SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.
Ruth E TimmeJacquelina WoodsJessica L JonesKevin R CalciRachel RodriguezCandace BarnesElizabeth LeardMark CravenHaifeng ChenCameron BoernerChristopher GrimAmanda M WindsorPadmini RamachandranTim MuruvandaHugh RandBereket TesfaldetJasmine AmirzadeganTunc KayikciogluTamara WalskyMarc William AllardMaria BalkeyCandace Hope BiasEric BrownKathryn JudyTina PfeferSandra M TallentMaria Hoffmannnull nullJames PettengillPublished in: mSystems (2024)
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.
Keyphrases
- sars cov
- respiratory syndrome coronavirus
- public health
- electronic health record
- single cell
- wastewater treatment
- big data
- copy number
- gram negative
- primary care
- healthcare
- antimicrobial resistance
- anaerobic digestion
- quality improvement
- coronavirus disease
- machine learning
- risk assessment
- artificial intelligence
- data analysis
- network analysis
- life cycle
- high throughput sequencing