印度尼西亚西加里曼丹的 Omicron 系 BA.2.40 进口病例消失。

IF 1.6 Q2 MEDICINE, GENERAL & INTERNAL Iranian Journal of Medical Sciences Pub Date : 2024-03-01 DOI:10.30476/ijms.2023.97513.2935
Delima Fajar Liana, Virhan Novianry, Andriani Andriani, Mahyarudin Mahyarudin, Puji Astuti
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引用次数: 0

摘要

背景:世界卫生组织已宣布 Omicron 为第五个令人担忧的变种,它有 50 多个突变,特别是在尖峰蛋白中。由于变异导致病毒传染性增强,因此必须在全球范围内对严重急性呼吸系统综合征 2(SARS-CoV-2)进行基因组监测和检测。本研究旨在追踪印度尼西亚西加里曼丹省的 Omicron 系 BA.2.40:2022年5月至8月,从前往西加里曼丹的国际旅行者(主动监测)和因感染SARS-CoV-2而住院的患者(基线监测)中采集了鼻咽拭子样本(n=3,642)。根据 ORF1ab、N 和 HV69-70del 基因对样本进行了 Omicron 系检测,然后进行了全基因组测序。然后使用两个基因组数据库对序列进行鉴定,与参考基因组(Wuhan/Hu-1/2019)进行比对,再与全球检测到的 BA.2.40 系进行比较。使用分子进化遗传学分析软件对样本和其他 SARS-CoV-2 分离物进行了系统进化分析:结果:根据基因组数据库,10 个分离株被确定为 BA.2.40。所有样本的 ORF1ab 和 N 基因均呈阳性,但 HV69-70del 基因呈阴性,而 HV69-70del 基因是检测 Omicron 变种的标记。系统发育分析表明,这些分离物与马来西亚的一个分离物关系密切,而马来西亚是 BA.2.40 的主要分布区:欧米克隆品系 BA.2.40 的尖峰蛋白中没有 HV69-70 缺失,而 HV69-70 是用于筛选欧米克隆变异体的标记。BA.2.40与马来西亚的一个分离株高度相似,并且只在特定时期被检测到,这表明国际输入病例的影响。
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Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia.

Background: The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia.

Methods: In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software.

Results: Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40.

Conclusion: Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.

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来源期刊
Iranian Journal of Medical Sciences
Iranian Journal of Medical Sciences MEDICINE, GENERAL & INTERNAL-
CiteScore
3.20
自引率
0.00%
发文量
84
审稿时长
12 weeks
期刊介绍: The Iranian Journal of Medical Sciences (IJMS) is an international quarterly biomedical publication, which is sponsored by Shiraz University of Medical Sciences. The IJMS intends to provide a scientific medium of com­muni­cation for researchers throughout the globe. The journal welcomes original clinical articles as well as clinically oriented basic science re­search experiences on prevalent diseases in the region and analysis of various regional problems.
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