台湾地区奥密克戎变异株 BA.5 至 XBB.1 的流行病学和系统进化趋势

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

机构信息

Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.

Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.

出版信息

J Infect Public Health. 2024 Nov;17(11):102556. doi: 10.1016/j.jiph.2024.102556. Epub 2024 Sep 29.

DOI:10.1016/j.jiph.2024.102556

PMID:39388868

Abstract

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.

摘要

背景

奥密克戎（Omicron）是一种严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）的变体，于 2021 年底传入台湾。台湾政府于 2022 年 3 月结束了“零新冠”政策。2022 年 4 月开始出现多起 2019 年冠状病毒病（COVID-19）疫情。我们监测了奥密克戎 BA.1/BA.2 后亚变体的替代情况，并分析了它们与 COVID-19 疫情的相关性。

方法

我们收集了来自台湾高雄医学大学附设医院（KMUH）的 SARS-CoV-2 实时 qRT-PCR 阳性鼻咽拭子，并对在 Vero E6 细胞中表现出细胞病变效应的标本进行测序，以确定其分支和谱系。我们分析了 COVID-19 患者的病历，并确定了住院的危险因素。我们从 GISAID 检索了在台湾确定的 SARS-CoV-2 序列，并分析了它们与台湾疾病管制署的 COVID-19 数据的相关性。

结果

我们分析了 KMUH-47 到 KMUH-104（本文中鉴定的 SARS-CoV-2 分离株）和所有奥密克戎亚变体（BA.5 到 XBB.1，n=1930）的系统发生。年龄和合并症是住院的危险因素。男性的死亡率普遍高于女性。COVID-19 相关死亡主要发生在 70 岁以上的人群中。COVID-19 相关病死率随核苷酸（NT）和氨基酸（AA）替换的增加而增加。随着 2022 年 8 月至 2023 年 10 月期间每次疫情的发生，COVID-19 相关病例和死亡人数逐渐减少。