Genomic Analysis and Tracking of SARS-CoV-2 Variants in Gwangju, South Korea, From 2020 to 2022

IF 4.3 4区医学 Q1 INFECTIOUS DISEASES

Influenza and Other Respiratory Viruses Pub Date : 2024-06-25 DOI:10.1111/irv.13350

Yeong-Un Lee, Kwangho Lee, Hongsu Lee, Jung Wook Park, Sun-Ju Cho, Ji-Su Park, Jeongeun Mun, Sujung Park, Cheong-mi Lee, Juhye Lee, Jinjong Seo, Yonghwan Kim, Sun-Hee Kim, Yoon-Seok Chung

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Abstract

Background

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, in December 2019, it has spread rapidly, and many coronavirus disease (COVID-19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID-19 epidemic have increased interest in the characteristics of epidemics in this region, and pathogen genetic analysis is required for infection control and prevention.

Methods

In this study, SARS-CoV-2 whole-genome analysis was performed on samples from patients with COVID-19 in Gwangju from 2020 to 2022 to identify the trends in COVID-19 prevalence and to analyze the phylogenetic relationships of dominant variants. B.41 and B.1.497 prevailed in 2020, the early stage of the COVID-19 outbreak; then, B.1.619.1 mainly occurred until June 2021. B.1.617.2, classified as sublineages AY.69 and AY.122, occurred continuously from July to December 2021. Since strict measures to strengthen national quarantine management had been implemented in South Korea until this time, the analysis of mutations was also able to infer the epidemiological relationship between infection transmission routes. Since the first identification of the Omicron variant in late December 2021, the spread of infection has been very rapid, and weekly whole-genome analysis of specimens has enabled us to monitor new Omicron sublineages occurring in Gwangju.

Conclusions

Our study suggests that conducting regional surveillance in addition to nation-level genomic surveillance will enable more rapid and detailed variant surveillance, which will be helpful in the overall prevention and management of infectious diseases.

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2020 年至 2022 年韩国光州 SARS-CoV-2 变异基因组分析与追踪。

背景：自2019年12月中国武汉首次报告严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）以来，该病毒迅速传播，韩国光州也发生了多起冠状病毒病（COVID-19）病例。COVID-19疫情发生后的病毒变异使人们对这一地区的疫情特点更加关注，感染控制和预防需要对病原体基因进行分析：本研究对 2020 年至 2022 年光州 COVID-19 患者样本进行了 SARS-CoV-2 全基因组分析，以确定 COVID-19 的流行趋势，并分析优势变异株的系统发育关系。2020 年，即 COVID-19 爆发初期，B.41 和 B.1.497 占主导地位；之后，B.1.619.1 主要出现在 2021 年 6 月之前。2021 年 7 月至 12 月，B.1.617.2（分为 AY.69 和 AY.122 亚系）持续出现。在此之前，韩国一直在采取严格的措施加强国家检疫管理，因此通过对变异的分析也可以推断出感染传播途径之间的流行病学关系。自 2021 年 12 月底首次发现 Omicron 变种以来，感染的传播速度非常快，每周对标本进行的全基因组分析使我们能够监测光州出现的新 Omicron 亚系：我们的研究表明，在国家级基因组监测的基础上进行区域性监测，可以更迅速、更详细地监测变异情况，这将有助于传染病的整体预防和管理。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Influenza and Other Respiratory Viruses 医学-病毒学

CiteScore

7.20

自引率

4.50%

发文量

120

审稿时长

6-12 weeks

期刊介绍： Influenza and Other Respiratory Viruses is the official journal of the International Society of Influenza and Other Respiratory Virus Diseases - an independent scientific professional society - dedicated to promoting the prevention, detection, treatment, and control of influenza and other respiratory virus diseases. Influenza and Other Respiratory Viruses is an Open Access journal. Copyright on any research article published by Influenza and Other Respiratory Viruses is retained by the author(s). Authors grant Wiley a license to publish the article and identify itself as the original publisher. Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.