针对SARS-CoV-2废水变体的监测:利用FDA的GenomeTrakr网络进行流行病应对
Ruth E Timme1, Jacquelina Woods2, Jessica L Jones2
1Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA.
mSystems
|May 31, 2024
概括
美国食品和药物管理局 FDA
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
- 公共卫生监督是对公共卫生的监督.
背景情况:
- 废水监测是人口层面病原体监测的关键工具.
- 美国食品和药物管理局的GenomeTrakr计划适应了其对SARS-CoV-2的食物传播病原体测序能力.
- 美国救援计划法案的资金支持了这一倡议.
研究的目的:
- 总结SARS-CoV-2废水监测项目的基因组和上下文数据.
- 概述从环境样本收集人口级下一代测序 (NGS) 数据的最佳实践.
- 建立培养独立的病原体监测能力.
主要方法:
- 从美国各地的2517个废水样本中测序SARS-CoV-2 (2021年9月至2023年6月).
- 开发和发布版本控制的协议,用于样本采集到变种分析.
- 创建一个定制的数据分析工具和公共仪表板,用于实时数据可视化.
- 将序列数据提交给NCBI (BioProject PRJNA757291) 并使用质量控制标签.
主要成果:
- 追踪了废水中SARS-CoV-2变种,包括Delta和Omicron的流行情况.
- 在2021年晚些时候,Delta的广泛传播和Omicron随后的多样化.
- 成功生成和共享适时的基因组数据,以应对流行病.
结论:
- 使用NGS建立了环境监测的最佳实践.
- 证明了FDA在废水中进行培养独立的病原体监测的能力.
- 为SARS-CoV-2循环动态提供了有价值的基因组洞察力.
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