废水基因组测序用于SARS-CoV-2变种的废水基础流行病学应用中的监测
Xiaoqing Xu1, Yu Deng1, Jiahui Ding1
1Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
Water research
|August 14, 2023
概括
废水基因组测序可靠地跟踪SARS-CoV-2变种,比临床数据更早地检测趋势. 这种方法增强了基于废水的流行病学 (WBE) 用于公共卫生监测.
科学领域:
- 环境微生物学环境微生物学
- 病毒学 病毒学
- 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) 补充了针对SARS-CoV-2的临床监测.
- 废水的基因组测序为病毒多样性提供了洞察力,但在变体检测和量化方面面临挑战.
研究的目的:
- 评估测序吞吐量对废水中SARS-CoV-2基因组分析的影响.
- 用模拟数据集评估变体解卷管道的性能.
- 为了证明废水基因组测序在香港公共卫生监测中的实用性.
主要方法:
- 通过将SARS-CoV-2变种RNA入废水RNA,创建模拟废水样本.
- 评估测序吞吐量对基因组覆盖范围,突变检测和变异解的影响.
- 在7个月内对超过600万人的86个废水样本进行了测序.
- 使用in silico模拟数据集来测试变体解卷管道性能.
主要成果:
- 测序吞吐量>0.5 Gb提供了可靠的基因组分析结果.
- 成功追踪的变种替代 (Delta by Omicron) 和Omicron亚系流行率.
- 废水基因组数据比临床数据早16天发现了变异趋势.
- 证明了在尖基因中识别新突变和独特基因的潜力.
结论:
- 废水基因组监测对于监测SARS-CoV-2变种的出现和趋势至关重要.
- 在WBE中为新兴病毒建立基因组分析方法的基础.
- 强调WBE在早期检测公共卫生威胁方面的价值.
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