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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 &lt;48 hours from raw sample to analyzed data. The high-throughput method 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, and we envision their use for infectious disease epidemiology in the 21 st  Century.

Sequencing the pandemic: rapid and high-throughput processing and analysis of COVID-19 clinical samples for 21st century public health