Methods for sequencing the pandemic: Benefits of rapid or high-throughput processing
- Folkerts, M.L.
- Lemmer, D.
- Pfeiffer, A.
- Vasquez, D.
- French, C.
- Jones, A.
- Nguyen, M.
- Larsen, B.
- Porter, W.T.
- Sheridan, K.
- Bowers, J.R.
- Engelthaler, D.M.
DOIAbstract
Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks. Here, we report two genomic sequencing and analysis strategies for rapid-turnaround or high-throughput processing of metagenomic samples. The rapid-turnaround method was designed to provide a quick phylogenetic snapshot of samples at the heart of active outbreaks, and has a total turnaround time of <48 hours from raw sample to analyzed data. The high-throughput method, first reported here for SARS-CoV2, was designed for semi-retrospective data analysis, and is both cost effective and highly scalable. Though these methods were developed and utilized for the SARS-CoV-2 pandemic response in Arizona, U.S, we envision their u...
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