Sequencing the pandemic: rapid and high-throughput processing and analysis of COVID-19 clinical samples for 21 st century public health.
Megan L FolkertsDarrin LemmerAshlyn PfeifferDanielle VasquezChris FrenchAmber JonesMarjorie NguyenBrendan LarsenW Tanner PorterKrystal SheridanJolene R BowersDavid M EngelthalerPublished in: F1000Research (2021)
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 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.
Keyphrases
- sars cov
- high throughput
- data analysis
- single cell
- infectious diseases
- coronavirus disease
- public health
- respiratory syndrome coronavirus
- loop mediated isothermal amplification
- cross sectional
- risk factors
- copy number
- heart failure
- electronic health record
- big data
- dna methylation
- atrial fibrillation
- gene expression
- machine learning
- quantum dots
- microbial community
- global health
- anaerobic digestion