Full genomic sequence characterization of the chikungunya virus from an imported case with serum viral concentration below culturable level

IF 3.5 Q1 PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH Biosafety and Health Pub Date : 2024-10-01 DOI:10.1016/j.bsheal.2024.09.003
Mengling Jiang , Muchun Wan , Qinghong Fan , Yuyi Min , Guofang Tang , Yingfen Wen , Yaqing Lin , Ruiying He , Jiaojiao Li , Yue Tang , Yun Lan , Feng Li
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Abstract

Chikungunya virus (CHIKV) infection, responsible for chikungunya fever and occasionally severe symptoms, has emerged as an increasing global health concern following several large-scale outbreaks from Africa, Asia, Europe, and America. Over the past two decades, South and Southeast Asia regions have gradually become hot spots for outbreaks involving multiple CHIKV lineages. In China, most CHIKV infections are imported, making it crucial to trace the origins and transmission routes for effective prevention and control. In January 2024, a case of imported chikungunya fever was confirmed in Guangzhou City, Guangdong Province, China. However, the serum CHIKV viral concentration was too low for cultivation [reverse transcription-polymerase chain reaction (RT-PCR) detection, cycle threshold = 32.62]. Despite this, we successfully obtained the viral genome sequence directly from the whole blood sample using an optimized metatranscriptomic sequencing strategy, achieving a full-length viral genome with an average depth of 54.3X. Further analysis confirmed that the CHIKV virus belonged to the Asian lineage, traced to Timor-Leste, where an endemic CHIKV outbreak had been reported in January 2024, consistent with the patient’s travel history. Finally, we analyzed genetic evolutionary trends and amino acid site variations. This study highlights the identification of a CHIKV infection origin using direct whole-blood metatranscriptomic sequencing, a valuable method for rapidly sequencing low viral-load samples.
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从血清病毒浓度低于可培养水平的输入病例中鉴定基孔肯雅病毒的全基因组序列特征
基孔肯雅病毒(CHIKV)感染是导致基孔肯雅热和偶尔出现严重症状的原因,在非洲、亚洲、欧洲和美洲爆发几次大规模疫情后,基孔肯雅病毒已成为全球日益关注的健康问题。在过去二十年中,南亚和东南亚地区逐渐成为涉及多种 CHIKV 系的疫情爆发热点。在中国,大多数 CHIKV 感染病例都是输入性的,因此追踪病源和传播途径对于有效防控至关重要。2024 年 1 月,中国广东省广州市确诊一例输入性基孔肯雅热病例。然而,血清中的CHIKV病毒浓度太低,无法进行培养[反转录聚合酶链反应(RT-PCR)检测,周期阈值=32.62]。尽管如此,我们还是采用优化的元转录组测序策略,成功地从全血样本中直接获得了病毒基因组序列,获得了平均深度为 54.3 倍的全长病毒基因组。进一步分析证实,该 CHIKV 病毒属于亚洲系,可追溯到 2024 年 1 月东帝汶爆发的地方性 CHIKV 疫情,这与患者的旅行史相符。最后,我们分析了基因进化趋势和氨基酸位点变异。这项研究强调了利用直接全血元转录组测序鉴定 CHIKV 感染来源,这是一种对低病毒载量样本进行快速测序的重要方法。
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来源期刊
Biosafety and Health
Biosafety and Health Medicine-Infectious Diseases
CiteScore
7.60
自引率
0.00%
发文量
116
审稿时长
66 days
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