评估不同的下一代测序技术,以废水为基础的流行病学
Anika John1, David Dreifuss1, Seju Kang2
1Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
Water research
|October 10, 2024
概括
使用下一代测序的废水流行病学有效追踪SARS-CoV-2变种. 不同的测序技术为公共卫生监测提供了成本,速度和准确性的权衡.
科学领域:
- 环境微生物学环境微生物学
- 公共卫生监督是对公共卫生的监督.
- 基因组流行病学基因组流行病学
背景情况:
- 基于废水的流行病学 (WBE) 是一个有价值的工具,用于人口层面的疾病监测,特别是COVID-19.
- 下一代测序 (NGS) 对于在废水中识别和量化SARS-CoV-2菌株至关重要.
- 测序技术的选择会影响WBE中的数据质量,及时性和实用性.
研究的目的:
- 系统地对废水中SARS-CoV-2监测的不同NGS技术进行基准测试.
- 评估测序平台之间在变种检测成本,速度和准确性方面的权衡.
主要方法:
- 来自Illumina NovaSeq 6000,Element Aviti和牛津纳米孔技术 (ONT) R9.4.1的测序数据的比较分析.
- 利用了来自瑞士污水处理厂的废水样本和入实验的时间序列.
- 评估病毒变种丰度估计的准确性和测序运行时间的影响.
主要成果:
- 所有测试的测序技术都使SARS-CoV-2变体的跟踪成为可能.
- ONT纳米孔测序显示出更高的错误率,影响了变体丰度的准确性,但显示了整体趋势的一致性.
- 在ONT纳米孔测序运行时间可以减少到五小时,而不会对变异估计质量产生重大影响.
结论:
- 在废水中跟踪SARS-CoV-2变种在多个NGS平台上是可行的.
- 与Illumina相比,ONT纳米孔测序提供了一个快速的选择,尽管与Illumina相比,具有潜在的准确性权衡.
- 对于WBE的技术选择应考虑具体的项目需求,包括成本,及时性和所需的准确性.
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