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结合短读和长读测序技术,识别废水中的SARS-CoV-2变种

Gabrielle Jayme¹, Ju-Ling Liu^2,3, Jose Hector Galvez⁴

¹Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

|September 28, 2024

概括

在疫情期间,废水监测有效追踪了SARS-CoV-2变种. 将Illumina和Nanopore测序进行比较,揭示了在检测不同变体系谱方面具有明显的优势,改善了公共卫生洞察力.

科学领域:

环境微生物学环境微生物学
基因组学就是基因组学.
公共卫生病毒学.

背景情况:

对SARS-CoV-2 RNA的废水监测为社区层面提供了有关COVID-19大流行期间感染动态和变种演变的见解.
随着SARS-CoV-2亚系的日益多样化,在混合废水样本中复杂地识别变体,特别是在新型或低丰度变体中.

研究的目的:

为了比较Illumina (短读) 和牛津纳米孔技术 (长读) 测序的有效性,用于检测废水中不同丰度的SARS-CoV-2变体.
评估两种用于变种识别的分析方法:特征突变的存在和在片内同时发生的突变.

主要方法:

使用Illumina和牛津纳米孔测序平台分析了来自北克和安大略省的248个废水样本.
基于特征突变和在安普利康中突变同时发生的变体鉴定.

主要成果:

照明测序显示出更高的灵敏度来检测低丰度或以前未知的血统.
纳米孔测序显示出更大的能力来检测像B.1.1.7 (阿尔法) 这样的高丰度变异,并识别同一个amplicon.内同时发生的突变.

结论:

这两种测序技术在废水中检测SARS-CoV-2变种时具有互补的优势.
结合短读和长读测序的集成工作流可以在复杂的环境样本中全面识别各种SARS-CoV-2血统.

关键词:

照明的顺序是照明的顺序.纳米孔测序的测序这就是SARS-CoV-2病毒.冠状病毒冠状病毒变种变种的变种废水监管监督废水的情况.

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