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.
Highlights
Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks
Targeted amplification SARS-CoV2 RNA was amplified for both of the sequencing methods described below following the nCoV-2019 sequencing protocol V.121 and using the ARTIC v3 primer set[22]
A Ct of 35, ~18% of samples yielded a complete genome, and breadth of coverage dropped below 57% (SD 31.65, 95% confidence interval (95%CI) 48.70-59.08) (Table 2)
Summary
Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks. We report two genomic sequencing and analysis strategies for rapidturnaround 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
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