including BA.1, BA.2, BA.5, followed by JN.1, KP.3, and NB.1.8.1, were seen to circulate sequentially over time. The nucleotide diversity of the SARS-CoV-2 genome gradually increased after the JN.1 outbreak. Of the tested variants, hamster antiserum neutralization analysis indicated that Omicron NB.1.8.1, which began to circulate in 2025, exhibited the lowest neutralization activity, with an approximately 6.6-fold decrease compared to JN.1. This suggests a potential expansion in the dominance of new variants with enhanced immune evasion. As the transmission of SARS-CoV-2 continues, new variants with novel characteristics may emerge; therefore, continuous national genomic surveillance and immunological characterization are considered crucial for early detection of emerging variants and for guiding effective public health responses.

• Publisher: MDPI AG
• Subject: Animals / Antibodies / Antibodies, Neutralizing - immunology / Antibodies, Viral - immunology / Antisera / Biological diversity / Comparative analysis / COVID-19 / COVID-19 - epidemiology / COVID-19 - immunology / COVID-19 - virology / COVID-19 vaccines / DNA sequencing / Epidemics / Genetic diversity / Genetic Variation / Genome, Viral / Genomes / genomic epidemiology / genomic surveillance / Genomics / Hamsters / Health aspects / Humans / Immune Evasion / Immune response / Immunization / Infectious diseases / Mutation / neutralization antibodies / Nucleotide sequencing / Pandemics / Phylogenetics / Phylogeny / Public health / Republic of Korea - epidemiology / SARS-CoV-2 / SARS-CoV-2 - classification / SARS-CoV-2 - genetics / SARS-CoV-2 - immunology / Severe acute respiratory syndrome coronavirus 2 / Spike Glycoprotein, Coronavirus - genetics / variant / Viruses / Whole Genome Sequencing