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Updated: Sep 28, 2025

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
Published on: August 18, 2023
Methods for sequencing the pandemic: benefits of rapid or high-throughput processing
Megan L Folkerts1, Darrin Lemmer1, Ashlyn Pfeiffer1
1Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA.
Abstract:
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 use for infectious disease epidemiology in the 21 st Century.
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