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高分辨率和实时废水病毒监测通过纳米孔测序

Xiaoqing Xu¹, Yu Deng¹, Jiahui Ding¹

¹Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.

|April 24, 2024

概括

这项研究验证了纳米孔测序用于对SARS-CoV-2的废水监测,显示了其用于变种识别和实时监测的准确性. 建议在废水样本中对碎片化病毒基因组进行较短的PCR放大.

科学领域:

环境微生物学环境微生物学
基因组流行病学基因组流行病学
传染病监测传染病监测传染病监测传染病监测

背景情况:

废水基因组测序对于人口级别的病毒监测至关重要.
之前的纳米孔测序版本面临废水分析的准确性问题.
R10.4.1纳米孔版本为实时基因组数据提供了更高的准确性.

研究的目的:

评估最新的纳米孔测序 (R10.4.1) 对于废水中SARS-CoV-2监测的有效性.
为了将纳米孔测序与Illumina进行比较,以获得变体识别可靠性.
为了证明纳米孔测序在公共卫生中的早期预警信号的能力.

主要方法:

为了最佳的废水病毒基因组分析,比较了400bp和1200bp的安普利康长度.
利用废水模拟样本验证纳米孔测序对Illumina.
监测香港的废水处理厂,以进行变种流行和突变概况.

主要成果:

较短的PCR放大片 (400 bp) 更适合废水中的细分病毒RNA.
纳米孔测序证明了变体识别的高可靠性,与Illumina.
只有0.001Gb的纳米孔数据提供了准确的变体流行率,SNVs和indels的精度高于99%,变化频率高于50%.
观察到从BA.5到XBB系的转变,在香港的废水中XBB.1.5占主导地位.

结论:

该R10.4.1纳米孔测序平台是有效的实时SARS-CoV-2废水监测.
这项技术为早期检测病毒变体和公共卫生早期预警提供了巨大的潜力.
使用纳米孔测序的基于废水的流行病学可以扩展到监测其他流行病病毒.

关键词:

突变突变是一种突变.纳米孔测序的测序这就是SARS-CoV-2病毒.病毒监测病毒监测废水是废水,废水就是废水.基于废水的流行病学.

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