通过长读单分子实时测序识别SARS-CoV-2联合感染和重组
Pauline Trémeaux1, Justine Latour1, Noémie Ranger1
1Virology Laboratory, Toulouse University Hospital, Toulouse, France.
Microbiology spectrum
|June 1, 2023
概括
使用先进的测序检测了与多个SARS-CoV-2菌株的同时感染,包括Omicron变种. 这项研究强调了长读测序对于识别病毒重组事件和跟踪流行病演变的有用性.
科学领域:
- 病毒学 病毒学
- 基因组学就是基因组学.
- 流行病学 流行病学
背景情况:
- 病毒重组,由多个菌株的联合感染驱动,是遗传多样化的关键机制.
- 了解SARS-CoV-2联合感染和重组流行率对于监测病毒演变和流行病动态至关重要.
- 之前关于SARS-CoV-2联合感染的报道主要涉及Delta/Omicron或早期Omicron亚变体组合.
研究的目的:
- 调查SARS-CoV-2联合感染和相关重组事件的流行率.
- 评估长期以来PacBio单分子实时测序 (SMRT) 的有效性,以检测共感染和复合变异.
- 评估SARS-CoV-2联合感染的临床影响和进化意义.
主要方法:
- 整个基因组和目标区域测序使用长期阅读的PacBio SMRT技术.
- 分析了2022年1月至10月期间收集的6829个SARS-CoV-2样本.
- 鉴定和表征涉及不同SARS-CoV-2菌群的共感染,并检测重组小单元型.
主要成果:
- 在6829个样本中发现了17例SARS-CoV-2联合感染,患病率为0.25%.
- 同时感染包括Delta/Omicron (3例) 和Omicron/Omicron (14例) 变种,其中包括最近的Omicron菌群 (22A,22B,22C,22E).
- 24%的同时感染的患者携带了重组小单元类型,其中一个病例显示在慢性感染期间选择了重组病毒.
结论:
- 长期阅读的SMRT测序是检测SARS-CoV-2联合感染和重组事件的强大工具.
- 同时感染虽然很少见,但有助于病毒遗传多样化,需要持续监测.
- 这项技术为评估临床影响和理解SARS-CoV-2流行病演变提供了精确的指标.
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