台湾从BA.5到XBB.1的Omicron亚变体的流行病学和系统发育趋势。

IF 4.7 3区医学 Q1 INFECTIOUS DISEASES

Journal of Infection and Public Health Pub Date : 2024-09-29 DOI:10.1016/j.jiph.2024.102556

Jih-Jin Tsai , Shyh-Shin Chiou , Po-Chih Chen , Chun-Hong Chen , Ping-Chang Lin , Ching-Yi Tsai , Wan-Long Chuang , Shang-Jyh Hwang , Inn-Wen Chong , Li-Teh Liu

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引用次数: 0

摘要

背景：严重急性呼吸系统综合症冠状病毒 2（SARS-CoV-2）变种 Omicron 于 2021 年底进入台湾。台湾政府于 2022 年 3 月结束了 "零冠状病毒 "政策。2022 年 4 月开始爆发多种冠状病毒病 2019（COVID-19）。我们监测了BA.1/BA.2之后Omicron亚变体的替换情况，并分析了它们与COVID-19爆发的相关性：方法：我们从台湾高雄市高雄医学大学附设医院（KMUH）采集了SARS-CoV-2实时qRTPCR阳性鼻咽拭子，并对在Vero E6细胞中表现出细胞病理效应的标本进行测序，以确定其支系和系谱。我们分析了 COVID-19 患者的医疗记录，并确定了住院风险因素。我们从 GISAID 中检索了在台湾发现的 SARS-CoV-2 序列，并分析了它们与台湾疾病控制中心提供的 COVID-19 数据的相关性：我们分析了KMUH-47到KMUH-104（本文发现的SARS-CoV-2分离株）以及从BA.5到XBB.1的所有Omicron亚变异株（n = 1930）的系统发育。年龄和合并症是住院风险因素。男性的死亡率普遍高于女性。与COVID-19相关的死亡病例主要发生在70岁以上的人群中。随着核苷酸（NT）和氨基酸（AA）置换的增加，COVID-19相关病例死亡率也随之增加。2022年8月至2023年10月期间，COVID-19相关病例和死亡人数随着每次疫情爆发而逐渐减少：结论：住院治疗与年龄和合并症有关。COVID-19相关死亡病例与性别、年龄以及新出现的Omicron亚变体中NT和AA替代的累积有关。

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The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan

Background

Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its "zero-COVID" policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks.

Methods

We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control.

Results

We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023.

Conclusion

Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants.

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来源期刊

Journal of Infection and Public Health PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH -INFECTIOUS DISEASES

CiteScore

13.10

自引率

1.50%

发文量

203

审稿时长

96 days

期刊介绍： The Journal of Infection and Public Health, first official journal of the Saudi Arabian Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences and the Saudi Association for Public Health, aims to be the foremost scientific, peer-reviewed journal encompassing infection prevention and control, microbiology, infectious diseases, public health and the application of healthcare epidemiology to the evaluation of health outcomes. The point of view of the journal is that infection and public health are closely intertwined and that advances in one area will have positive consequences on the other. The journal will be useful to all health professionals who are partners in the management of patients with communicable diseases, keeping them up to date. The journal is proud to have an international and diverse editorial board that will assist and facilitate the publication of articles that reflect a global view on infection control and public health, as well as emphasizing our focus on supporting the needs of public health practitioners. It is our aim to improve healthcare by reducing risk of infection and related adverse outcomes by critical review, selection, and dissemination of new and relevant information in the field of infection control, public health and infectious diseases in all healthcare settings and the community.