PDF(Pubmed)
Abstract：
Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA\'s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA\'s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA.
OBJECTIVE: This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA\'s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
OBJECTIVE: This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA\'s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
摘要：
废水监测已成为人口水平病原体监测的重要公共卫生工具。在2021年美国救援计划法案的资助下，FDA的基因组流行病学计划，GenomeTrakr,被用来从美国各地的污水处理厂对SARS-CoV-2进行测序。这一举措需要评估，优化，发展,并发布新的方法和分析工具，通过变异分析进行样本收集。开发了该过程每个步骤的版本控制协议，并在protocols.io上发布。构建了自定义数据分析工具和可公开访问的仪表板，以促进对收集的数据进行实时可视化，重点关注整个项目中不同样本和地点的SARS-CoV-2变体和亚谱系的相对丰度。从2021年9月到2023年6月，共收集了3389个废水样本，在BioProject的保护下，有2,517个正在进行测序并提交给NCBI，PRJNA757291。在所有序列记录上使用明确的质量控制（QC）标签发布序列数据，传达我们对数据质量的信心。变异分析显示，在2021年秋季，Delta的广泛循环，并在采样期结束时捕获了Omicron的扫描以及该谱系的随后多样化。该项目成功实现了FDAGenomeTrakr计划的两个重要目标：第一，为SARS-CoV-2大流行反应提供及时的基因组数据，第二,建立独立于文化的能力和最佳实践，对FDA感兴趣的其他病原体进行人群级环境监测。
目的：本文服务于两个主要目的。首先,它总结了在新冠肺炎大流行应对项目期间收集的基因组和背景数据，利用FDA的实验室网络，传统上用于对食源性病原体进行测序，用于对废水样品中的SARS-CoV-2进行测序。第二,它概述了收集和组织为无文化收集的群体级下一代测序（NGS）数据的最佳实践，监测来自环境样本的病原体。
目的：本文服务于两个主要目的。首先,它总结了在新冠肺炎大流行应对项目期间收集的基因组和背景数据，利用FDA的实验室网络，传统上用于对食源性病原体进行测序，用于对废水样品中的SARS-CoV-2进行测序。第二,它概述了收集和组织为无文化收集的群体级下一代测序（NGS）数据的最佳实践，监测来自环境样本的病原体。
